diff --git a/.Rbuildignore b/.Rbuildignore index 7379796b3..ffb1702ff 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -22,3 +22,4 @@ vignettes/articles ^pkgdown ^\.github$ test_data/ +^CODE_OF_CONDUCT\.md$ diff --git a/.github/workflows/Deploy-pkgdown.yaml b/.github/workflows/Deploy-pkgdown.yaml index 11d1c1c42..03b204ba9 100644 --- a/.github/workflows/Deploy-pkgdown.yaml +++ b/.github/workflows/Deploy-pkgdown.yaml @@ -1,48 +1,45 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: - - CRAN - - main - tags: - -'*' + branches: [CRAN, main] + tags: ['*'] name: Deploy-pkgdown jobs: deploy-pkgdown: - runs-on: macOS-latest + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 - - uses: r-lib/actions/setup-pandoc@v1 - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - - name: Restore R package cache - uses: actions/cache@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + extra-packages: any::pkgdown, any::bench, any::dplyr, any::landscapetools, any::purrr, any::stars, local::. + needs: website - name: Install dependencies run: | - remotes::install_deps(dependencies = TRUE) - install.packages("pkgdown", type = "binary") + install.packages(c("remotes")) + remotes::install_version(package = "SDMTools", version = "1.1-221.2") shell: Rscript {0} - - name: Install package - run: R CMD INSTALL . + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) + shell: Rscript {0} - - name: Deploy package - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@4.1.4 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 14939fccc..5534ccd28 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,14 +1,11 @@ -# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. -# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions +# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help + on: push: - branches: - - CRAN - - main + branches: [CRAN, main, development] pull_request: - branches: - - CRAN - - main + branches: [CRAN, main] name: R-CMD-check @@ -23,61 +20,40 @@ jobs: fail-fast: false matrix: config: - - {os: windows-latest, r: 'release'} - {os: macOS-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'release'} env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 - with: - r-version: ${{ matrix.config.r }} - - uses: r-lib/actions/setup-pandoc@v1 - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} + - uses: r-lib/actions/setup-pandoc@v2 - - name: Restore R package cache - uses: actions/cache@v2 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + - name: Install spatial dependencies + if: runner.os == 'macOS' + run: | + brew install gdal + brew install proj - - name: Install system dependencies + - name : Install libudunits2 if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') + run: sudo apt-get install libudunits2-dev - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true diff --git a/.github/workflows/Render-README.yaml b/.github/workflows/Render-README.yaml index 1e1da1883..fcd8f28f5 100644 --- a/.github/workflows/Render-README.yaml +++ b/.github/workflows/Render-README.yaml @@ -1,39 +1,37 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: - - CRAN - - main - paths: - - README.Rmd + paths: ["README.Rmd"] name: Render-README jobs: render-readme: - name: Render README - runs-on: macOS-latest + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 - - uses: r-lib/actions/setup-pandoc@v1 + - name: Checkout repo + uses: actions/checkout@v2 + with: + fetch-depth: 0 - - name: Install rmarkdown, remotes, and the local package - run: | - install.packages("remotes") - remotes::install_cran("rmarkdown") - remotes::install_cran("landscapetools") - remotes::install_local(".") - shell: Rscript {0} + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rmarkdown, any::landscapemetrics, any::landscapetools - - name: Render README + - name: Render README files run: Rscript -e 'rmarkdown::render("README.Rmd")' - - name: Commit results + - name: Commit README run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" git add README.md man/figures/README-* git commit -m "Re-build README.md" || echo "No changes to commit" git push origin || echo "No changes to commit" diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml index e3f261e43..ec9037ddf 100644 --- a/.github/workflows/Test-coverage.yaml +++ b/.github/workflows/Test-coverage.yaml @@ -1,45 +1,33 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help + on: push: - branches: - - CRAN - - main + branches: [CRAN, main, development] + pull_request: + branches: [CRAN, main] name: Test-coverage jobs: test-coverage: if: "!contains(github.event.commits[0].message, '[skip-ci]')" - runs-on: macOS-latest + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 - - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Restore R package cache - uses: actions/cache@v2 + - uses: r-lib/actions/setup-r@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + use-public-rspm: true - - name: Install dependencies - run: | - install.packages(c("remotes")) - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("covr") - shell: Rscript {0} + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::stars + needs: coverage - name: Test coverage - run: covr::codecov() + run: covr::codecov(quiet = FALSE) shell: Rscript {0} diff --git a/.github/workflows/Write-codemeta.yaml b/.github/workflows/Write-codemeta.yaml new file mode 100644 index 000000000..320d3062b --- /dev/null +++ b/.github/workflows/Write-codemeta.yaml @@ -0,0 +1,35 @@ +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help + +on: + push: + paths: ['DESCRIPTION'] + +name: Write-codemeta + +jobs: + render-readme: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - name: Checkout repo + uses: actions/checkout@v2 + with: + fetch-depth: 0 + + - uses: r-lib/actions/setup-r@v2 + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::codemeta + + - name: Write codemeta file + run: Rscript -e 'codemeta::write_codemeta()' + + - name: Commit codemeta file + run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + git add codemeta.json + git commit -m "Re-write codemeta.json" || echo "No changes to commit" + git push origin || echo "No changes to commit" diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 24aa0a3cd..762fc7224 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,25 +1,126 @@ -# Contributor Code of Conduct +# Contributor Covenant Code of Conduct -As contributors and maintainers of this project, we pledge to respect all people who -contribute through reporting issues, posting feature requests, updating documentation, -submitting pull requests or patches, and other activities. +## Our Pledge -We are committed to making participation in this project a harassment-free experience for -everyone, regardless of level of experience, gender, gender identity and expression, -sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion. +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity and +orientation. -Examples of unacceptable behavior by participants include the use of sexual language or -imagery, derogatory comments or personal attacks, trolling, public or private harassment, -insults, or other unprofessional conduct. +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. -Project maintainers have the right and responsibility to remove, edit, or reject comments, -commits, code, wiki edits, issues, and other contributions that are not aligned to this -Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed -from the project team. +## Our Standards -Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by -opening an issue or contacting one or more of the project maintainers. +Examples of behavior that contributes to a positive environment for our +community include: -This Code of Conduct is adapted from the Contributor Covenant -(http://contributor-covenant.org), version 1.0.0, available at -http://contributor-covenant.org/version/1/0/0/ +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, +and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall +community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or +advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email +address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a +professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards +of acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies +when an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail +address, posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at mhk.hesselbarth@gmail.com. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, +available at . + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +. Translations are available at . diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d96e398ec..3088bf6ea 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,27 +2,67 @@ ### Please contribute! -We love collaboration. -In fact, this was one of the main ideas to start the work on this package. -This includes suggestions or even implementations of new landscape metrics. -Of course, you are also welcome to suggest general improvements to the package structure or to whatsoever. -We appreciate any contribution and collaboration. +We love collaboration. In fact, this was one of the main ideas to start the work on this package. This includes suggestions or even implementations of new landscape metrics. Of course, you are also welcome to suggest general improvements to the package structure or to whatsoever. We appreciate any contribution and collaboration. -### Bugs? +#### Code of Conduct -* Submit an issue on the Issues page [here](https://github.com/r-spatialecology/landscapemetrics/issues) +Please note that the **landscapemetrics** project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project you agree to abide by its terms. -### Code contributions +## How to contribute -1. Fork this repo to your GitHub account -2. Clone your version to your machine, e.g., `git clone https://github.com/r-spatialecology/landscapemetrics.git` -3. Make sure to track progress upstream (i.e., our version of `landscapemetrics` at `r-spatialecology/landscapemetrics`) by doing `git remote add upstream https://github.com/r-spatialecology/landscapemetrics.git` -Before making any changes, make sure to pull changes in from upstream by either doing `git fetch upstream` then merge later, or `git pull upstream` to fetch and merge in one step -4. Make your changes (bonus points for making changes on a new branch) -5. If you alter package functionality at all (e.g., the code itself, not just documentation) please do write some tests to cover the new functionality. -6. Push changes to your account -7. Submit a pull request to the main branch at `r-spatialecology/landscapemetrics` +### Ask a question :interrobang: -### Questions? Get in touch: [sciaini.marco@gmail.com](mailto:sciaini.marco@gmail.com) or [mhk.hesselbarth@gmail.com](mailto:mhk.hesselbarth@gmail.com) +Browse the [documentation](https://r-spatialecology.github.io/landscapemetrics/) to see if you can find a solution. Still stuck? Open an [issue on GitHub](https://github.com/r-spatialecology/landscapemetrics/issues) on GitHub. We'll try to do our best to address it, as questions often lead to better documentation or the discovery of bugs. -### Thanks for contributing! +If you want to ask a question in private get in contact by [mhk.hesselbarth\gmail.com](mailto:mhk.hesselbarth@gmail.com) or [sciaini.marcogmail.com](mailto:sciaini.marco@gmail.com). + +Please try to include a reproducible example using for example the [`reprex`](https://reprex.tidyverse.org) package. + +### Propose an idea :bulb: + +Take a look at the [documentation](https://r-spatialecology.github.io/landscapemetrics/) and [issue on GitHub](https://github.com/r-spatialecology/landscapemetrics/issues) list to see if it isn't included or suggested yet. If not, please open a new issue! + +While we can't promise to implement your idea, it helps to: + +* Explain in detail how it would work. +* Keep the scope as narrow as possible. + +### Report a bug :bug: + +Report it as an [issue on GitHub](https://github.com/r-spatialecology/landscapemetrics/issue) so we can fix it. A good bug report makes it easier for us to do so, so please include: + +* The content of `utils::sessionInfo()`. +* Any details about your local setup that might be helpful in troubleshooting. +* Detailed steps to reproduce the bug + +Again, please try to include a reproducible example using for example the [`reprex`](https://reprex.tidyverse.org) package. + +### Improve the documentation :book: + +Good documentation makes all the difference, so your help to improve it is very welcome! + +We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation. + +### Pull request process :arrow_up_down: + +We try to follow the [GitHub flow](https://guides.github.com/introduction/flow/) for development. + +1. Fork [the repo](https://github.com/r-spatialecology/landscapemetrics) and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/). Don't forget to pull all new changes before starting to work! + +2. Open the RStudio project file (`.Rproj`) and install all development dependencies with (e.g., using `devtools::install_dev_deps()`). Make sure the package passes R CMD check by running `devtools::check()`. + +3. Create a new Git branch and use a name that briefly describes the proposed changes. + +4. Make your changes: + * Write your code. + * Test your code (bonus points for adding unit tests using the [`testthat`](https://testthat.r-lib.org) package). + * Document your code (see function documentation above). + * Check your code with `devtools::check()` and aim for 0 errors, warnings and notes. +5. Commit and push your changes. +6. Submit a [pull request](https://guides.github.com/activities/forking/#making-a-pull-request). + +New code should follow the tidyverse [style guide](https://style.tidyverse.org). + +#### References + +This CONTRIBUTING.md is adapted from [here](https://gist.github.com/peterdesmet/e90a1b0dc17af6c12daf6e8b2f044e7c) and [here](https://github.com/r-lib/usethis/blob/main/inst/templates/tidy-contributing.md). diff --git a/DESCRIPTION b/DESCRIPTION index 7b063caef..e80ebf48d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: landscapemetrics Title: Landscape Metrics for Categorical Map Patterns -Version: 1.5.4 -Authors@R: c(person("Maximillian H.K.", "Hesselbarth", +Version: 1.5.5 +Authors@R: c(person("Maximilian H.K.", "Hesselbarth", role = c("aut", "cre"), email = "mhk.hesselbarth@gmail.com", comment = c(ORCID = "0000-0003-1125-9918")), @@ -36,10 +36,10 @@ Authors@R: c(person("Maximillian H.K.", "Hesselbarth", role = "ctb", comment = "Bugfix in sample_metrics()") ) -Maintainer: Maximillian H.K. Hesselbarth +Maintainer: Maximilian H.K. Hesselbarth Description: Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from - 'FRAGSTATS' () + 'FRAGSTATS' () and new ones from the current literature on landscape metrics. This package supports 'raster' spatial objects and takes RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the @@ -78,6 +78,6 @@ ByteCompile: true Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.1 +RoxygenNote: 7.2.1 SystemRequirements: C++11 VignetteBuilder: knitr diff --git a/NEWS.md b/NEWS.md index db82733d2..946bb2f14 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# landscapemetrics 1.5.5 +* Improvements + * `get_patches` returns a unique patch id for all classes + * Adds adds the ability to use a circular window in `window_lsm()` + * Various + * Fix typo in Maintainer name + # landscapemetrics 1.5.4 * Improvements * Improved memory performance related to perimeter and edge calculations diff --git a/R/calculate_lsm.R b/R/calculate_lsm.R index 2c42cfbf3..aa3ce1e4c 100644 --- a/R/calculate_lsm.R +++ b/R/calculate_lsm.R @@ -57,7 +57,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export calculate_lsm <- function(landscape, diff --git a/R/extract_lsm.R b/R/extract_lsm.R index 11fdd8069..d1ca1f50e 100644 --- a/R/extract_lsm.R +++ b/R/extract_lsm.R @@ -170,21 +170,7 @@ extract_lsm_internal <- function(landscape, } # get patches of landscape - landscape_labeled <- get_patches(landscape, - directions = directions, - class = "all", - to_disk = getOption("to_disk", default = FALSE), - return_raster = TRUE)[[1]] - - # label patch id continuously - for (i in seq_len(length(landscape_labeled) - 1)) { - - # max patch id of current layer - max_patch_id <- max(raster::values(landscape_labeled[[i]]), na.rm = TRUE) - - # add max patch id to ids of next layer - landscape_labeled[[i + 1]] <- landscape_labeled[[i + 1]] + max_patch_id - } + landscape_labeled <- get_patches(landscape, directions = directions,)[[1]] # combine to one raster layer landscape_id <- raster::merge(raster::stack(landscape_labeled)) diff --git a/R/get_centroids.R b/R/get_centroids.R index 221606f63..eee47a800 100644 --- a/R/get_centroids.R +++ b/R/get_centroids.R @@ -27,14 +27,14 @@ get_centroids <- function(landscape, directions = 8, cell_center = FALSE, return_sp = FALSE, verbose = TRUE) { + landscape <- landscape_as_list(landscape) + if (return_sp) { - crs <- raster::crs(landscape) + crs <- raster::crs(landscape[[1]]) } - landscape <- landscape_as_list(landscape) - result <- lapply(X = landscape, FUN = get_centroids_calc, directions = directions, diff --git a/R/get_patches.R b/R/get_patches.R index 975228c07..d69707050 100644 --- a/R/get_patches.R +++ b/R/get_patches.R @@ -53,47 +53,54 @@ get_patches <- function(landscape, class = "all", directions = 8, landscape <- landscape_as_list(landscape) - result <- lapply(X = landscape, - FUN = function(x, class, directions, return_raster, to_disk) { + result <- lapply(X = landscape, FUN = function(i) { - # convert to matrix - if (!inherits(x = x, what = "matrix")) { + res_temp <- get_patches_int(landscape = i, class = "all", directions = directions, + return_raster = return_raster, to_disk = to_disk) - x_matrix <- raster::as.matrix(x) + # filter returned classes + if (all(class != "all")) { - } else { + res_temp <- res_temp[names(res_temp) == paste0("class_", class)] - x_matrix <- x + if (length(res_temp) == 0) { - } + stop("Selected class not present in landscape.", call. = FALSE) - result_temp <- get_patches_int(x_matrix, class, directions) + } - if ((return_raster || to_disk) && !inherits(x = x, what = "matrix")) { + } - result_temp <- lapply(result_temp, FUN = matrix_to_raster, - landscape = x, to_disk = to_disk) + return(res_temp) + }) - } else if ((return_raster || to_disk) && inherits(x = x, what = "matrix")) { + names(result) <- paste0("layer_", 1:length(landscape)) - warning("'return_raster = TRUE' or 'to_disk = TRUE' not able for matrix input.", - call. = FALSE) + return(result) - } +} - return(result_temp) - }, class = class, directions = directions, - return_raster = return_raster, to_disk = to_disk) +get_patches_int <- function(landscape, class, directions, + return_raster = FALSE, to_disk = FALSE) { - names(result) <- paste0("layer_", 1:length(landscape)) + # convert to matrix + if (!inherits(x = landscape, what = "matrix")) { - return(result) + landscape_mat <- raster::as.matrix(landscape) -} + # already a matrix + } else { + + landscape_mat <- landscape + + if (return_raster || to_disk) { -get_patches_int <- function(landscape, - class, - directions) { + return_raster <- FALSE + + warning("'return_raster' or 'to_disk' not possible for matrix input.", call. = FALSE) + + } + } # check if directions argument is valid if (directions != 4 && directions != 8) { @@ -104,72 +111,64 @@ get_patches_int <- function(landscape, directions <- 8 } - # get unique classes - unique_classes <- get_unique_values_int(landscape, verbose = FALSE) + if (class == "all") { - # set-up filter matrix - filter_matrix <- matrix(NA, - nrow = nrow(landscape), - ncol = ncol(landscape)) + # get unique class id + unique_classes <- get_unique_values_int(landscape_mat, verbose = FALSE) - # class is specified - if (any(class != "all")) { + } else { - # check if class is present in landscape - if (!any(class %in% unique_classes)) { - stop("Not all provided classes present in landscape") - } + unique_classes <- class - patch_landscape <- lapply(X = class, FUN = function(current_class) { + } - # set all values in filter_matrix to 1 that belong to class (at same spot as in original landscape) - filter_matrix[landscape == current_class] <- 1L + # init highest patch id + counter_id <- 0 - # connected labeling with 4 neighbours - if (directions == 4) { - #patch_landscape <- .Call('ccl_4', filter_matrix, PACKAGE = 'landscapemetrics') - rcpp_ccl(filter_matrix, 4) - patch_landscape_temp <- filter_matrix - } + # init list with classes + patch_landscape <- vector(mode = "list", length = length(unique_classes)) - # connected labeling with 8 neighbours - if (directions == 8) { - #patch_landscape <- .Call('ccl_8', filter_matrix, PACKAGE = 'landscapemetrics') - rcpp_ccl(filter_matrix, 8) - patch_landscape_temp <- filter_matrix - } + # CCL all classes + for (i in 1:length(unique_classes)) { - return(patch_landscape_temp) - }) + # set-up filter matrix + landscape_temp <- matrix(NA, nrow = nrow(landscape_mat), + ncol = ncol(landscape_mat)) - names(patch_landscape) <- paste0("class_", class) + # set all values in filter_matrix to 1 that belong to class (at same spot as in original landscape) + landscape_temp[landscape_mat == unique_classes[i]] <- 1L - } else { + # connected labeling with 4 neighbours + if (directions == 4) { - patch_landscape <- lapply(X = unique_classes, FUN = function(class) { + rcpp_ccl(landscape_temp, 4) - filter_matrix[landscape == class] <- 1L + # connected labeling with 8 neighbours + } else if (directions == 8) { - # connected labeling with 4 neighbours - if (directions == 4) { - rcpp_ccl(filter_matrix, 4) - patch_landscape_temp <- filter_matrix - } + rcpp_ccl(landscape_temp, 8) - # connected labeling with 8 neighbours - if (directions == 8) { - rcpp_ccl(filter_matrix, 8) - patch_landscape_temp <- filter_matrix - } + } - return(patch_landscape_temp) - }) + # increase patch id by highest value so far + landscape_temp <- landscape_temp + counter_id - names(patch_landscape) <- paste0("class_", unique_classes) + # update highest patch id + counter_id <- max(landscape_temp, na.rm = TRUE) - patch_landscape <- patch_landscape[order(nchar(names(patch_landscape)), names(patch_landscape))] + # return matrix to + if (return_raster) { + + landscape_temp <- matrix_to_raster(matrix = landscape_temp, + landscape = landscape, to_disk = to_disk) + } + + patch_landscape[[i]] <- landscape_temp } + # set class names + names(patch_landscape) <- paste0("class_", unique_classes) + return(patch_landscape) } diff --git a/R/get_unique_values.R b/R/get_unique_values.R index 0450e328b..a3a97d72b 100644 --- a/R/get_unique_values.R +++ b/R/get_unique_values.R @@ -75,5 +75,5 @@ get_unique_values_int <- function(landscape, verbose) { } - rcpp_get_unique_values(landscape) + sort(rcpp_get_unique_values(landscape)) } diff --git a/R/landscapemetrics-package.R b/R/landscapemetrics-package.R index 63f7c8517..0d17b1f8e 100644 --- a/R/landscapemetrics-package.R +++ b/R/landscapemetrics-package.R @@ -14,7 +14,7 @@ #' @docType package #' @useDynLib landscapemetrics #' @importFrom Rcpp sourceCpp -# nocov start +#' @keywords internal "_PACKAGE" globalVariables(c("class_name", @@ -51,5 +51,3 @@ globalVariables(c("class_name", "x_centroid", "y", "y_centroid")) - -# nocov end diff --git a/R/list_lsm.R b/R/list_lsm.R index 3e0dbda51..923f01ab4 100644 --- a/R/list_lsm.R +++ b/R/list_lsm.R @@ -37,7 +37,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export list_lsm <- function(level = NULL, diff --git a/R/lsm_c_ai.R b/R/lsm_c_ai.R index cb9864cba..44a0bdc54 100644 --- a/R/lsm_c_ai.R +++ b/R/lsm_c_ai.R @@ -34,7 +34,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' He, H. S., DeZonia, B. E., & Mladenoff, D. J. 2000. An aggregation index (AI) #' to quantify spatial patterns of landscapes. Landscape ecology, 15(7), 591-601. diff --git a/R/lsm_c_area_cv.R b/R/lsm_c_area_cv.R index 07a3cdedf..d5349d1be 100644 --- a/R/lsm_c_area_cv.R +++ b/R/lsm_c_area_cv.R @@ -40,7 +40,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_area_cv <- function(landscape, directions = 8) { diff --git a/R/lsm_c_area_mn.R b/R/lsm_c_area_mn.R index e24425571..e3dbd6f9a 100644 --- a/R/lsm_c_area_mn.R +++ b/R/lsm_c_area_mn.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_area_mn <- function(landscape, directions = 8) { diff --git a/R/lsm_c_area_sd.R b/R/lsm_c_area_sd.R index 40765bfe7..ddfde8a15 100644 --- a/R/lsm_c_area_sd.R +++ b/R/lsm_c_area_sd.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_area_sd <- function(landscape, directions = 8) { diff --git a/R/lsm_c_ca.R b/R/lsm_c_ca.R index c2f2f0611..ca755baf8 100644 --- a/R/lsm_c_ca.R +++ b/R/lsm_c_ca.R @@ -40,7 +40,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_ca <- function(landscape, directions = 8) { diff --git a/R/lsm_c_cai_cv.R b/R/lsm_c_cai_cv.R index 3a6d901e1..17b3a25f6 100644 --- a/R/lsm_c_cai_cv.R +++ b/R/lsm_c_cai_cv.R @@ -49,7 +49,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_cai_cv <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_cai_mn.R b/R/lsm_c_cai_mn.R index cb11fc2cf..3e6019ac2 100644 --- a/R/lsm_c_cai_mn.R +++ b/R/lsm_c_cai_mn.R @@ -46,7 +46,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_cai_mn <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_cai_sd.R b/R/lsm_c_cai_sd.R index e29e4be14..4494b622b 100644 --- a/R/lsm_c_cai_sd.R +++ b/R/lsm_c_cai_sd.R @@ -48,7 +48,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_cai_sd <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_circle_cv.R b/R/lsm_c_circle_cv.R index 3e8333151..4ba1ae214 100644 --- a/R/lsm_c_circle_cv.R +++ b/R/lsm_c_circle_cv.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of #' landscape structure using the GRASS geographical information system. diff --git a/R/lsm_c_circle_mn.R b/R/lsm_c_circle_mn.R index 4f1611334..926823ba9 100644 --- a/R/lsm_c_circle_mn.R +++ b/R/lsm_c_circle_mn.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of #' landscape structure using the GRASS geographical information system. diff --git a/R/lsm_c_circle_sd.R b/R/lsm_c_circle_sd.R index 39979b67f..6883e7a9a 100644 --- a/R/lsm_c_circle_sd.R +++ b/R/lsm_c_circle_sd.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of #' landscape structure using the GRASS geographical information system. diff --git a/R/lsm_c_clumpy.R b/R/lsm_c_clumpy.R index 168f5ebbf..142877677 100644 --- a/R/lsm_c_clumpy.R +++ b/R/lsm_c_clumpy.R @@ -35,7 +35,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_clumpy <- function(landscape) { diff --git a/R/lsm_c_cohesion.R b/R/lsm_c_cohesion.R index d0fe95f06..7aaafe552 100644 --- a/R/lsm_c_cohesion.R +++ b/R/lsm_c_cohesion.R @@ -38,7 +38,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Schumaker, N. H. 1996. Using landscape indices to predict habitat #' connectivity. Ecology, 77(4), 1210-1225. diff --git a/R/lsm_c_contig_cv.R b/R/lsm_c_contig_cv.R index 2de23d27d..7cd52e737 100644 --- a/R/lsm_c_contig_cv.R +++ b/R/lsm_c_contig_cv.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' LaGro, J. 1991. Assessing patch shape in landscape mosaics. #' Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/R/lsm_c_contig_mn.R b/R/lsm_c_contig_mn.R index c3b1d04a1..09e4ee7ca 100644 --- a/R/lsm_c_contig_mn.R +++ b/R/lsm_c_contig_mn.R @@ -49,7 +49,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' LaGro, J. 1991. Assessing patch shape in landscape mosaics. #' Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/R/lsm_c_contig_sd.R b/R/lsm_c_contig_sd.R index e8bab91d4..0986cc470 100644 --- a/R/lsm_c_contig_sd.R +++ b/R/lsm_c_contig_sd.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' LaGro, J. 1991. Assessing patch shape in landscape mosaics. #' Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/R/lsm_c_core_cv.R b/R/lsm_c_core_cv.R index 6c125ca74..b722afa3c 100644 --- a/R/lsm_c_core_cv.R +++ b/R/lsm_c_core_cv.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_core_cv <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_core_mn.R b/R/lsm_c_core_mn.R index 22de75232..fec73f929 100644 --- a/R/lsm_c_core_mn.R +++ b/R/lsm_c_core_mn.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_core_mn <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_core_sd.R b/R/lsm_c_core_sd.R index 1630b0b2d..23b6c2ee2 100644 --- a/R/lsm_c_core_sd.R +++ b/R/lsm_c_core_sd.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_core_sd <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_cpland.R b/R/lsm_c_cpland.R index 7afd9080f..814cfc707 100644 --- a/R/lsm_c_cpland.R +++ b/R/lsm_c_cpland.R @@ -40,7 +40,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_cpland <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_dcad.R b/R/lsm_c_dcad.R index 9a1dbecd6..dbaa61b1f 100644 --- a/R/lsm_c_dcad.R +++ b/R/lsm_c_dcad.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_dcad <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_dcore_cv.R b/R/lsm_c_dcore_cv.R index d58d7ed2c..badafd31b 100644 --- a/R/lsm_c_dcore_cv.R +++ b/R/lsm_c_dcore_cv.R @@ -48,7 +48,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_dcore_cv <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_dcore_mn.R b/R/lsm_c_dcore_mn.R index 31bc7ab63..deffa61fa 100644 --- a/R/lsm_c_dcore_mn.R +++ b/R/lsm_c_dcore_mn.R @@ -45,7 +45,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_dcore_mn <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_dcore_sd.R b/R/lsm_c_dcore_sd.R index bd92417fb..097ce7de5 100644 --- a/R/lsm_c_dcore_sd.R +++ b/R/lsm_c_dcore_sd.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_dcore_sd <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_division.R b/R/lsm_c_division.R index 2f7c0e58c..914c84605 100644 --- a/R/lsm_c_division.R +++ b/R/lsm_c_division.R @@ -36,7 +36,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh #' size: new measures of landscape fragmentation. diff --git a/R/lsm_c_ed.R b/R/lsm_c_ed.R index 238ed4da1..191432ffb 100644 --- a/R/lsm_c_ed.R +++ b/R/lsm_c_ed.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_ed <- function(landscape, diff --git a/R/lsm_c_enn_cv.R b/R/lsm_c_enn_cv.R index d117498e6..989e95f04 100644 --- a/R/lsm_c_enn_cv.R +++ b/R/lsm_c_enn_cv.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' McGarigal, K., and McComb, W. C. (1995). Relationships between landscape #' structure and breeding birds in the Oregon Coast Range. diff --git a/R/lsm_c_enn_mn.R b/R/lsm_c_enn_mn.R index b5053a952..7ffc63330 100644 --- a/R/lsm_c_enn_mn.R +++ b/R/lsm_c_enn_mn.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' McGarigal, K., and McComb, W. C. (1995). Relationships between landscape #' structure and breeding birds in the Oregon Coast Range. diff --git a/R/lsm_c_enn_sd.R b/R/lsm_c_enn_sd.R index 96e81869d..3fb11ecc3 100644 --- a/R/lsm_c_enn_sd.R +++ b/R/lsm_c_enn_sd.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' McGarigal, K., and McComb, W. C. (1995). Relationships between landscape #' structure and breeding birds in the Oregon Coast Range. diff --git a/R/lsm_c_frac_cv.R b/R/lsm_c_frac_cv.R index 21fb1bcec..de7eae62a 100644 --- a/R/lsm_c_frac_cv.R +++ b/R/lsm_c_frac_cv.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. #' San Francisco. W. H. Freeman and Company. diff --git a/R/lsm_c_frac_mn.R b/R/lsm_c_frac_mn.R index ef0e71912..675129cb1 100644 --- a/R/lsm_c_frac_mn.R +++ b/R/lsm_c_frac_mn.R @@ -40,7 +40,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. #' San Francisco. W. H. Freeman and Company. diff --git a/R/lsm_c_frac_sd.R b/R/lsm_c_frac_sd.R index 6e71b6dfb..102a3b189 100644 --- a/R/lsm_c_frac_sd.R +++ b/R/lsm_c_frac_sd.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. #' San Francisco. W. H. Freeman and Company. diff --git a/R/lsm_c_gyrate_cv.R b/R/lsm_c_gyrate_cv.R index 066205ecd..b3f23fef9 100644 --- a/R/lsm_c_gyrate_cv.R +++ b/R/lsm_c_gyrate_cv.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales #' in fragmented landscapes. Conservation ecology, 1(1). diff --git a/R/lsm_c_gyrate_mn.R b/R/lsm_c_gyrate_mn.R index b51e97f29..68e853a3c 100644 --- a/R/lsm_c_gyrate_mn.R +++ b/R/lsm_c_gyrate_mn.R @@ -48,7 +48,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales #' in fragmented landscapes. Conservation ecology, 1(1). diff --git a/R/lsm_c_gyrate_sd.R b/R/lsm_c_gyrate_sd.R index cc0b8869b..6ac96ac1d 100644 --- a/R/lsm_c_gyrate_sd.R +++ b/R/lsm_c_gyrate_sd.R @@ -49,7 +49,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales #' in fragmented landscapes. Conservation ecology, 1(1). diff --git a/R/lsm_c_iji.R b/R/lsm_c_iji.R index 5982ba698..bd9bb144a 100644 --- a/R/lsm_c_iji.R +++ b/R/lsm_c_iji.R @@ -35,7 +35,7 @@ #'McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #'Program for Categorical and Continuous Maps. Computer software program produced by #'the authors at the University of Massachusetts, Amherst. Available at the following -#'web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#'web site: https://www.umass.edu/landeco/ #' #'McGarigal, K., & Marks, B. J. 1995. FRAGSTATS: spatial pattern analysis #'program for quantifying landscape structure. Gen. Tech. Rep. PNW-GTR-351. diff --git a/R/lsm_c_lpi.R b/R/lsm_c_lpi.R index f47b57dcf..4240425b5 100644 --- a/R/lsm_c_lpi.R +++ b/R/lsm_c_lpi.R @@ -37,7 +37,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_lpi <- function(landscape, directions = 8) { diff --git a/R/lsm_c_lsi.R b/R/lsm_c_lsi.R index 44f431d9c..f17ad7195 100644 --- a/R/lsm_c_lsi.R +++ b/R/lsm_c_lsi.R @@ -35,7 +35,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_c_mesh.R b/R/lsm_c_mesh.R index ea46bd5cc..f9dc00a30 100644 --- a/R/lsm_c_mesh.R +++ b/R/lsm_c_mesh.R @@ -38,7 +38,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh #' size: new measures of landscape fragmentation. diff --git a/R/lsm_c_ndca.R b/R/lsm_c_ndca.R index 92757dce6..bb9ebad06 100644 --- a/R/lsm_c_ndca.R +++ b/R/lsm_c_ndca.R @@ -45,7 +45,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_ndca <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_nlsi.R b/R/lsm_c_nlsi.R index b83cebbd4..4455eb045 100644 --- a/R/lsm_c_nlsi.R +++ b/R/lsm_c_nlsi.R @@ -39,7 +39,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_c_np.R b/R/lsm_c_np.R index 4c35636c2..b1af49f2d 100644 --- a/R/lsm_c_np.R +++ b/R/lsm_c_np.R @@ -33,7 +33,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_np <- function(landscape, directions = 8) { diff --git a/R/lsm_c_pafrac.R b/R/lsm_c_pafrac.R index 0eb8a9c25..ed60ded66 100644 --- a/R/lsm_c_pafrac.R +++ b/R/lsm_c_pafrac.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Burrough, P. A. 1986. Principles of Geographical Information Systems for #' Land Resources Assessment. Monographs on Soil and Resources Survey No. 12. diff --git a/R/lsm_c_para_cv.R b/R/lsm_c_para_cv.R index 22587d59a..f02d84821 100644 --- a/R/lsm_c_para_cv.R +++ b/R/lsm_c_para_cv.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_para_cv <- function(landscape, directions = 8) { diff --git a/R/lsm_c_para_mn.R b/R/lsm_c_para_mn.R index 5ee1ea117..e43dd1bfd 100644 --- a/R/lsm_c_para_mn.R +++ b/R/lsm_c_para_mn.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_para_mn <- function(landscape, directions = 8) { diff --git a/R/lsm_c_para_sd.R b/R/lsm_c_para_sd.R index dfa570713..0dc37dd62 100644 --- a/R/lsm_c_para_sd.R +++ b/R/lsm_c_para_sd.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_para_sd <- function(landscape, directions = 8) { diff --git a/R/lsm_c_pd.R b/R/lsm_c_pd.R index 472526bc6..2874d7a09 100644 --- a/R/lsm_c_pd.R +++ b/R/lsm_c_pd.R @@ -38,7 +38,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_pd <- function(landscape, directions = 8) { diff --git a/R/lsm_c_pladj.R b/R/lsm_c_pladj.R index d560c9fdf..5b663e80b 100644 --- a/R/lsm_c_pladj.R +++ b/R/lsm_c_pladj.R @@ -31,7 +31,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html. +#' web site: https://www.umass.edu/landeco/. #' #' @export lsm_c_pladj <- function(landscape) { diff --git a/R/lsm_c_pland.R b/R/lsm_c_pland.R index 5efa51c7e..5d279c945 100644 --- a/R/lsm_c_pland.R +++ b/R/lsm_c_pland.R @@ -36,7 +36,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_pland <- function(landscape, directions = 8) { diff --git a/R/lsm_c_shape_cv.R b/R/lsm_c_shape_cv.R index 26324c5e1..e18e7df11 100644 --- a/R/lsm_c_shape_cv.R +++ b/R/lsm_c_shape_cv.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_c_shape_mn.R b/R/lsm_c_shape_mn.R index af1d670e5..a85ca1663 100644 --- a/R/lsm_c_shape_mn.R +++ b/R/lsm_c_shape_mn.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_c_shape_sd.R b/R/lsm_c_shape_sd.R index 41365ef97..8116fea7d 100644 --- a/R/lsm_c_shape_sd.R +++ b/R/lsm_c_shape_sd.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_c_split.R b/R/lsm_c_split.R index cbc0f3660..588f03d82 100644 --- a/R/lsm_c_split.R +++ b/R/lsm_c_split.R @@ -36,7 +36,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh #' size: new measures of landscape fragmentation. diff --git a/R/lsm_c_tca.R b/R/lsm_c_tca.R index 6b7e36c8c..fdff5c0f1 100644 --- a/R/lsm_c_tca.R +++ b/R/lsm_c_tca.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_tca <- function(landscape, directions = 8, consider_boundary = FALSE, edge_depth = 1) { diff --git a/R/lsm_c_te.R b/R/lsm_c_te.R index 995e4bf0d..e98eebb4a 100644 --- a/R/lsm_c_te.R +++ b/R/lsm_c_te.R @@ -15,7 +15,7 @@ #' all other classes k. It measures the configuration of the landscape because a highly #' fragmented landscape will have many edges. However, total edge is an absolute measure, #' making comparisons among landscapes with different total areas difficult. If -#' \code{cound_boundary = TRUE} also edges to the landscape boundary are included. +#' \code{count_boundary = TRUE} also edges to the landscape boundary are included. #' #' \subsection{Units}{Meters} #' \subsection{Range}{TE >= 0} @@ -38,7 +38,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_c_te <- function(landscape, diff --git a/R/lsm_l_ai.R b/R/lsm_l_ai.R index a042d9bb6..27e378909 100644 --- a/R/lsm_l_ai.R +++ b/R/lsm_l_ai.R @@ -35,7 +35,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' He, H. S., DeZonia, B. E., & Mladenoff, D. J. 2000. An aggregation index (AI) #' to quantify spatial patterns of landscapes. Landscape ecology, 15(7), 591-601. diff --git a/R/lsm_l_area_cv.R b/R/lsm_l_area_cv.R index a627b0a62..7175b817f 100644 --- a/R/lsm_l_area_cv.R +++ b/R/lsm_l_area_cv.R @@ -40,7 +40,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_area_cv <- function(landscape, directions = 8) { diff --git a/R/lsm_l_area_mn.R b/R/lsm_l_area_mn.R index fad3f3a1a..99e170e6f 100644 --- a/R/lsm_l_area_mn.R +++ b/R/lsm_l_area_mn.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_area_mn <- function(landscape, directions = 8) { diff --git a/R/lsm_l_area_sd.R b/R/lsm_l_area_sd.R index 0aa9b0747..d8f50f02f 100644 --- a/R/lsm_l_area_sd.R +++ b/R/lsm_l_area_sd.R @@ -39,7 +39,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_area_sd <- function(landscape, directions = 8) { diff --git a/R/lsm_l_cai_cv.R b/R/lsm_l_cai_cv.R index dcb4ff6a2..7b94a0fc6 100644 --- a/R/lsm_l_cai_cv.R +++ b/R/lsm_l_cai_cv.R @@ -49,7 +49,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_cai_cv <- function(landscape, diff --git a/R/lsm_l_cai_mn.R b/R/lsm_l_cai_mn.R index 80f1aa164..680715b2b 100644 --- a/R/lsm_l_cai_mn.R +++ b/R/lsm_l_cai_mn.R @@ -46,7 +46,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_cai_mn <- function(landscape, diff --git a/R/lsm_l_cai_sd.R b/R/lsm_l_cai_sd.R index 6c6c06533..59ae872f5 100644 --- a/R/lsm_l_cai_sd.R +++ b/R/lsm_l_cai_sd.R @@ -48,7 +48,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_cai_sd <- function(landscape, diff --git a/R/lsm_l_circle_cv.R b/R/lsm_l_circle_cv.R index 68d51406d..beea372c1 100644 --- a/R/lsm_l_circle_cv.R +++ b/R/lsm_l_circle_cv.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of #' landscape structure using the GRASS geographical information system. diff --git a/R/lsm_l_circle_mn.R b/R/lsm_l_circle_mn.R index 92cdd5d60..eab4a0343 100644 --- a/R/lsm_l_circle_mn.R +++ b/R/lsm_l_circle_mn.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of #' landscape structure using the GRASS geographical information system. diff --git a/R/lsm_l_circle_sd.R b/R/lsm_l_circle_sd.R index abd1b7bca..0e89a5fff 100644 --- a/R/lsm_l_circle_sd.R +++ b/R/lsm_l_circle_sd.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of #' landscape structure using the GRASS geographical information system. diff --git a/R/lsm_l_cohesion.R b/R/lsm_l_cohesion.R index 06a0c0e3a..3b42b18ee 100644 --- a/R/lsm_l_cohesion.R +++ b/R/lsm_l_cohesion.R @@ -33,7 +33,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Schumaker, N. H. 1996. Using landscape indices to predict habitat #' connectivity. Ecology, 77(4), 1210-1225. diff --git a/R/lsm_l_contag.R b/R/lsm_l_contag.R index 89b5276ae..908fba1a9 100644 --- a/R/lsm_l_contag.R +++ b/R/lsm_l_contag.R @@ -38,7 +38,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Riitters, K.H., O’Neill, R.V., Wickham, J.D. & Jones, K.B. (1996). A note on #' contagion indices for landscape analysis. Landscape ecology, 11, 197–202. diff --git a/R/lsm_l_contig_cv.R b/R/lsm_l_contig_cv.R index 2f61822b4..e1547e4c2 100644 --- a/R/lsm_l_contig_cv.R +++ b/R/lsm_l_contig_cv.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' LaGro, J. 1991. Assessing patch shape in landscape mosaics. #' Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/R/lsm_l_contig_mn.R b/R/lsm_l_contig_mn.R index a5096b5f3..2833aaba6 100644 --- a/R/lsm_l_contig_mn.R +++ b/R/lsm_l_contig_mn.R @@ -49,7 +49,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' LaGro, J. 1991. Assessing patch shape in landscape mosaics. #' Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/R/lsm_l_contig_sd.R b/R/lsm_l_contig_sd.R index 7f2cfcdfa..2f6062eb9 100644 --- a/R/lsm_l_contig_sd.R +++ b/R/lsm_l_contig_sd.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' LaGro, J. 1991. Assessing patch shape in landscape mosaics. #' Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/R/lsm_l_core_cv.R b/R/lsm_l_core_cv.R index c8184a13c..560eb80c5 100644 --- a/R/lsm_l_core_cv.R +++ b/R/lsm_l_core_cv.R @@ -46,7 +46,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_core_cv <- function(landscape, diff --git a/R/lsm_l_core_mn.R b/R/lsm_l_core_mn.R index c803064ce..8aa529347 100644 --- a/R/lsm_l_core_mn.R +++ b/R/lsm_l_core_mn.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_core_mn <- function(landscape, diff --git a/R/lsm_l_core_sd.R b/R/lsm_l_core_sd.R index eabf1e633..3241573cf 100644 --- a/R/lsm_l_core_sd.R +++ b/R/lsm_l_core_sd.R @@ -45,7 +45,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_core_sd <- function(landscape, diff --git a/R/lsm_l_dcad.R b/R/lsm_l_dcad.R index 762e0780e..813da280a 100644 --- a/R/lsm_l_dcad.R +++ b/R/lsm_l_dcad.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_dcad <- function(landscape, diff --git a/R/lsm_l_dcore_cv.R b/R/lsm_l_dcore_cv.R index 5b7403cfd..82adee80f 100644 --- a/R/lsm_l_dcore_cv.R +++ b/R/lsm_l_dcore_cv.R @@ -48,7 +48,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_dcore_cv <- function(landscape, diff --git a/R/lsm_l_dcore_mn.R b/R/lsm_l_dcore_mn.R index 4f4c6eeda..269eb00a4 100644 --- a/R/lsm_l_dcore_mn.R +++ b/R/lsm_l_dcore_mn.R @@ -45,7 +45,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_dcore_mn <- function(landscape, diff --git a/R/lsm_l_dcore_sd.R b/R/lsm_l_dcore_sd.R index 532fa338e..9e459d403 100644 --- a/R/lsm_l_dcore_sd.R +++ b/R/lsm_l_dcore_sd.R @@ -47,7 +47,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_dcore_sd <- function(landscape, diff --git a/R/lsm_l_division.R b/R/lsm_l_division.R index 55182982e..13a4465e9 100644 --- a/R/lsm_l_division.R +++ b/R/lsm_l_division.R @@ -36,7 +36,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh #' size: new measures of landscape fragmentation. diff --git a/R/lsm_l_ed.R b/R/lsm_l_ed.R index 26ea29d3f..9578a8616 100644 --- a/R/lsm_l_ed.R +++ b/R/lsm_l_ed.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_ed <- function(landscape, diff --git a/R/lsm_l_enn_cv.R b/R/lsm_l_enn_cv.R index 5eb979a87..f25ef6e0c 100644 --- a/R/lsm_l_enn_cv.R +++ b/R/lsm_l_enn_cv.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' McGarigal, K., and McComb, W. C. (1995). Relationships between landscape #' structure and breeding birds in the Oregon Coast Range. diff --git a/R/lsm_l_enn_mn.R b/R/lsm_l_enn_mn.R index c97a0b005..5581239e9 100644 --- a/R/lsm_l_enn_mn.R +++ b/R/lsm_l_enn_mn.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' McGarigal, K., and McComb, W. C. (1995). Relationships between landscape #' structure and breeding birds in the Oregon Coast Range. diff --git a/R/lsm_l_enn_sd.R b/R/lsm_l_enn_sd.R index 1daa1ab11..97b8cb12c 100644 --- a/R/lsm_l_enn_sd.R +++ b/R/lsm_l_enn_sd.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' McGarigal, K., and McComb, W. C. (1995). Relationships between landscape #' structure and breeding birds in the Oregon Coast Range. diff --git a/R/lsm_l_frac_cv.R b/R/lsm_l_frac_cv.R index 08d54f3bd..2537f60d7 100644 --- a/R/lsm_l_frac_cv.R +++ b/R/lsm_l_frac_cv.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. #' San Francisco. W. H. Freeman and Company. diff --git a/R/lsm_l_frac_mn.R b/R/lsm_l_frac_mn.R index eeee85862..5a3d71f5c 100644 --- a/R/lsm_l_frac_mn.R +++ b/R/lsm_l_frac_mn.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. #' San Francisco. W. H. Freeman and Company. diff --git a/R/lsm_l_frac_sd.R b/R/lsm_l_frac_sd.R index a0b54faf4..7a7408c45 100644 --- a/R/lsm_l_frac_sd.R +++ b/R/lsm_l_frac_sd.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. #' San Francisco. W. H. Freeman and Company. diff --git a/R/lsm_l_gyrate_cv.R b/R/lsm_l_gyrate_cv.R index 70229e92b..11761407b 100644 --- a/R/lsm_l_gyrate_cv.R +++ b/R/lsm_l_gyrate_cv.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales #' in fragmented landscapes. Conservation ecology, 1(1). diff --git a/R/lsm_l_gyrate_mn.R b/R/lsm_l_gyrate_mn.R index 3c00a6852..25bab9d09 100644 --- a/R/lsm_l_gyrate_mn.R +++ b/R/lsm_l_gyrate_mn.R @@ -48,7 +48,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales #' in fragmented landscapes. Conservation ecology, 1(1). diff --git a/R/lsm_l_gyrate_sd.R b/R/lsm_l_gyrate_sd.R index e5ec395a2..637452488 100644 --- a/R/lsm_l_gyrate_sd.R +++ b/R/lsm_l_gyrate_sd.R @@ -49,7 +49,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales #' in fragmented landscapes. Conservation ecology, 1(1). diff --git a/R/lsm_l_iji.R b/R/lsm_l_iji.R index ab2b251b1..bc894c8a7 100644 --- a/R/lsm_l_iji.R +++ b/R/lsm_l_iji.R @@ -36,7 +36,7 @@ #'McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #'Program for Categorical and Continuous Maps. Computer software program produced by #'the authors at the University of Massachusetts, Amherst. Available at the following -#'web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#'web site: https://www.umass.edu/landeco/ #' #'McGarigal, K., & Marks, B. J. 1995. FRAGSTATS: spatial pattern analysis #'program for quantifying landscape structure. Gen. Tech. Rep. PNW-GTR-351. diff --git a/R/lsm_l_lpi.R b/R/lsm_l_lpi.R index 40068fa99..f43575bd7 100644 --- a/R/lsm_l_lpi.R +++ b/R/lsm_l_lpi.R @@ -37,7 +37,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_lpi <- function(landscape, directions = 8) { diff --git a/R/lsm_l_lsi.R b/R/lsm_l_lsi.R index aecc05cde..12b50169e 100644 --- a/R/lsm_l_lsi.R +++ b/R/lsm_l_lsi.R @@ -35,7 +35,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_l_mesh.R b/R/lsm_l_mesh.R index 2f029aa04..b5e1efb10 100644 --- a/R/lsm_l_mesh.R +++ b/R/lsm_l_mesh.R @@ -38,7 +38,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh #' size: new measures of landscape fragmentation. diff --git a/R/lsm_l_msidi.R b/R/lsm_l_msidi.R index eaa0c6d7a..7ae051238 100644 --- a/R/lsm_l_msidi.R +++ b/R/lsm_l_msidi.R @@ -32,7 +32,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Simpson, E. H. 1949. Measurement of diversity. Nature 163:688 #' diff --git a/R/lsm_l_msiei.R b/R/lsm_l_msiei.R index 545bb7303..dc9bfb4a4 100644 --- a/R/lsm_l_msiei.R +++ b/R/lsm_l_msiei.R @@ -32,7 +32,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Simpson, E. H. 1949. Measurement of diversity. Nature 163:688 #' diff --git a/R/lsm_l_ndca.R b/R/lsm_l_ndca.R index d8baa5d82..5d05a037a 100644 --- a/R/lsm_l_ndca.R +++ b/R/lsm_l_ndca.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_ndca <- function(landscape, diff --git a/R/lsm_l_np.R b/R/lsm_l_np.R index 7e0e4a999..6f19de277 100644 --- a/R/lsm_l_np.R +++ b/R/lsm_l_np.R @@ -34,7 +34,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_np <- function(landscape, directions = 8) { diff --git a/R/lsm_l_pafrac.R b/R/lsm_l_pafrac.R index f84a6cb53..85056d142 100644 --- a/R/lsm_l_pafrac.R +++ b/R/lsm_l_pafrac.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Burrough, P. A. 1986. Principles of Geographical Information Systems for #' Land Resources Assessment. Monographs on Soil and Resources Survey No. 12. diff --git a/R/lsm_l_para_cv.R b/R/lsm_l_para_cv.R index 091bb95b1..15b3d1968 100644 --- a/R/lsm_l_para_cv.R +++ b/R/lsm_l_para_cv.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_para_cv <- function(landscape, directions = 8) { diff --git a/R/lsm_l_para_mn.R b/R/lsm_l_para_mn.R index 1e985e183..e7111da3f 100644 --- a/R/lsm_l_para_mn.R +++ b/R/lsm_l_para_mn.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_para_mn <- function(landscape, directions = 8) { diff --git a/R/lsm_l_para_sd.R b/R/lsm_l_para_sd.R index b2b39f653..00cb417e5 100644 --- a/R/lsm_l_para_sd.R +++ b/R/lsm_l_para_sd.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_para_sd <- function(landscape, directions = 8) { diff --git a/R/lsm_l_pd.R b/R/lsm_l_pd.R index be99b3483..4183be275 100644 --- a/R/lsm_l_pd.R +++ b/R/lsm_l_pd.R @@ -38,7 +38,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_pd <- function(landscape, directions = 8) { diff --git a/R/lsm_l_pladj.R b/R/lsm_l_pladj.R index 63980e86c..17b993b64 100644 --- a/R/lsm_l_pladj.R +++ b/R/lsm_l_pladj.R @@ -31,7 +31,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html. +#' web site: https://www.umass.edu/landeco/. #' #' @export lsm_l_pladj <- function(landscape) { diff --git a/R/lsm_l_pr.R b/R/lsm_l_pr.R index a583e0b83..9527f5cf2 100644 --- a/R/lsm_l_pr.R +++ b/R/lsm_l_pr.R @@ -29,7 +29,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_pr <- function(landscape){ diff --git a/R/lsm_l_prd.R b/R/lsm_l_prd.R index feaa044d5..16d058bcb 100644 --- a/R/lsm_l_prd.R +++ b/R/lsm_l_prd.R @@ -33,7 +33,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_prd <- function(landscape, directions = 8) { diff --git a/R/lsm_l_rpr.R b/R/lsm_l_rpr.R index d2050a805..b83fb3e1d 100644 --- a/R/lsm_l_rpr.R +++ b/R/lsm_l_rpr.R @@ -33,7 +33,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Romme, W. H. 1982. Fire and landscapediversity in subalpine forests of #' Yellowstone National Park.Ecol.Monogr. 52:199-221 diff --git a/R/lsm_l_shape_cv.R b/R/lsm_l_shape_cv.R index 9372a0b13..10ba6ba10 100644 --- a/R/lsm_l_shape_cv.R +++ b/R/lsm_l_shape_cv.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_l_shape_mn.R b/R/lsm_l_shape_mn.R index c7db16a23..a2889f501 100644 --- a/R/lsm_l_shape_mn.R +++ b/R/lsm_l_shape_mn.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_l_shape_sd.R b/R/lsm_l_shape_sd.R index 7daf22736..09e25c787 100644 --- a/R/lsm_l_shape_sd.R +++ b/R/lsm_l_shape_sd.R @@ -41,7 +41,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/lsm_l_shdi.R b/R/lsm_l_shdi.R index 355d31301..161b20114 100644 --- a/R/lsm_l_shdi.R +++ b/R/lsm_l_shdi.R @@ -32,7 +32,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Shannon, C., and W. Weaver. 1949. The mathematical theory of #' communication. Univ. IllinoisPress, Urbana diff --git a/R/lsm_l_shei.R b/R/lsm_l_shei.R index a0c79564a..916597b31 100644 --- a/R/lsm_l_shei.R +++ b/R/lsm_l_shei.R @@ -34,7 +34,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Shannon, C., and W. Weaver. 1949. The mathematical theory of #' communication. Univ. IllinoisPress, Urbana diff --git a/R/lsm_l_sidi.R b/R/lsm_l_sidi.R index f5c251cce..805d06865 100644 --- a/R/lsm_l_sidi.R +++ b/R/lsm_l_sidi.R @@ -37,7 +37,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Simpson, E. H. 1949. Measurement of diversity. Nature 163:688 #' diff --git a/R/lsm_l_siei.R b/R/lsm_l_siei.R index 188f13c48..3021b1710 100644 --- a/R/lsm_l_siei.R +++ b/R/lsm_l_siei.R @@ -37,7 +37,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Simpson, E. H. 1949. Measurement of diversity. Nature 163:688 #' diff --git a/R/lsm_l_split.R b/R/lsm_l_split.R index e2872d778..fb9ed6165 100644 --- a/R/lsm_l_split.R +++ b/R/lsm_l_split.R @@ -36,7 +36,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh #' size: new measures of landscape fragmentation. diff --git a/R/lsm_l_ta.R b/R/lsm_l_ta.R index 1996f8289..8f2eb164e 100644 --- a/R/lsm_l_ta.R +++ b/R/lsm_l_ta.R @@ -35,7 +35,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_ta <- function(landscape, directions = 8) { diff --git a/R/lsm_l_tca.R b/R/lsm_l_tca.R index 57a7c6ec9..ce6c2208f 100644 --- a/R/lsm_l_tca.R +++ b/R/lsm_l_tca.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_tca <- function(landscape, diff --git a/R/lsm_l_te.R b/R/lsm_l_te.R index 5913b760c..aae830014 100644 --- a/R/lsm_l_te.R +++ b/R/lsm_l_te.R @@ -12,7 +12,7 @@ #' TE is an 'Area and edge metric'. Total edge includes all edges. It measures the #' configuration of the landscape because a highly fragmented landscape will have many #' edges. However, total edge is an absolute measure, making comparisons among landscapes -#' with different total areas difficult. If \code{cound_boundary = TRUE} also edges to the +#' with different total areas difficult. If \code{count_boundary = TRUE} also edges to the #' landscape boundary are included. #' #' \subsection{Units}{Meters} @@ -36,7 +36,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_l_te <- function(landscape, count_boundary = FALSE) { diff --git a/R/lsm_p_area.R b/R/lsm_p_area.R index bd8bcc985..7b81662ab 100644 --- a/R/lsm_p_area.R +++ b/R/lsm_p_area.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_p_area <- function(landscape, directions = 8) { @@ -65,6 +65,7 @@ lsm_p_area_calc <- function(landscape, directions, resolution = NULL){ # convert to matrix if (!inherits(x = landscape, what = "matrix")) { + resolution <- raster::res(landscape) landscape <- raster::as.matrix(landscape) diff --git a/R/lsm_p_cai.R b/R/lsm_p_cai.R index b81be2d17..de7c029bd 100644 --- a/R/lsm_p_cai.R +++ b/R/lsm_p_cai.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_p_cai <- function(landscape, diff --git a/R/lsm_p_circle.R b/R/lsm_p_circle.R index ff99fbccb..11c6374ed 100644 --- a/R/lsm_p_circle.R +++ b/R/lsm_p_circle.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of #' landscape structure using the GRASS geographical information system. diff --git a/R/lsm_p_contig.R b/R/lsm_p_contig.R index 2eeadad99..21f7342f1 100644 --- a/R/lsm_p_contig.R +++ b/R/lsm_p_contig.R @@ -51,7 +51,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' LaGro, J. 1991. Assessing patch shape in landscape mosaics. #' Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/R/lsm_p_core.R b/R/lsm_p_core.R index f3ef2a817..8c8260e88 100644 --- a/R/lsm_p_core.R +++ b/R/lsm_p_core.R @@ -50,7 +50,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_p_core <- function(landscape, directions = 8, diff --git a/R/lsm_p_enn.R b/R/lsm_p_enn.R index 7a269518b..d0b5fab94 100644 --- a/R/lsm_p_enn.R +++ b/R/lsm_p_enn.R @@ -44,7 +44,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' McGarigal, K., and McComb, W. C. (1995). Relationships between landscape #' structure and breeding birds in the Oregon Coast Range. diff --git a/R/lsm_p_frac.R b/R/lsm_p_frac.R index b0c458b81..af2688306 100644 --- a/R/lsm_p_frac.R +++ b/R/lsm_p_frac.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. #' San Francisco. W. H. Freeman and Company. diff --git a/R/lsm_p_gyrate.R b/R/lsm_p_gyrate.R index cb8f4f787..205b62a22 100644 --- a/R/lsm_p_gyrate.R +++ b/R/lsm_p_gyrate.R @@ -45,7 +45,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales #' in fragmented landscapes. Conservation ecology, 1(1). diff --git a/R/lsm_p_ncore.R b/R/lsm_p_ncore.R index 0bbd020f4..6bb2606d8 100644 --- a/R/lsm_p_ncore.R +++ b/R/lsm_p_ncore.R @@ -53,7 +53,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_p_ncore <- function(landscape, diff --git a/R/lsm_p_para.R b/R/lsm_p_para.R index ce0c20652..8939ec425 100644 --- a/R/lsm_p_para.R +++ b/R/lsm_p_para.R @@ -43,7 +43,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_p_para <- function(landscape, directions = 8) { diff --git a/R/lsm_p_perim.R b/R/lsm_p_perim.R index c5ff1f0b4..61425e8a2 100644 --- a/R/lsm_p_perim.R +++ b/R/lsm_p_perim.R @@ -32,7 +32,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' @export lsm_p_perim <- function(landscape, directions = 8) { diff --git a/R/lsm_p_shape.R b/R/lsm_p_shape.R index 0528d8ef2..288d0cece 100644 --- a/R/lsm_p_shape.R +++ b/R/lsm_p_shape.R @@ -42,7 +42,7 @@ #' McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +#' web site: https://www.umass.edu/landeco/ #' #' Patton, D. R. 1975. A diversity index for quantifying habitat "edge". #' Wildl. Soc.Bull. 3:171-173. diff --git a/R/show_cores.R b/R/show_cores.R index 515c64a5f..d50b4027f 100644 --- a/R/show_cores.R +++ b/R/show_cores.R @@ -77,16 +77,6 @@ show_cores_internal <- function(landscape, directions, class, labels, nrow, ncol landscape_labeled <- get_patches(landscape, directions = directions)[[1]] - for (i in seq_len(length(landscape_labeled) - 1)) { - - max(get_unique_values_int(raster::as.matrix(landscape_labeled[[i]]), - verbose = FALSE)) - - max_patch_id <- max(raster::values(landscape_labeled[[i]]), na.rm = TRUE) - - landscape_labeled[[i + 1]] <- landscape_labeled[[i + 1]] + max_patch_id - } - boundary <- lapply(X = landscape_labeled, FUN = function(patches_class) { class_edge <- get_boundaries(patches_class, diff --git a/R/show_lsm.R b/R/show_lsm.R index 5e57eddc8..7308af19a 100644 --- a/R/show_lsm.R +++ b/R/show_lsm.R @@ -80,13 +80,6 @@ show_lsm_internal <- function(landscape, what, class, landscape_labeled <- get_patches(landscape, directions = directions)[[1]] - for (i in seq_len(length(landscape_labeled) - 1)) { - - max_id <- max(raster::values(landscape_labeled[[i]]), na.rm = TRUE) - - landscape_labeled[[i + 1]] <- landscape_labeled[[i + 1]] + max_id - } - lsm_fun <- match.fun(what) if (what %in% c("lsm_p_core", "lsm_p_ncore")) { diff --git a/R/show_patches.R b/R/show_patches.R index a6527f7f2..a26b99b6c 100644 --- a/R/show_patches.R +++ b/R/show_patches.R @@ -55,13 +55,6 @@ show_patches_internal <- function(landscape, class, directions, labels, nrow, nc landscape_labeled <- get_patches(landscape, directions = directions)[[1]] - for (i in seq_len(length(landscape_labeled) - 1)) { - - max_patch_id <- max(raster::values(landscape_labeled[[i]]), na.rm = TRUE) - - landscape_labeled[[i + 1]] <- landscape_labeled[[i + 1]] + max_patch_id - } - if (any(class == "global")) { patches_tibble <- raster::as.data.frame(sum(raster::stack(landscape_labeled), diff --git a/R/spatialize_lsm.R b/R/spatialize_lsm.R index 1e51bbd4e..cb0a98644 100644 --- a/R/spatialize_lsm.R +++ b/R/spatialize_lsm.R @@ -36,16 +36,10 @@ #' @rdname spatialize_lsm #' #' @export -spatialize_lsm <- function(landscape, - level = "patch", - metric = NULL, - name = NULL, - type = NULL, - what = NULL, - directions = 8, - progress = FALSE, - to_disk = getOption("to_disk", default = FALSE), - ...) { +spatialize_lsm <- function(landscape, level = "patch", metric = NULL, name = NULL, + type = NULL, what = NULL, directions = 8, progress = FALSE, + to_disk = getOption("to_disk", default = FALSE), + ...) { landscape <- landscape_as_list(landscape) @@ -75,12 +69,8 @@ spatialize_lsm <- function(landscape, return(result) } -spatialize_lsm_internal <- function(landscape, - level, metric, name, type, what, - directions, - progress, - to_disk, - ...) { +spatialize_lsm_internal <- function(landscape, level, metric, name, type, what, + directions, progress, to_disk, ...) { # get name of metrics metrics <- list_lsm(level = level, @@ -110,14 +100,6 @@ spatialize_lsm_internal <- function(landscape, to_disk = to_disk, return_raster = TRUE)[[1]] - # continuous, unique patch id - for (i in seq_len(length(landscape_labeled) - 1)) { - - max_id <- max(raster::values(landscape_labeled[[i]]), na.rm = TRUE) - - landscape_labeled[[i + 1]] <- landscape_labeled[[i + 1]] + max_id - } - # get dataframe with patch ID and coordinates to merge with result of metric # MH: Do we really want to remove NA? patches_tibble <- raster::as.data.frame(sum(raster::stack(landscape_labeled), @@ -205,9 +187,9 @@ spatialize_lsm_internal <- function(landscape, return(result) }})}, warning = function(cond) { - warning_messages <<- c(warning_messages, conditionMessage(cond)) + warning_messages <<- c(warning_messages, conditionMessage(cond)) - invokeRestart("muffleWarning")} + invokeRestart("muffleWarning")} ) # using metrics to name list diff --git a/R/window_lsm.R b/R/window_lsm.R index baa7dd696..ac3f66333 100644 --- a/R/window_lsm.R +++ b/R/window_lsm.R @@ -33,6 +33,9 @@ #' window <- matrix(1, nrow = 5,ncol = 5) #' window_lsm(landscape, window = window, what = c("lsm_l_pr", "lsm_l_joinent")) #' window_lsm(landscape_stack, window = window, what = c("lsm_l_pr", "lsm_l_joinent")) +#' +#' window_circular <- matrix(c(NA, 1, NA, 1, 1, 1, NA, 1, NA), nrow = 3, ncol = 3) +#' window_lsm(landscape, window = window_circular, what = c("lsm_l_pr", "lsm_l_joinent")) #' } #' #' @aliases window_lsm @@ -49,7 +52,7 @@ #' McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis #' Program for Categorical and Continuous Maps. Computer software program produced by #' the authors at the University of Massachusetts, Amherst. Available at the following -#' website: +#' website: #' #' @export window_lsm <- function(landscape, @@ -129,10 +132,6 @@ window_lsm_int <- function(landscape, # resolution of original raster resolution <- raster::res(landscape) - # get dimensions of window - n_row = nrow(window) - n_col = ncol(window) - # create object for warning messages warning_messages <- character(0) @@ -147,8 +146,7 @@ window_lsm_int <- function(landscape, raster::focal(x = landscape, w = window, fun = function(x) { calculate_lsm_focal(landscape = x, - n_row = n_row, - n_col = n_col, + raster_window = window, resolution = resolution, points = points, what = metrics_list[[current_metric]], @@ -179,15 +177,14 @@ window_lsm_int <- function(landscape, } calculate_lsm_focal <- function(landscape, - n_row, - n_col, + raster_window, resolution, points, what, ...) { # convert focal window to matrix - raster_window <- matrix(landscape, n_row, n_col) + raster_window[!is.na(raster_window)] <- landscape # get internal calculation function what <- paste0(what, "_calc") diff --git a/README.Rmd b/README.Rmd index ee9ab6bd9..1c499c57a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,9 +1,7 @@ --- -output: - github_document: - html_preview: false -editor_options: - chunk_output_type: console +output: + github_document: + html_preview: false --- ```{r setup, include = FALSE} @@ -15,16 +13,18 @@ knitr::opts_chunk$set( ) ``` +# landscapemetrics + -| CI | Development | CRAN | License | -|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------| -| [![R-CMD-check](https://github.com/r-spatialecology/landscapemetrics/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)](https://github.com/r-spatialecology/landscapemetrics/actions/workflows/R-CMD-check.yaml) | [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN status](https://www.r-pkg.org/badges/version/landscapemetrics)](https://cran.r-project.org/package=landscapemetrics) | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | -| [![Coverage](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/main/graph/badge.svg)](https://codecov.io/github/r-spatialecology/landscapemetrics?branch=main) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/landscapemetrics)](http://cran.rstudio.com/web/packages/landscapemetrics/index.html) | [![DOI](https://img.shields.io/badge/DOI-10.1111/ecog.04617-blue.svg)](https://doi.org/10.1111/ecog.04617) | + - +| CI | Development | CRAN | License | +|----|-------------|------|---------| +| [![R-CMD-check](https://github.com/r-spatialecology/landscapemetrics/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatialecology/landscapemetrics/actions/workflows/R-CMD-check.yaml) | [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN status](https://www.r-pkg.org/badges/version/landscapemetrics)](https://cran.r-project.org/package=landscapemetrics) | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | +| [![codecov](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/main/graph/badge.svg?token=xjYJMNMGBU)](https://codecov.io/gh/r-spatialecology/landscapemetrics) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/landscapemetrics)](http://cran.rstudio.com/web/packages/landscapemetrics/index.html) | [![DOI](https://img.shields.io/badge/DOI-10.1111/ecog.04617-blue.svg)](https://doi.org/10.1111/ecog.04617) | -# landscapemetrics + ## Overview @@ -32,7 +32,7 @@ knitr::opts_chunk$set( **landscapemetrics** supports `raster`, `terra`, and `stars` spatial objects and takes `RasterLayer`, `RasterStacks`, `RasterBricks` lists of `RasterLayer`, `SpatRaster`, or `stars` as input arguments. Every function can be used in a piped workflow, as it always takes the data as the first argument and returns a `tibble`. -### Citation +#### Citation To cite **landscapemetrics** or acknowledge its use, please cite the following Software note, substituting the version of the application that you used for 'ver. 0': @@ -97,7 +97,7 @@ All functions return an identical structured tibble: Every function follows the same implementation design, so the usage is quite straightforward: -```{r, message = FALSE, warning = FALSE} +```{r, message = FALSE, warning = FALSE, fig.align = "center", out.width = "75%"} library(landscapemetrics) library(landscapetools) @@ -125,7 +125,7 @@ calculate_lsm(landscape, level = "patch") Important building blocks of the package are exported to help facilitate analysis or the development of new metrics. They all start with the prefix `get_`. All of them are implemented with Rcpp and have either memory or performance advantages compared to raster functions. -For more details, see the [utility function](https://r-spatialecology.github.io/landscapemetrics/articles/articles/utility.html) vignette. +For more details, see the `vignette("utility")`. ### Contributing @@ -135,5 +135,6 @@ Maintainers and contributors must follow this repository’s [CODE OF CONDUCT](C ### References -- McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: -- Nowosad J., TF Stepinski. 2019. Information theory as a consistent framework for quantification and classification of landscape patterns. https://doi.org/10.1007/s10980-019-00830-x +McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: + +Nowosad J., TF Stepinski. 2019. Information theory as a consistent framework for quantification and classification of landscape patterns. https://doi.org/10.1007/s10980-019-00830-x diff --git a/README.md b/README.md index b8748dbce..384b27e3e 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,15 @@ - +# landscapemetrics -| CI | Development | CRAN | License | -| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------- | -| [![R-CMD-check](https://github.com/r-spatialecology/landscapemetrics/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)](https://github.com/r-spatialecology/landscapemetrics/actions/workflows/R-CMD-check.yaml) | [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN status](https://www.r-pkg.org/badges/version/landscapemetrics)](https://cran.r-project.org/package=landscapemetrics) | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | -| [![Coverage](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/main/graph/badge.svg)](https://codecov.io/github/r-spatialecology/landscapemetrics?branch=main) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/landscapemetrics)](http://cran.rstudio.com/web/packages/landscapemetrics/index.html) | [![DOI](https://img.shields.io/badge/DOI-10.1111/ecog.04617-blue.svg)](https://doi.org/10.1111/ecog.04617) | + + - +| CI | Development | CRAN | License | +|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------| +| [![R-CMD-check](https://github.com/r-spatialecology/landscapemetrics/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatialecology/landscapemetrics/actions/workflows/R-CMD-check.yaml) | [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN status](https://www.r-pkg.org/badges/version/landscapemetrics)](https://cran.r-project.org/package=landscapemetrics) | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | +| [![codecov](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/main/graph/badge.svg?token=xjYJMNMGBU)](https://codecov.io/gh/r-spatialecology/landscapemetrics) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/landscapemetrics)](http://cran.rstudio.com/web/packages/landscapemetrics/index.html) | [![DOI](https://img.shields.io/badge/DOI-10.1111/ecog.04617-blue.svg)](https://doi.org/10.1111/ecog.04617) | -# landscapemetrics + ## Overview @@ -27,18 +28,16 @@ objects and takes `RasterLayer`, `RasterStacks`, `RasterBricks` lists of function can be used in a piped workflow, as it always takes the data as the first argument and returns a `tibble`. -### Citation +#### Citation To cite **landscapemetrics** or acknowledge its use, please cite the following Software note, substituting the version of the application that you used for ‘ver. 0’:

- Hesselbarth, M.H.K., Sciaini, M., With, K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open‐source R tool to calculate landscape metrics. Ecography, 42: 1648-1657 (ver. 0). -

For more information see [Publication @@ -82,26 +81,26 @@ of the function name is the abbreviation of the corresponding metric # general structure lsm_"level"_"metric" - + # Patch level ## lsm_p_"metric" lsm_p_enn() - + # Class level ## lsm_c_"metric" lsm_c_enn() - + # Landscape level ## lsm_p_"metric" lsm_l_enn() All functions return an identical structured tibble: -| layer | level | class | id | metric | value | -| ----- | --------- | ----- | -- | ---------------- | ----- | -| 1 | patch | 1 | 1 | landscape metric | x | -| 1 | class | 1 | NA | landscape metric | x | -| 1 | landscape | NA | NA | landscape metric | x | +| layer | level | class | id | metric | value | +|-------|-----------|-------|-----|------------------|-------| +| 1 | patch | 1 | 1 | landscape metric | x | +| 1 | class | 1 | NA | landscape metric | x | +| 1 | landscape | NA | NA | landscape metric | x | ### Using metric functions @@ -116,7 +115,7 @@ library(landscapetools) show_landscape(landscape, discrete = TRUE) ``` - + ``` r @@ -187,9 +186,7 @@ analysis or the development of new metrics. They all start with the prefix `get_`. All of them are implemented with Rcpp and have either memory or performance advantages compared to raster functions. -For more details, see the [utility -function](https://r-spatialecology.github.io/landscapemetrics/articles/articles/utility.html) -vignette. +For more details, see the `vignette("utility")`. ### Contributing @@ -198,7 +195,7 @@ provide an open-source code collection of landscape metrics. This includes, besides bug reports, especially the idea to include new metrics and functions. Therefore, in case you want to suggest new metrics or functions and in the best case even contribute code, we -warmly welcome to do so\! For more information see +warmly welcome to do so! For more information see [CONTRIBUTING](CONTRIBUTING.md). Maintainers and contributors must follow this repository’s [CODE OF @@ -206,11 +203,12 @@ CONDUCT](CODE_OF_CONDUCT.md). ### References - - McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial - Pattern Analysis Program for Categorical and Continuous Maps. - Computer software program produced by the authors at the University - of Massachusetts, Amherst. Available at the following website: - - - Nowosad J., TF Stepinski. 2019. Information theory as a consistent - framework for quantification and classification of landscape - patterns. +McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial +Pattern Analysis Program for Categorical and Continuous Maps. Computer +software program produced by the authors at the University of +Massachusetts, Amherst. Available at the following website: + + +Nowosad J., TF Stepinski. 2019. Information theory as a consistent +framework for quantification and classification of landscape patterns. + diff --git a/_pkgdown.yml b/_pkgdown.yml index ad79f8b56..ade01ddf2 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,234 +1,126 @@ -title: landscapemetrics | Landscape Metrics for Categorical Map Patterns +url: https://r-spatialecology.github.io/landscapemetrics/ template: - params: - bootswatch: sandstone + bootstrap: 5 + bootswatch: sandstone reference: - title: Internal Datasets contents: - - lsm_abbreviations_names - - landscape - - augusta_nlcd - - podlasie_ccilc - - fragstats_patch_landscape - - fragstats_patch_augusta_nlcd - - fragstats_patch_podlasie - - fragstats_class_landscape - - fragstats_class_augusta_nlcd - - fragstats_class_podlasie - - fragstats_landscape_landscape - - fragstats_landscape_augusta_nlcd - - fragstats_landscape_podlasie + - lsm_abbreviations_names + - landscape + - augusta_nlcd + - podlasie_ccilc + - fragstats_patch_landscape + - fragstats_patch_augusta_nlcd + - fragstats_patch_podlasie + - fragstats_class_landscape + - fragstats_class_augusta_nlcd + - fragstats_class_podlasie + - fragstats_landscape_landscape + - fragstats_landscape_augusta_nlcd + - fragstats_landscape_podlasie + - title: Options for landscapemetrics contents: - - options_landscapemetrics + - options_landscapemetrics + - title: Auxiliary/Utility functions contents: - - calculate_correlation - - check_landscape - - list_lsm - - get_adjacencies - - get_boundaries - - get_circumscribingcircle - - get_nearestneighbour - - get_patches - - get_unique_values - - extract_lsm - - sample_lsm - - scale_sample - - scale_window - - spatialize_lsm - - window_lsm + - calculate_correlation + - check_landscape + - extract_lsm + - get_adjacencies + - get_boundaries + - get_centroids + - get_circumscribingcircle + - get_nearestneighbour + - get_patches + - get_unique_values + - landscape_as_list + - list_lsm + - sample_lsm + - scale_sample + - scale_window + - spatialize_lsm + - window_lsm + - title: Visualisation functions contents: - - show_patches - - show_cores - - show_correlation - - show_lsm + - show_patches + - show_cores + - show_correlation + - show_lsm + - title: Patch Level Metrics contents: - - lsm_p_area - - lsm_p_cai - - lsm_p_circle - - lsm_p_contig - - lsm_p_core - - lsm_p_enn - - lsm_p_frac - - lsm_p_gyrate - - lsm_p_ncore - - lsm_p_para - - lsm_p_perim - - lsm_p_shape + - starts_with("lsm_p_") + - title: Class Level Metrics contents: - - lsm_c_ai - - lsm_c_area_cv - - lsm_c_area_mn - - lsm_c_area_sd - - lsm_c_ca - - lsm_c_cai_cv - - lsm_c_cai_mn - - lsm_c_cai_sd - - lsm_c_circle_cv - - lsm_c_circle_mn - - lsm_c_circle_sd - - lsm_c_clumpy - - lsm_c_cohesion - - lsm_c_contig_cv - - lsm_c_contig_mn - - lsm_c_contig_sd - - lsm_c_core_cv - - lsm_c_core_mn - - lsm_c_core_sd - - lsm_c_tca - - lsm_c_cpland - - lsm_c_dcad - - lsm_c_dcore_cv - - lsm_c_dcore_mn - - lsm_c_dcore_sd - - lsm_c_division - - lsm_c_ed - - lsm_c_enn_cv - - lsm_c_enn_mn - - lsm_c_enn_sd - - lsm_c_frac_cv - - lsm_c_frac_mn - - lsm_c_frac_sd - - lsm_c_gyrate_cv - - lsm_c_gyrate_mn - - lsm_c_gyrate_sd - - lsm_c_iji - - lsm_c_lpi - - lsm_c_lsi - - lsm_c_mesh - - lsm_c_ndca - - lsm_c_nlsi - - lsm_c_np - - lsm_c_pafrac - - lsm_c_para_cv - - lsm_c_para_mn - - lsm_c_para_sd - - lsm_c_pd - - lsm_c_pladj - - lsm_c_pland - - lsm_c_shape_cv - - lsm_c_shape_mn - - lsm_c_shape_sd - - lsm_c_split - - lsm_c_te + - starts_with("lsm_c_") + - title: Landscape Level Metrics contents: - - lsm_l_ai - - lsm_l_area_cv - - lsm_l_area_mn - - lsm_l_area_sd - - lsm_l_cai_cv - - lsm_l_cai_mn - - lsm_l_cai_sd - - lsm_l_circle_cv - - lsm_l_circle_mn - - lsm_l_circle_sd - - lsm_l_cohesion - - lsm_l_condent - - lsm_l_contag - - lsm_l_contig_cv - - lsm_l_contig_mn - - lsm_l_contig_sd - - lsm_l_core_cv - - lsm_l_core_mn - - lsm_l_core_sd - - lsm_l_ent - - lsm_l_tca - - lsm_l_dcad - - lsm_l_dcore_cv - - lsm_l_dcore_mn - - lsm_l_dcore_sd - - lsm_l_division - - lsm_l_ed - - lsm_l_enn_cv - - lsm_l_enn_mn - - lsm_l_enn_sd - - lsm_l_frac_cv - - lsm_l_frac_mn - - lsm_l_frac_sd - - lsm_l_gyrate_cv - - lsm_l_gyrate_mn - - lsm_l_gyrate_sd - - lsm_l_iji - - lsm_l_joinent - - lsm_l_lpi - - lsm_l_lsi - - lsm_l_mesh - - lsm_l_msidi - - lsm_l_msiei - - lsm_l_mutinf - - lsm_l_ndca - - lsm_l_np - - lsm_l_pafrac - - lsm_l_para_cv - - lsm_l_para_mn - - lsm_l_para_sd - - lsm_l_pd - - lsm_l_pladj - - lsm_l_pr - - lsm_l_prd - - lsm_l_relmutinf - - lsm_l_rpr - - lsm_l_shape_cv - - lsm_l_shape_mn - - lsm_l_shape_sd - - lsm_l_shdi - - lsm_l_shei - - lsm_l_sidi - - lsm_l_siei - - lsm_l_split - - lsm_l_ta - - lsm_l_te + - starts_with("lsm_l_") + - title: Wrapper around all metrics contents: - - calculate_lsm + - calculate_lsm navbar: - title: landscapemetrics - left: - - text: "Get Started" + structure: + left: [getstarted, reference, articles, news] + right: [github, contact, search] + components: + getstarted: + text: "Get Started" icon: fa fa-magic - href: articles/getstarted.html - - text: "More" + href: articles/get_started.html + + reference: + icon: fa-gears + text: "Functions" + href: reference/index.html + + articles: icon: fa-graduation-cap + text: "More" menu: - text: "General Background" icon: fa-book - href: articles/articles/general-background.html + href: articles/general_background.html - text: "Differences FRAGSTATS|landscapemetrics" icon: fa-edit - href: articles/articles/comparing_tools.html + href: articles/comparing_tools.html - text: "New Metrics outside FRAGSTATS" icon: fa-sticky-note - href: articles/articles/new_metrics.html + href: articles/new_metrics.html - text: "Utility functions" icon: fa-comment - href: articles/articles/utility.html + href: articles/utility.html - text: "Moving window" icon: fa-comment - href: articles/articles/guide_moving_window.html + href: articles/guide_moving_window.html - text: "Sample metrics" icon: fa-comment - href: articles/articles/guide_sample_lsm.html + href: articles/guide_sample_lsm.html - text: "Landscape distribution statistics" icon: fa-comment - href: articles/articles/landscape_distribution_statistics.html + href: articles/landscape_distribution_statistics.html - text: "Publication Record" icon: fa-file-text-o - href: articles/articles/publication_record.html - right: - - icon: fa-newspaper-o - text: "news" + href: articles/publication_record.html + + news: + icon: fa-newspaper-o + text: "News" href: news/index.html - - icon: fa-gears - text: "functions" - href: reference/index.html - - icon: fa-github fa-lg - text: "github" - href: https://github.com/r-spatialecology/landscapemetrics + + contact: + icon: fa-user + hreft: https://mhesselbarth.rbind.io + +home: + sidebar: + structure: [authors, license, community] diff --git a/codemeta.json b/codemeta.json index cce4acf4c..80059667b 100644 --- a/codemeta.json +++ b/codemeta.json @@ -1,22 +1,19 @@ { - "@context": [ - "https://doi.org/10.5063/schema/codemeta-2.0", - "http://schema.org" - ], + "@context": "https://doi.org/10.5063/schema/codemeta-2.0", "@type": "SoftwareSourceCode", "identifier": "landscapemetrics", - "description": "Calculates landscape metrics for categorical landscape patterns in \n a tidy workflow. 'landscapemetrics' reimplements the most common metrics from\n 'FRAGSTATS' () \n and new ones from the current literature on landscape metrics.\n This package supports 'raster' spatial objects and takes \n RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the\n 'raster' package as input arguments. It further provides utility functions\n to visualize patches, select metrics and building blocks to develop new \n metrics.", + "description": "Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' () and new ones from the current literature on landscape metrics. This package supports 'raster' spatial objects and takes RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the 'raster' package as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.", "name": "landscapemetrics: Landscape Metrics for Categorical Map Patterns", - "codeRepository": "https://github.com/r-spatialecology/landscapemetrics", + "codeRepository": "https://r-spatialecology.github.io/landscapemetrics/", "issueTracker": "https://github.com/r-spatialecology/landscapemetrics/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "1.5.2", + "version": "1.5.5", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.0.3 (2020-10-10)", + "runtimePlatform": "R version 4.2.1 (2022-06-23)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -26,7 +23,7 @@ "author": [ { "@type": "Person", - "givenName": "Maximillian H.K.", + "givenName": "Maximilian H.K.", "familyName": "Hesselbarth", "email": "mhk.hesselbarth@gmail.com", "@id": "https://orcid.org/0000-0003-1125-9918" @@ -83,12 +80,10 @@ "familyName": "Strimas-Mackey" } ], - "copyrightHolder": {}, - "funder": {}, "maintainer": [ { "@type": "Person", - "givenName": "Maximillian H.K.", + "givenName": "Maximilian H.K.", "familyName": "Hesselbarth", "email": "mhk.hesselbarth@gmail.com", "@id": "https://orcid.org/0000-0003-1125-9918" @@ -155,6 +150,18 @@ }, "sameAs": "https://CRAN.R-project.org/package=rmarkdown" }, + { + "@type": "SoftwareApplication", + "identifier": "terra", + "name": "terra", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=terra" + }, { "@type": "SoftwareApplication", "identifier": "testthat", @@ -168,14 +175,14 @@ "sameAs": "https://CRAN.R-project.org/package=testthat" } ], - "softwareRequirements": [ - { + "softwareRequirements": { + "1": { "@type": "SoftwareApplication", "identifier": "R", "name": "R", "version": ">= 3.1" }, - { + "2": { "@type": "SoftwareApplication", "identifier": "cli", "name": "cli", @@ -187,7 +194,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=cli" }, - { + "3": { "@type": "SoftwareApplication", "identifier": "ggplot2", "name": "ggplot2", @@ -199,12 +206,12 @@ }, "sameAs": "https://CRAN.R-project.org/package=ggplot2" }, - { + "4": { "@type": "SoftwareApplication", "identifier": "methods", "name": "methods" }, - { + "5": { "@type": "SoftwareApplication", "identifier": "raster", "name": "raster", @@ -216,7 +223,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=raster" }, - { + "6": { "@type": "SoftwareApplication", "identifier": "Rcpp", "name": "Rcpp", @@ -228,7 +235,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=Rcpp" }, - { + "7": { "@type": "SoftwareApplication", "identifier": "sp", "name": "sp", @@ -240,12 +247,12 @@ }, "sameAs": "https://CRAN.R-project.org/package=sp" }, - { + "8": { "@type": "SoftwareApplication", "identifier": "stats", "name": "stats" }, - { + "9": { "@type": "SoftwareApplication", "identifier": "tibble", "name": "tibble", @@ -257,16 +264,9 @@ }, "sameAs": "https://CRAN.R-project.org/package=tibble" }, - { - "@type": "SoftwareApplication", - "identifier": "https://sysreqs.r-hub.io/get/cxx11" - } - ], - "relatedLink": ["https://r-spatialecology.github.io/landscapemetrics/", "https://CRAN.R-project.org/package=landscapemetrics"], - "releaseNotes": "https://github.com/r-spatialecology/landscapemetrics/blob/master/NEWS.md", - "fileSize": "16580.046KB", - "contIntegration": "https://codecov.io/github/r-spatialecology/landscapemetrics?branch=main", - "developmentStatus": ["https://www.tidyverse.org/lifecycle/#stable", "http://www.repostatus.org/#active"], + "SystemRequirements": "C++11" + }, + "fileSize": "1885.14KB", "citation": [ { "@type": "ScholarlyArticle", diff --git a/cran-comments.md b/cran-comments.md index a83474707..6ec5463d6 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,7 @@ +# landscapemetrics 1.5.5 +- Improved user experience +- Fix typo in Maintainer name + # landscapemetrics 1.5.4 Computational improvements diff --git a/man/calculate_lsm.Rd b/man/calculate_lsm.Rd index ced9f87a5..5cd07e05a 100644 --- a/man/calculate_lsm.Rd +++ b/man/calculate_lsm.Rd @@ -97,7 +97,7 @@ calculate_lsm(landscape, level = c("class", "landscape"), type = "aggregation me McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{list_lsm}} diff --git a/man/figures/README-unnamed-chunk-1-1.png b/man/figures/README-unnamed-chunk-1-1.png deleted file mode 100644 index 5e7fecd03..000000000 Binary files a/man/figures/README-unnamed-chunk-1-1.png and /dev/null differ diff --git a/man/figures/README-unnamed-chunk-2-1.png b/man/figures/README-unnamed-chunk-2-1.png index c9e0be885..cc3835526 100644 Binary files a/man/figures/README-unnamed-chunk-2-1.png and b/man/figures/README-unnamed-chunk-2-1.png differ diff --git a/man/landscapemetrics.Rd b/man/landscapemetrics.Rd index 4ca6e4b9e..58d8dd505 100644 --- a/man/landscapemetrics.Rd +++ b/man/landscapemetrics.Rd @@ -24,7 +24,7 @@ Useful links: } \author{ -\strong{Maintainer}: Maximillian H.K. Hesselbarth \email{mhk.hesselbarth@gmail.com} (\href{https://orcid.org/0000-0003-1125-9918}{ORCID}) +\strong{Maintainer}: Maximilian H.K. Hesselbarth \email{mhk.hesselbarth@gmail.com} (\href{https://orcid.org/0000-0003-1125-9918}{ORCID}) Authors: \itemize{ @@ -44,3 +44,4 @@ Other contributors: } } +\keyword{internal} diff --git a/man/list_lsm.Rd b/man/list_lsm.Rd index 7aaa08259..329833d89 100644 --- a/man/list_lsm.Rd +++ b/man/list_lsm.Rd @@ -59,5 +59,5 @@ list_lsm(what = c("lsm_c_tca", "lsm_l_ta")) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } diff --git a/man/lsm_c_ai.Rd b/man/lsm_c_ai.Rd index 5bd01aa5d..c01f8070a 100644 --- a/man/lsm_c_ai.Rd +++ b/man/lsm_c_ai.Rd @@ -38,7 +38,7 @@ lsm_c_ai(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ He, H. S., DeZonia, B. E., & Mladenoff, D. J. 2000. An aggregation index (AI) to quantify spatial patterns of landscapes. Landscape ecology, 15(7), 591-601. diff --git a/man/lsm_c_area_cv.Rd b/man/lsm_c_area_cv.Rd index 7d25a33af..dc86e2880 100644 --- a/man/lsm_c_area_cv.Rd +++ b/man/lsm_c_area_cv.Rd @@ -39,7 +39,7 @@ lsm_c_area_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_c_area_mn.Rd b/man/lsm_c_area_mn.Rd index 82cf209ba..ba032b8c5 100644 --- a/man/lsm_c_area_mn.Rd +++ b/man/lsm_c_area_mn.Rd @@ -40,7 +40,7 @@ lsm_c_area_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_c_area_sd.Rd b/man/lsm_c_area_sd.Rd index 94e8855ba..4028fd337 100644 --- a/man/lsm_c_area_sd.Rd +++ b/man/lsm_c_area_sd.Rd @@ -40,7 +40,7 @@ lsm_c_area_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_c_ca.Rd b/man/lsm_c_ca.Rd index 64adcd332..5e520f7de 100644 --- a/man/lsm_c_ca.Rd +++ b/man/lsm_c_ca.Rd @@ -43,7 +43,7 @@ lsm_c_ca(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_c_cai_cv.Rd b/man/lsm_c_cai_cv.Rd index 2261be2c1..98369b410 100644 --- a/man/lsm_c_cai_cv.Rd +++ b/man/lsm_c_cai_cv.Rd @@ -55,7 +55,7 @@ lsm_c_cai_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_cai}}, diff --git a/man/lsm_c_cai_mn.Rd b/man/lsm_c_cai_mn.Rd index d528fd539..8d8625183 100644 --- a/man/lsm_c_cai_mn.Rd +++ b/man/lsm_c_cai_mn.Rd @@ -52,7 +52,7 @@ lsm_c_cai_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_cai}}, diff --git a/man/lsm_c_cai_sd.Rd b/man/lsm_c_cai_sd.Rd index 3b45555b0..3127beb5b 100644 --- a/man/lsm_c_cai_sd.Rd +++ b/man/lsm_c_cai_sd.Rd @@ -54,7 +54,7 @@ lsm_c_cai_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_cai}}, diff --git a/man/lsm_c_circle_cv.Rd b/man/lsm_c_circle_cv.Rd index 317794bc9..168275e96 100644 --- a/man/lsm_c_circle_cv.Rd +++ b/man/lsm_c_circle_cv.Rd @@ -43,7 +43,7 @@ lsm_c_circle_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. diff --git a/man/lsm_c_circle_mn.Rd b/man/lsm_c_circle_mn.Rd index 0b6ef61c4..45e655bd4 100644 --- a/man/lsm_c_circle_mn.Rd +++ b/man/lsm_c_circle_mn.Rd @@ -41,7 +41,7 @@ lsm_c_circle_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. diff --git a/man/lsm_c_circle_sd.Rd b/man/lsm_c_circle_sd.Rd index 06f39d3d0..6fe9f4b2f 100644 --- a/man/lsm_c_circle_sd.Rd +++ b/man/lsm_c_circle_sd.Rd @@ -41,7 +41,7 @@ lsm_c_circle_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. diff --git a/man/lsm_c_clumpy.Rd b/man/lsm_c_clumpy.Rd index 7b8289beb..bde22716f 100644 --- a/man/lsm_c_clumpy.Rd +++ b/man/lsm_c_clumpy.Rd @@ -42,5 +42,5 @@ lsm_c_clumpy(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } diff --git a/man/lsm_c_cohesion.Rd b/man/lsm_c_cohesion.Rd index b30374061..965bc6e40 100644 --- a/man/lsm_c_cohesion.Rd +++ b/man/lsm_c_cohesion.Rd @@ -41,7 +41,7 @@ lsm_c_cohesion(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Schumaker, N. H. 1996. Using landscape indices to predict habitat connectivity. Ecology, 77(4), 1210-1225. diff --git a/man/lsm_c_contig_cv.Rd b/man/lsm_c_contig_cv.Rd index 234405bcf..49fac8501 100644 --- a/man/lsm_c_contig_cv.Rd +++ b/man/lsm_c_contig_cv.Rd @@ -25,10 +25,12 @@ where \eqn{CONTIG[patch_{ij}]} is the contiguity of each patch. CONTIG_CV is a 'Shape metric'. It summarises each class as the mean of each patch belonging to class i. CONTIG_CV asses the spatial connectedness (contiguity) of cells in patches. The metric coerces patch values to a value of 1 and the background -to NA. A nine cell focal filter matrix:\preformatted{filter_matrix <- matrix(c(1, 2, 1, +to NA. A nine cell focal filter matrix: + +\if{html}{\out{
}}\preformatted{filter_matrix <- matrix(c(1, 2, 1, 2, 1, 2, 1, 2, 1), 3, 3, byrow = T) -} +}\if{html}{\out{
}} ... is then used to weight orthogonally contiguous pixels more heavily than diagonally contiguous pixels. Therefore, larger and more connections between @@ -48,7 +50,7 @@ lsm_c_contig_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ LaGro, J. 1991. Assessing patch shape in landscape mosaics. Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/man/lsm_c_contig_mn.Rd b/man/lsm_c_contig_mn.Rd index 39a2dbe9e..ad26f92f6 100644 --- a/man/lsm_c_contig_mn.Rd +++ b/man/lsm_c_contig_mn.Rd @@ -25,10 +25,12 @@ where \eqn{CONTIG[patch_{ij}]} is the contiguity of each patch. CONTIG_MN is a 'Shape metric'. It summarises each class as the mean of each patch belonging to class i. CONTIG_MN asses the spatial connectedness (contiguity) of cells in patches. The metric coerces patch values to a value of 1 and the background -to NA. A nine cell focal filter matrix:\preformatted{filter_matrix <- matrix(c(1, 2, 1, +to NA. A nine cell focal filter matrix: + +\if{html}{\out{
}}\preformatted{filter_matrix <- matrix(c(1, 2, 1, 2, 1, 2, 1, 2, 1), 3, 3, byrow = T) -} +}\if{html}{\out{
}} ... is then used to weight orthogonally contiguous pixels more heavily than diagonally contiguous pixels. Therefore, larger and more connections between @@ -47,7 +49,7 @@ lsm_c_contig_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ LaGro, J. 1991. Assessing patch shape in landscape mosaics. Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/man/lsm_c_contig_sd.Rd b/man/lsm_c_contig_sd.Rd index 16317a743..4b4e3597e 100644 --- a/man/lsm_c_contig_sd.Rd +++ b/man/lsm_c_contig_sd.Rd @@ -25,10 +25,12 @@ where \eqn{CONTIG[patch_{ij}]} is the contiguity of each patch. CONTIG_SD is a 'Shape metric'. It summarises each class as the mean of each patch belonging to class i. CONTIG_SD asses the spatial connectedness (contiguity) of cells in patches. The metric coerces patch values to a value of 1 and the background -to NA. A nine cell focal filter matrix:\preformatted{filter_matrix <- matrix(c(1, 2, 1, +to NA. A nine cell focal filter matrix: + +\if{html}{\out{
}}\preformatted{filter_matrix <- matrix(c(1, 2, 1, 2, 1, 2, 1, 2, 1), 3, 3, byrow = T) -} +}\if{html}{\out{
}} ... is then used to weight orthogonally contiguous pixels more heavily than diagonally contiguous pixels. Therefore, larger and more connections between @@ -48,7 +50,7 @@ lsm_c_contig_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ LaGro, J. 1991. Assessing patch shape in landscape mosaics. Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/man/lsm_c_core_cv.Rd b/man/lsm_c_core_cv.Rd index ec6c18d5f..0a6da4ef5 100644 --- a/man/lsm_c_core_cv.Rd +++ b/man/lsm_c_core_cv.Rd @@ -51,7 +51,7 @@ lsm_c_core_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_c_core_mn.Rd b/man/lsm_c_core_mn.Rd index 2621c62c3..ae1e09c43 100644 --- a/man/lsm_c_core_mn.Rd +++ b/man/lsm_c_core_mn.Rd @@ -49,7 +49,7 @@ lsm_c_core_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_c_core_sd.Rd b/man/lsm_c_core_sd.Rd index 5c54326bb..19dae1c19 100644 --- a/man/lsm_c_core_sd.Rd +++ b/man/lsm_c_core_sd.Rd @@ -50,7 +50,7 @@ lsm_c_core_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_c_cpland.Rd b/man/lsm_c_cpland.Rd index 88be534ac..89fbb86ce 100644 --- a/man/lsm_c_cpland.Rd +++ b/man/lsm_c_cpland.Rd @@ -53,7 +53,7 @@ lsm_c_cpland(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}} and \code{\link{lsm_l_ta}} diff --git a/man/lsm_c_dcad.Rd b/man/lsm_c_dcad.Rd index ddc8b0d93..df732adc6 100644 --- a/man/lsm_c_dcad.Rd +++ b/man/lsm_c_dcad.Rd @@ -54,7 +54,7 @@ lsm_c_dcad(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_ndca}}, diff --git a/man/lsm_c_dcore_cv.Rd b/man/lsm_c_dcore_cv.Rd index f4e552140..707979e2b 100644 --- a/man/lsm_c_dcore_cv.Rd +++ b/man/lsm_c_dcore_cv.Rd @@ -54,7 +54,7 @@ lsm_c_dcore_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_ncore}}, diff --git a/man/lsm_c_dcore_mn.Rd b/man/lsm_c_dcore_mn.Rd index 926a1ef7a..38acfcec1 100644 --- a/man/lsm_c_dcore_mn.Rd +++ b/man/lsm_c_dcore_mn.Rd @@ -51,7 +51,7 @@ lsm_c_dcore_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_ncore}}, diff --git a/man/lsm_c_dcore_sd.Rd b/man/lsm_c_dcore_sd.Rd index 213c4d8b6..17a1064b0 100644 --- a/man/lsm_c_dcore_sd.Rd +++ b/man/lsm_c_dcore_sd.Rd @@ -54,7 +54,7 @@ lsm_c_dcore_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_ncore}}, diff --git a/man/lsm_c_division.Rd b/man/lsm_c_division.Rd index 7edf38d2c..181e02da7 100644 --- a/man/lsm_c_division.Rd +++ b/man/lsm_c_division.Rd @@ -39,7 +39,7 @@ lsm_c_division(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh size: new measures of landscape fragmentation. diff --git a/man/lsm_c_ed.Rd b/man/lsm_c_ed.Rd index d6035e589..433a3fbb3 100644 --- a/man/lsm_c_ed.Rd +++ b/man/lsm_c_ed.Rd @@ -45,7 +45,7 @@ lsm_c_ed(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_te}}, diff --git a/man/lsm_c_enn_cv.Rd b/man/lsm_c_enn_cv.Rd index 66b3d49f4..005073e06 100644 --- a/man/lsm_c_enn_cv.Rd +++ b/man/lsm_c_enn_cv.Rd @@ -44,7 +44,7 @@ lsm_c_enn_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., and McComb, W. C. (1995). Relationships between landscape structure and breeding birds in the Oregon Coast Range. diff --git a/man/lsm_c_enn_mn.Rd b/man/lsm_c_enn_mn.Rd index f52b07d9c..f7bdbd472 100644 --- a/man/lsm_c_enn_mn.Rd +++ b/man/lsm_c_enn_mn.Rd @@ -44,7 +44,7 @@ lsm_c_enn_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., and McComb, W. C. (1995). Relationships between landscape structure and breeding birds in the Oregon Coast Range. diff --git a/man/lsm_c_enn_sd.Rd b/man/lsm_c_enn_sd.Rd index 46c37bf9d..1f6aeeceb 100644 --- a/man/lsm_c_enn_sd.Rd +++ b/man/lsm_c_enn_sd.Rd @@ -44,7 +44,7 @@ lsm_c_enn_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., and McComb, W. C. (1995). Relationships between landscape structure and breeding birds in the Oregon Coast Range. diff --git a/man/lsm_c_frac_cv.Rd b/man/lsm_c_frac_cv.Rd index 1faf84b87..7939a57ca 100644 --- a/man/lsm_c_frac_cv.Rd +++ b/man/lsm_c_frac_cv.Rd @@ -42,7 +42,7 @@ lsm_c_frac_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. San Francisco. W. H. Freeman and Company. diff --git a/man/lsm_c_frac_mn.Rd b/man/lsm_c_frac_mn.Rd index 751174424..931bdac18 100644 --- a/man/lsm_c_frac_mn.Rd +++ b/man/lsm_c_frac_mn.Rd @@ -38,7 +38,7 @@ lsm_c_frac_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. San Francisco. W. H. Freeman and Company. diff --git a/man/lsm_c_frac_sd.Rd b/man/lsm_c_frac_sd.Rd index 6679265de..09cb94634 100644 --- a/man/lsm_c_frac_sd.Rd +++ b/man/lsm_c_frac_sd.Rd @@ -41,7 +41,7 @@ lsm_c_frac_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. San Francisco. W. H. Freeman and Company. diff --git a/man/lsm_c_gyrate_cv.Rd b/man/lsm_c_gyrate_cv.Rd index 8995c8469..2e4455e4f 100644 --- a/man/lsm_c_gyrate_cv.Rd +++ b/man/lsm_c_gyrate_cv.Rd @@ -50,7 +50,7 @@ lsm_c_gyrate_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales in fragmented landscapes. Conservation ecology, 1(1). diff --git a/man/lsm_c_gyrate_mn.Rd b/man/lsm_c_gyrate_mn.Rd index c7d0d51a2..7f1cda2b1 100644 --- a/man/lsm_c_gyrate_mn.Rd +++ b/man/lsm_c_gyrate_mn.Rd @@ -48,7 +48,7 @@ lsm_c_gyrate_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales in fragmented landscapes. Conservation ecology, 1(1). diff --git a/man/lsm_c_gyrate_sd.Rd b/man/lsm_c_gyrate_sd.Rd index edee9f403..1275d8174 100644 --- a/man/lsm_c_gyrate_sd.Rd +++ b/man/lsm_c_gyrate_sd.Rd @@ -49,7 +49,7 @@ lsm_c_gyrate_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales in fragmented landscapes. Conservation ecology, 1(1). diff --git a/man/lsm_c_iji.Rd b/man/lsm_c_iji.Rd index 6416c0073..0b62eb76a 100644 --- a/man/lsm_c_iji.Rd +++ b/man/lsm_c_iji.Rd @@ -39,7 +39,7 @@ lsm_c_iji(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., & Marks, B. J. 1995. FRAGSTATS: spatial pattern analysis program for quantifying landscape structure. Gen. Tech. Rep. PNW-GTR-351. diff --git a/man/lsm_c_lpi.Rd b/man/lsm_c_lpi.Rd index 9e6ac9f4d..75ea3f4c6 100644 --- a/man/lsm_c_lpi.Rd +++ b/man/lsm_c_lpi.Rd @@ -40,7 +40,7 @@ lsm_c_lpi(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_c_lsi.Rd b/man/lsm_c_lsi.Rd index 19192e7de..7413b5900 100644 --- a/man/lsm_c_lsi.Rd +++ b/man/lsm_c_lsi.Rd @@ -38,7 +38,7 @@ lsm_c_lsi(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_c_mesh.Rd b/man/lsm_c_mesh.Rd index 275d55a4d..c54a1f755 100644 --- a/man/lsm_c_mesh.Rd +++ b/man/lsm_c_mesh.Rd @@ -41,7 +41,7 @@ lsm_c_mesh(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh size: new measures of landscape fragmentation. diff --git a/man/lsm_c_ndca.Rd b/man/lsm_c_ndca.Rd index 5a983eaed..12b95ec35 100644 --- a/man/lsm_c_ndca.Rd +++ b/man/lsm_c_ndca.Rd @@ -55,7 +55,7 @@ lsm_c_ndca(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_tca}}, \cr diff --git a/man/lsm_c_nlsi.Rd b/man/lsm_c_nlsi.Rd index 2b1b11bd1..b8f993ecd 100644 --- a/man/lsm_c_nlsi.Rd +++ b/man/lsm_c_nlsi.Rd @@ -42,7 +42,7 @@ lsm_c_nlsi(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_c_np.Rd b/man/lsm_c_np.Rd index 0d62a33e7..c5c13c068 100644 --- a/man/lsm_c_np.Rd +++ b/man/lsm_c_np.Rd @@ -38,7 +38,7 @@ lsm_c_np(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_l_np}} diff --git a/man/lsm_c_pafrac.Rd b/man/lsm_c_pafrac.Rd index c48879ade..689e1a9e5 100644 --- a/man/lsm_c_pafrac.Rd +++ b/man/lsm_c_pafrac.Rd @@ -45,7 +45,7 @@ lsm_c_pafrac(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Burrough, P. A. 1986. Principles of Geographical Information Systems for Land Resources Assessment. Monographs on Soil and Resources Survey No. 12. diff --git a/man/lsm_c_para_cv.Rd b/man/lsm_c_para_cv.Rd index ebc676fb1..4e25a068a 100644 --- a/man/lsm_c_para_cv.Rd +++ b/man/lsm_c_para_cv.Rd @@ -42,7 +42,7 @@ lsm_c_para_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_para}}, diff --git a/man/lsm_c_para_mn.Rd b/man/lsm_c_para_mn.Rd index ac3aeda5d..c5656bf25 100644 --- a/man/lsm_c_para_mn.Rd +++ b/man/lsm_c_para_mn.Rd @@ -42,7 +42,7 @@ lsm_c_para_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_para}}, diff --git a/man/lsm_c_para_sd.Rd b/man/lsm_c_para_sd.Rd index 1168a4f4b..e8852cc56 100644 --- a/man/lsm_c_para_sd.Rd +++ b/man/lsm_c_para_sd.Rd @@ -42,7 +42,7 @@ lsm_c_para_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_para}}, diff --git a/man/lsm_c_pd.Rd b/man/lsm_c_pd.Rd index f3fef6dee..894928f60 100644 --- a/man/lsm_c_pd.Rd +++ b/man/lsm_c_pd.Rd @@ -41,7 +41,7 @@ lsm_c_pd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_np}}, diff --git a/man/lsm_c_pladj.Rd b/man/lsm_c_pladj.Rd index d7b4bfed7..f461d04bd 100644 --- a/man/lsm_c_pladj.Rd +++ b/man/lsm_c_pladj.Rd @@ -38,5 +38,5 @@ lsm_c_pladj(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html. +web site: https://www.umass.edu/landeco/. } diff --git a/man/lsm_c_pland.Rd b/man/lsm_c_pland.Rd index 63e254719..1575cf5c8 100644 --- a/man/lsm_c_pland.Rd +++ b/man/lsm_c_pland.Rd @@ -40,7 +40,7 @@ lsm_c_pland(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_ca}}, diff --git a/man/lsm_c_shape_cv.Rd b/man/lsm_c_shape_cv.Rd index 3c1696ba9..62e19439e 100644 --- a/man/lsm_c_shape_cv.Rd +++ b/man/lsm_c_shape_cv.Rd @@ -40,7 +40,7 @@ lsm_c_shape_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_c_shape_mn.Rd b/man/lsm_c_shape_mn.Rd index 953ff8246..44463f94f 100644 --- a/man/lsm_c_shape_mn.Rd +++ b/man/lsm_c_shape_mn.Rd @@ -40,7 +40,7 @@ lsm_c_shape_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_c_shape_sd.Rd b/man/lsm_c_shape_sd.Rd index 828d86bd7..610bca41d 100644 --- a/man/lsm_c_shape_sd.Rd +++ b/man/lsm_c_shape_sd.Rd @@ -40,7 +40,7 @@ lsm_c_shape_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_c_split.Rd b/man/lsm_c_split.Rd index b65b75e73..f27ee250c 100644 --- a/man/lsm_c_split.Rd +++ b/man/lsm_c_split.Rd @@ -39,7 +39,7 @@ lsm_c_split(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh size: new measures of landscape fragmentation. diff --git a/man/lsm_c_tca.Rd b/man/lsm_c_tca.Rd index 1f413578a..fb629414b 100644 --- a/man/lsm_c_tca.Rd +++ b/man/lsm_c_tca.Rd @@ -50,7 +50,7 @@ lsm_c_tca(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_c_te.Rd b/man/lsm_c_te.Rd index a4311556e..84e80d5c4 100644 --- a/man/lsm_c_te.Rd +++ b/man/lsm_c_te.Rd @@ -27,7 +27,7 @@ TE is an 'Area and edge metric'. Total (class) edge includes all edges between c all other classes k. It measures the configuration of the landscape because a highly fragmented landscape will have many edges. However, total edge is an absolute measure, making comparisons among landscapes with different total areas difficult. If -\code{cound_boundary = TRUE} also edges to the landscape boundary are included. +\code{count_boundary = TRUE} also edges to the landscape boundary are included. \subsection{Units}{Meters} \subsection{Range}{TE >= 0} @@ -42,7 +42,7 @@ lsm_c_te(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_perim}} diff --git a/man/lsm_l_ai.Rd b/man/lsm_l_ai.Rd index dabea12a2..62626a3e1 100644 --- a/man/lsm_l_ai.Rd +++ b/man/lsm_l_ai.Rd @@ -40,7 +40,7 @@ lsm_l_ai(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ He, H. S., DeZonia, B. E., & Mladenoff, D. J. 2000. An aggregation index (AI) to quantify spatial patterns of landscapes. Landscape ecology, 15(7), 591-601. diff --git a/man/lsm_l_area_cv.Rd b/man/lsm_l_area_cv.Rd index d874829ef..3305ef529 100644 --- a/man/lsm_l_area_cv.Rd +++ b/man/lsm_l_area_cv.Rd @@ -39,7 +39,7 @@ lsm_l_area_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_l_area_mn.Rd b/man/lsm_l_area_mn.Rd index f6a81aa2a..d61da98ad 100644 --- a/man/lsm_l_area_mn.Rd +++ b/man/lsm_l_area_mn.Rd @@ -40,7 +40,7 @@ lsm_l_area_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_l_area_sd.Rd b/man/lsm_l_area_sd.Rd index 0686963ed..409fed19a 100644 --- a/man/lsm_l_area_sd.Rd +++ b/man/lsm_l_area_sd.Rd @@ -38,7 +38,7 @@ lsm_l_area_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_l_cai_cv.Rd b/man/lsm_l_cai_cv.Rd index 0f604751c..2ac9f61d7 100644 --- a/man/lsm_l_cai_cv.Rd +++ b/man/lsm_l_cai_cv.Rd @@ -55,7 +55,7 @@ lsm_l_cai_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_cai}}, diff --git a/man/lsm_l_cai_mn.Rd b/man/lsm_l_cai_mn.Rd index 08288ed1b..9e12c1d8b 100644 --- a/man/lsm_l_cai_mn.Rd +++ b/man/lsm_l_cai_mn.Rd @@ -52,7 +52,7 @@ lsm_l_cai_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_cai}}, diff --git a/man/lsm_l_cai_sd.Rd b/man/lsm_l_cai_sd.Rd index 22722c05d..64eb22533 100644 --- a/man/lsm_l_cai_sd.Rd +++ b/man/lsm_l_cai_sd.Rd @@ -54,7 +54,7 @@ lsm_l_cai_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_cai}}, diff --git a/man/lsm_l_circle_cv.Rd b/man/lsm_l_circle_cv.Rd index 0996b4e30..cd2330261 100644 --- a/man/lsm_l_circle_cv.Rd +++ b/man/lsm_l_circle_cv.Rd @@ -41,7 +41,7 @@ lsm_l_circle_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. diff --git a/man/lsm_l_circle_mn.Rd b/man/lsm_l_circle_mn.Rd index 1a1a5e4bf..339c6f80e 100644 --- a/man/lsm_l_circle_mn.Rd +++ b/man/lsm_l_circle_mn.Rd @@ -40,7 +40,7 @@ lsm_l_circle_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. diff --git a/man/lsm_l_circle_sd.Rd b/man/lsm_l_circle_sd.Rd index a6275b7ee..a26d86c8d 100644 --- a/man/lsm_l_circle_sd.Rd +++ b/man/lsm_l_circle_sd.Rd @@ -42,7 +42,7 @@ lsm_l_circle_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. diff --git a/man/lsm_l_cohesion.Rd b/man/lsm_l_cohesion.Rd index 74d9248d2..8bad3fce1 100644 --- a/man/lsm_l_cohesion.Rd +++ b/man/lsm_l_cohesion.Rd @@ -36,7 +36,7 @@ lsm_l_cohesion(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Schumaker, N. H. 1996. Using landscape indices to predict habitat connectivity. Ecology, 77(4), 1210-1225. diff --git a/man/lsm_l_contag.Rd b/man/lsm_l_contag.Rd index 846d837a7..daf6c12f7 100644 --- a/man/lsm_l_contag.Rd +++ b/man/lsm_l_contag.Rd @@ -46,7 +46,7 @@ lsm_l_contag(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Riitters, K.H., O’Neill, R.V., Wickham, J.D. & Jones, K.B. (1996). A note on contagion indices for landscape analysis. Landscape ecology, 11, 197–202. diff --git a/man/lsm_l_contig_cv.Rd b/man/lsm_l_contig_cv.Rd index fe631c729..77b6df6d2 100644 --- a/man/lsm_l_contig_cv.Rd +++ b/man/lsm_l_contig_cv.Rd @@ -25,10 +25,12 @@ where \eqn{CONTIG[patch_{ij}]} is the contiguity of each patch. CONTIG_CV is a 'Shape metric'. It summarises the landscape as the coefficient of variation of all patches in the landscape. CONTIG_CV asses the spatial connectedness (contiguity) of cells in patches. The metric coerces patch values to a value of 1 and the background -to NA. A nine cell focal filter matrix:\preformatted{filter_matrix <- matrix(c(1, 2, 1, +to NA. A nine cell focal filter matrix: + +\if{html}{\out{
}}\preformatted{filter_matrix <- matrix(c(1, 2, 1, 2, 1, 2, 1, 2, 1), 3, 3, byrow = T) -} +}\if{html}{\out{
}} ... is then used to weight orthogonally contiguous pixels more heavily than diagonally contiguous pixels. Therefore, larger and more connections between @@ -48,7 +50,7 @@ lsm_l_contig_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ LaGro, J. 1991. Assessing patch shape in landscape mosaics. Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/man/lsm_l_contig_mn.Rd b/man/lsm_l_contig_mn.Rd index 7e65f74b0..232a3508e 100644 --- a/man/lsm_l_contig_mn.Rd +++ b/man/lsm_l_contig_mn.Rd @@ -25,10 +25,12 @@ where \eqn{CONTIG[patch_{ij}]} is the contiguity of each patch. CONTIG_MN is a 'Shape metric'. It summarises the landscape as the mean of all patches in the landscape. CONTIG_MN asses the spatial connectedness (contiguity) of cells in patches. The metric coerces patch values to a value of 1 and the background -to NA. A nine cell focal filter matrix:\preformatted{filter_matrix <- matrix(c(1, 2, 1, +to NA. A nine cell focal filter matrix: + +\if{html}{\out{
}}\preformatted{filter_matrix <- matrix(c(1, 2, 1, 2, 1, 2, 1, 2, 1), 3, 3, byrow = T) -} +}\if{html}{\out{
}} ... is then used to weight orthogonally contiguous pixels more heavily than diagonally contiguous pixels. Therefore, larger and more connections between @@ -47,7 +49,7 @@ lsm_l_contig_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ LaGro, J. 1991. Assessing patch shape in landscape mosaics. Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/man/lsm_l_contig_sd.Rd b/man/lsm_l_contig_sd.Rd index 1465d7ed9..2d07e06f3 100644 --- a/man/lsm_l_contig_sd.Rd +++ b/man/lsm_l_contig_sd.Rd @@ -25,10 +25,12 @@ where \eqn{CONTIG[patch_{ij}]} is the contiguity of each patch. CONTIG_SD is a 'Shape metric'. It summarises the landscape as the standard deviation of all patches in the landscape. CONTIG_SD asses the spatial connectedness (contiguity) of cells in patches. The metric coerces patch values to a value of 1 and the background -to NA. A nine cell focal filter matrix:\preformatted{filter_matrix <- matrix(c(1, 2, 1, +to NA. A nine cell focal filter matrix: + +\if{html}{\out{
}}\preformatted{filter_matrix <- matrix(c(1, 2, 1, 2, 1, 2, 1, 2, 1), 3, 3, byrow = T) -} +}\if{html}{\out{
}} ... is then used to weight orthogonally contiguous pixels more heavily than diagonally contiguous pixels. Therefore, larger and more connections between @@ -48,7 +50,7 @@ lsm_l_contig_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ LaGro, J. 1991. Assessing patch shape in landscape mosaics. Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/man/lsm_l_core_cv.Rd b/man/lsm_l_core_cv.Rd index 6c11fc036..5d67f6de2 100644 --- a/man/lsm_l_core_cv.Rd +++ b/man/lsm_l_core_cv.Rd @@ -52,7 +52,7 @@ lsm_l_core_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_l_core_mn.Rd b/man/lsm_l_core_mn.Rd index ec4a8c225..82379ee13 100644 --- a/man/lsm_l_core_mn.Rd +++ b/man/lsm_l_core_mn.Rd @@ -50,7 +50,7 @@ lsm_l_core_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_l_core_sd.Rd b/man/lsm_l_core_sd.Rd index 1d63cabfa..b4ece829f 100644 --- a/man/lsm_l_core_sd.Rd +++ b/man/lsm_l_core_sd.Rd @@ -51,7 +51,7 @@ lsm_l_core_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_l_dcad.Rd b/man/lsm_l_dcad.Rd index 666b6f511..149ccc49e 100644 --- a/man/lsm_l_dcad.Rd +++ b/man/lsm_l_dcad.Rd @@ -54,7 +54,7 @@ lsm_l_dcad(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_ndca}}, diff --git a/man/lsm_l_dcore_cv.Rd b/man/lsm_l_dcore_cv.Rd index 91023567c..385971521 100644 --- a/man/lsm_l_dcore_cv.Rd +++ b/man/lsm_l_dcore_cv.Rd @@ -54,7 +54,7 @@ lsm_l_dcore_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_ncore}}, diff --git a/man/lsm_l_dcore_mn.Rd b/man/lsm_l_dcore_mn.Rd index d24b45846..72acf6850 100644 --- a/man/lsm_l_dcore_mn.Rd +++ b/man/lsm_l_dcore_mn.Rd @@ -51,7 +51,7 @@ lsm_l_dcore_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_ncore}}, diff --git a/man/lsm_l_dcore_sd.Rd b/man/lsm_l_dcore_sd.Rd index fd904e831..8d58b7897 100644 --- a/man/lsm_l_dcore_sd.Rd +++ b/man/lsm_l_dcore_sd.Rd @@ -53,7 +53,7 @@ lsm_l_dcore_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_ncore}}, diff --git a/man/lsm_l_division.Rd b/man/lsm_l_division.Rd index ad52466a5..e2ef2b83f 100644 --- a/man/lsm_l_division.Rd +++ b/man/lsm_l_division.Rd @@ -39,7 +39,7 @@ lsm_l_division(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh size: new measures of landscape fragmentation. diff --git a/man/lsm_l_ed.Rd b/man/lsm_l_ed.Rd index c14dd83d7..74c7c08bc 100644 --- a/man/lsm_l_ed.Rd +++ b/man/lsm_l_ed.Rd @@ -45,7 +45,7 @@ lsm_l_ed(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_l_te}}, diff --git a/man/lsm_l_enn_cv.Rd b/man/lsm_l_enn_cv.Rd index 7a9c23122..2f8e3e7aa 100644 --- a/man/lsm_l_enn_cv.Rd +++ b/man/lsm_l_enn_cv.Rd @@ -44,7 +44,7 @@ lsm_l_enn_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., and McComb, W. C. (1995). Relationships between landscape structure and breeding birds in the Oregon Coast Range. diff --git a/man/lsm_l_enn_mn.Rd b/man/lsm_l_enn_mn.Rd index 4f08312f5..7c9f1ddc6 100644 --- a/man/lsm_l_enn_mn.Rd +++ b/man/lsm_l_enn_mn.Rd @@ -44,7 +44,7 @@ lsm_l_enn_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., and McComb, W. C. (1995). Relationships between landscape structure and breeding birds in the Oregon Coast Range. diff --git a/man/lsm_l_enn_sd.Rd b/man/lsm_l_enn_sd.Rd index acb40fbfb..390a1e211 100644 --- a/man/lsm_l_enn_sd.Rd +++ b/man/lsm_l_enn_sd.Rd @@ -44,7 +44,7 @@ lsm_l_enn_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., and McComb, W. C. (1995). Relationships between landscape structure and breeding birds in the Oregon Coast Range. diff --git a/man/lsm_l_frac_cv.Rd b/man/lsm_l_frac_cv.Rd index 935a4370f..109790717 100644 --- a/man/lsm_l_frac_cv.Rd +++ b/man/lsm_l_frac_cv.Rd @@ -42,7 +42,7 @@ lsm_l_frac_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. San Francisco. W. H. Freeman and Company. diff --git a/man/lsm_l_frac_mn.Rd b/man/lsm_l_frac_mn.Rd index 35a2c4f3f..a09e125f1 100644 --- a/man/lsm_l_frac_mn.Rd +++ b/man/lsm_l_frac_mn.Rd @@ -41,7 +41,7 @@ lsm_l_frac_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. San Francisco. W. H. Freeman and Company. diff --git a/man/lsm_l_frac_sd.Rd b/man/lsm_l_frac_sd.Rd index 10871ec98..9486eff32 100644 --- a/man/lsm_l_frac_sd.Rd +++ b/man/lsm_l_frac_sd.Rd @@ -41,7 +41,7 @@ lsm_l_frac_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. San Francisco. W. H. Freeman and Company. diff --git a/man/lsm_l_gyrate_cv.Rd b/man/lsm_l_gyrate_cv.Rd index 8ee07dabc..d1091cd45 100644 --- a/man/lsm_l_gyrate_cv.Rd +++ b/man/lsm_l_gyrate_cv.Rd @@ -50,7 +50,7 @@ lsm_l_gyrate_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales in fragmented landscapes. Conservation ecology, 1(1). diff --git a/man/lsm_l_gyrate_mn.Rd b/man/lsm_l_gyrate_mn.Rd index 48cd1d92a..0ff231412 100644 --- a/man/lsm_l_gyrate_mn.Rd +++ b/man/lsm_l_gyrate_mn.Rd @@ -48,7 +48,7 @@ lsm_l_gyrate_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales in fragmented landscapes. Conservation ecology, 1(1). diff --git a/man/lsm_l_gyrate_sd.Rd b/man/lsm_l_gyrate_sd.Rd index 1474c97e2..fa83d8b73 100644 --- a/man/lsm_l_gyrate_sd.Rd +++ b/man/lsm_l_gyrate_sd.Rd @@ -49,7 +49,7 @@ lsm_l_gyrate_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales in fragmented landscapes. Conservation ecology, 1(1). diff --git a/man/lsm_l_iji.Rd b/man/lsm_l_iji.Rd index 44e82cbf1..33022bf90 100644 --- a/man/lsm_l_iji.Rd +++ b/man/lsm_l_iji.Rd @@ -40,7 +40,7 @@ lsm_l_iji(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., & Marks, B. J. 1995. FRAGSTATS: spatial pattern analysis program for quantifying landscape structure. Gen. Tech. Rep. PNW-GTR-351. diff --git a/man/lsm_l_lpi.Rd b/man/lsm_l_lpi.Rd index b2bb11d27..914c4b7b7 100644 --- a/man/lsm_l_lpi.Rd +++ b/man/lsm_l_lpi.Rd @@ -40,7 +40,7 @@ lsm_l_lpi(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_l_lsi.Rd b/man/lsm_l_lsi.Rd index 556f8fe6b..456a89648 100644 --- a/man/lsm_l_lsi.Rd +++ b/man/lsm_l_lsi.Rd @@ -38,7 +38,7 @@ lsm_l_lsi(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_l_mesh.Rd b/man/lsm_l_mesh.Rd index 9493c262a..1a6cf8c8c 100644 --- a/man/lsm_l_mesh.Rd +++ b/man/lsm_l_mesh.Rd @@ -41,7 +41,7 @@ lsm_l_mesh(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh size: new measures of landscape fragmentation. diff --git a/man/lsm_l_msidi.Rd b/man/lsm_l_msidi.Rd index 0995b7d54..b5298340c 100644 --- a/man/lsm_l_msidi.Rd +++ b/man/lsm_l_msidi.Rd @@ -37,7 +37,7 @@ lsm_l_msidi(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Simpson, E. H. 1949. Measurement of diversity. Nature 163:688 diff --git a/man/lsm_l_msiei.Rd b/man/lsm_l_msiei.Rd index ece9af766..735c1a846 100644 --- a/man/lsm_l_msiei.Rd +++ b/man/lsm_l_msiei.Rd @@ -35,7 +35,7 @@ lsm_l_msiei(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Simpson, E. H. 1949. Measurement of diversity. Nature 163:688 diff --git a/man/lsm_l_ndca.Rd b/man/lsm_l_ndca.Rd index 6f11d14e1..8dc778eef 100644 --- a/man/lsm_l_ndca.Rd +++ b/man/lsm_l_ndca.Rd @@ -55,7 +55,7 @@ lsm_l_ndca(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_tca}}, \cr diff --git a/man/lsm_l_np.Rd b/man/lsm_l_np.Rd index 78f7d5268..833108696 100644 --- a/man/lsm_l_np.Rd +++ b/man/lsm_l_np.Rd @@ -39,7 +39,7 @@ lsm_l_np(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_np}} diff --git a/man/lsm_l_pafrac.Rd b/man/lsm_l_pafrac.Rd index 13ccea4bb..1e5bd27be 100644 --- a/man/lsm_l_pafrac.Rd +++ b/man/lsm_l_pafrac.Rd @@ -45,7 +45,7 @@ lsm_l_pafrac(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Burrough, P. A. 1986. Principles of Geographical Information Systems for Land Resources Assessment. Monographs on Soil and Resources Survey No. 12. diff --git a/man/lsm_l_para_cv.Rd b/man/lsm_l_para_cv.Rd index 29c245823..2fb95297a 100644 --- a/man/lsm_l_para_cv.Rd +++ b/man/lsm_l_para_cv.Rd @@ -42,7 +42,7 @@ lsm_l_para_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_para}}, diff --git a/man/lsm_l_para_mn.Rd b/man/lsm_l_para_mn.Rd index c3537be83..7a145a7d9 100644 --- a/man/lsm_l_para_mn.Rd +++ b/man/lsm_l_para_mn.Rd @@ -42,7 +42,7 @@ lsm_l_para_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_para}}, diff --git a/man/lsm_l_para_sd.Rd b/man/lsm_l_para_sd.Rd index 619fda2dd..e9fadbc37 100644 --- a/man/lsm_l_para_sd.Rd +++ b/man/lsm_l_para_sd.Rd @@ -42,7 +42,7 @@ lsm_l_para_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_para}}, diff --git a/man/lsm_l_pd.Rd b/man/lsm_l_pd.Rd index 779c0e9de..3b331fef6 100644 --- a/man/lsm_l_pd.Rd +++ b/man/lsm_l_pd.Rd @@ -41,7 +41,7 @@ lsm_l_pd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_np}}, diff --git a/man/lsm_l_pladj.Rd b/man/lsm_l_pladj.Rd index d252c555a..5722a58f0 100644 --- a/man/lsm_l_pladj.Rd +++ b/man/lsm_l_pladj.Rd @@ -38,5 +38,5 @@ lsm_l_pladj(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html. +web site: https://www.umass.edu/landeco/. } diff --git a/man/lsm_l_pr.Rd b/man/lsm_l_pr.Rd index 747c56855..9920a6ebf 100644 --- a/man/lsm_l_pr.Rd +++ b/man/lsm_l_pr.Rd @@ -36,5 +36,5 @@ lsm_l_pr(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } diff --git a/man/lsm_l_prd.Rd b/man/lsm_l_prd.Rd index d8f9e4289..aa549a74d 100644 --- a/man/lsm_l_prd.Rd +++ b/man/lsm_l_prd.Rd @@ -41,5 +41,5 @@ lsm_l_prd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } diff --git a/man/lsm_l_rpr.Rd b/man/lsm_l_rpr.Rd index 091a5cc84..84ae216c9 100644 --- a/man/lsm_l_rpr.Rd +++ b/man/lsm_l_rpr.Rd @@ -42,7 +42,7 @@ lsm_l_rpr(landscape, classes_max = 5) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Romme, W. H. 1982. Fire and landscapediversity in subalpine forests of Yellowstone National Park.Ecol.Monogr. 52:199-221 diff --git a/man/lsm_l_shape_cv.Rd b/man/lsm_l_shape_cv.Rd index 1a67f2787..ed899a0ae 100644 --- a/man/lsm_l_shape_cv.Rd +++ b/man/lsm_l_shape_cv.Rd @@ -40,7 +40,7 @@ lsm_l_shape_cv(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_l_shape_mn.Rd b/man/lsm_l_shape_mn.Rd index 0415673a9..cc18ad729 100644 --- a/man/lsm_l_shape_mn.Rd +++ b/man/lsm_l_shape_mn.Rd @@ -40,7 +40,7 @@ lsm_l_shape_mn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_l_shape_sd.Rd b/man/lsm_l_shape_sd.Rd index bdb792261..5b83a5ece 100644 --- a/man/lsm_l_shape_sd.Rd +++ b/man/lsm_l_shape_sd.Rd @@ -40,7 +40,7 @@ lsm_l_shape_sd(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/lsm_l_shdi.Rd b/man/lsm_l_shdi.Rd index ff5d2f08f..2f5d6191d 100644 --- a/man/lsm_l_shdi.Rd +++ b/man/lsm_l_shdi.Rd @@ -36,7 +36,7 @@ lsm_l_shdi(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Shannon, C., and W. Weaver. 1949. The mathematical theory of communication. Univ. IllinoisPress, Urbana diff --git a/man/lsm_l_shei.Rd b/man/lsm_l_shei.Rd index 84ddba97d..010e5f576 100644 --- a/man/lsm_l_shei.Rd +++ b/man/lsm_l_shei.Rd @@ -37,7 +37,7 @@ lsm_l_shei(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Shannon, C., and W. Weaver. 1949. The mathematical theory of communication. Univ. IllinoisPress, Urbana diff --git a/man/lsm_l_sidi.Rd b/man/lsm_l_sidi.Rd index 89018d289..7ddd9e647 100644 --- a/man/lsm_l_sidi.Rd +++ b/man/lsm_l_sidi.Rd @@ -41,7 +41,7 @@ lsm_l_sidi(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Simpson, E. H. 1949. Measurement of diversity. Nature 163:688 } diff --git a/man/lsm_l_siei.Rd b/man/lsm_l_siei.Rd index 2c7996556..1ec5579d0 100644 --- a/man/lsm_l_siei.Rd +++ b/man/lsm_l_siei.Rd @@ -41,7 +41,7 @@ lsm_l_siei(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Simpson, E. H. 1949. Measurement of diversity. Nature 163:688 } diff --git a/man/lsm_l_split.Rd b/man/lsm_l_split.Rd index 0b5a598d9..18a52ecb0 100644 --- a/man/lsm_l_split.Rd +++ b/man/lsm_l_split.Rd @@ -39,7 +39,7 @@ lsm_l_split(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Jaeger, J. A. 2000. Landscape division, splitting index, and effective mesh size: new measures of landscape fragmentation. diff --git a/man/lsm_l_ta.Rd b/man/lsm_l_ta.Rd index 3c173734b..7ab063ece 100644 --- a/man/lsm_l_ta.Rd +++ b/man/lsm_l_ta.Rd @@ -38,7 +38,7 @@ lsm_l_ta(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_l_tca.Rd b/man/lsm_l_tca.Rd index fa82d0937..61e243eb5 100644 --- a/man/lsm_l_tca.Rd +++ b/man/lsm_l_tca.Rd @@ -49,7 +49,7 @@ lsm_l_tca(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_l_te.Rd b/man/lsm_l_te.Rd index a5db8b780..5114b718d 100644 --- a/man/lsm_l_te.Rd +++ b/man/lsm_l_te.Rd @@ -23,7 +23,7 @@ where \eqn{e_{ik}} is the edge lengths in meters. TE is an 'Area and edge metric'. Total edge includes all edges. It measures the configuration of the landscape because a highly fragmented landscape will have many edges. However, total edge is an absolute measure, making comparisons among landscapes -with different total areas difficult. If \code{cound_boundary = TRUE} also edges to the +with different total areas difficult. If \code{count_boundary = TRUE} also edges to the landscape boundary are included. \subsection{Units}{Meters} @@ -39,7 +39,7 @@ lsm_l_te(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_perim}} diff --git a/man/lsm_p_area.Rd b/man/lsm_p_area.Rd index ebf244724..d1c143bd3 100644 --- a/man/lsm_p_area.Rd +++ b/man/lsm_p_area.Rd @@ -40,7 +40,7 @@ lsm_p_area(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_area_mn}}, diff --git a/man/lsm_p_cai.Rd b/man/lsm_p_cai.Rd index 473195008..8d97d8c97 100644 --- a/man/lsm_p_cai.Rd +++ b/man/lsm_p_cai.Rd @@ -48,7 +48,7 @@ lsm_p_cai(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_core}}, diff --git a/man/lsm_p_circle.Rd b/man/lsm_p_circle.Rd index 8496a89e7..32a9f3ebf 100644 --- a/man/lsm_p_circle.Rd +++ b/man/lsm_p_circle.Rd @@ -42,7 +42,7 @@ lsm_p_circle(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Baker, W. L., and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. diff --git a/man/lsm_p_contig.Rd b/man/lsm_p_contig.Rd index d80fbfaa0..84cd50c8a 100644 --- a/man/lsm_p_contig.Rd +++ b/man/lsm_p_contig.Rd @@ -27,10 +27,12 @@ the size of the filter matrix (13 in this case). CONTIG is a 'Shape metric'. It asses the spatial connectedness (contiguity) of cells in patches. CONTIG coerces patch values to a value of 1 and the background -to NA. A nine cell focal filter matrix:\preformatted{filter_matrix <- matrix(c(1, 2, 1, +to NA. A nine cell focal filter matrix: + +\if{html}{\out{
}}\preformatted{filter_matrix <- matrix(c(1, 2, 1, 2, 1, 2, 1, 2, 1), 3, 3, byrow = T) -} +}\if{html}{\out{
}} ... is then used to weight orthogonally contiguous pixels more heavily than diagonally contiguous pixels. Therefore, larger and more connections between @@ -49,7 +51,7 @@ lsm_p_contig(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ LaGro, J. 1991. Assessing patch shape in landscape mosaics. Photogrammetric Engineering and Remote Sensing, 57(3), 285-293 diff --git a/man/lsm_p_core.Rd b/man/lsm_p_core.Rd index f9c5930bd..670e3852c 100644 --- a/man/lsm_p_core.Rd +++ b/man/lsm_p_core.Rd @@ -53,7 +53,7 @@ lsm_p_core(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_core_mn}}, diff --git a/man/lsm_p_enn.Rd b/man/lsm_p_enn.Rd index 42d78272b..360a537d1 100644 --- a/man/lsm_p_enn.Rd +++ b/man/lsm_p_enn.Rd @@ -45,7 +45,7 @@ lsm_p_enn(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ McGarigal, K., and McComb, W. C. (1995). Relationships between landscape structure and breeding birds in the Oregon Coast Range. diff --git a/man/lsm_p_frac.Rd b/man/lsm_p_frac.Rd index 8a64e26d2..21c26436b 100644 --- a/man/lsm_p_frac.Rd +++ b/man/lsm_p_frac.Rd @@ -41,7 +41,7 @@ lsm_p_frac(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Mandelbrot, B. B. 1977. Fractals: Form, Chance, and Dimension. San Francisco. W. H. Freeman and Company. diff --git a/man/lsm_p_gyrate.Rd b/man/lsm_p_gyrate.Rd index 14c72f400..c54fc1323 100644 --- a/man/lsm_p_gyrate.Rd +++ b/man/lsm_p_gyrate.Rd @@ -47,7 +47,7 @@ lsm_p_gyrate(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Keitt, T. H., Urban, D. L., & Milne, B. T. 1997. Detecting critical scales in fragmented landscapes. Conservation ecology, 1(1). diff --git a/man/lsm_p_ncore.Rd b/man/lsm_p_ncore.Rd index f88170d73..20f21d171 100644 --- a/man/lsm_p_ncore.Rd +++ b/man/lsm_p_ncore.Rd @@ -54,7 +54,7 @@ lsm_p_ncore(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_c_dcore_mn}}, diff --git a/man/lsm_p_para.Rd b/man/lsm_p_para.Rd index 55abca205..aa018f5ff 100644 --- a/man/lsm_p_para.Rd +++ b/man/lsm_p_para.Rd @@ -41,7 +41,7 @@ lsm_p_para(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } \seealso{ \code{\link{lsm_p_area}}, diff --git a/man/lsm_p_perim.Rd b/man/lsm_p_perim.Rd index bee655f3f..7fa90ca83 100644 --- a/man/lsm_p_perim.Rd +++ b/man/lsm_p_perim.Rd @@ -40,5 +40,5 @@ lsm_p_perim(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ } diff --git a/man/lsm_p_shape.Rd b/man/lsm_p_shape.Rd index f8142ee9e..289c74c8e 100644 --- a/man/lsm_p_shape.Rd +++ b/man/lsm_p_shape.Rd @@ -40,7 +40,7 @@ lsm_p_shape(landscape) McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -web site: http://www.umass.edu/landeco/research/fragstats/fragstats.html +web site: https://www.umass.edu/landeco/ Patton, D. R. 1975. A diversity index for quantifying habitat "edge". Wildl. Soc.Bull. 3:171-173. diff --git a/man/window_lsm.Rd b/man/window_lsm.Rd index ab8092d59..fbbdd4ec4 100644 --- a/man/window_lsm.Rd +++ b/man/window_lsm.Rd @@ -55,6 +55,9 @@ for selected landscape metrics). window <- matrix(1, nrow = 5,ncol = 5) window_lsm(landscape, window = window, what = c("lsm_l_pr", "lsm_l_joinent")) window_lsm(landscape_stack, window = window, what = c("lsm_l_pr", "lsm_l_joinent")) + +window_circular <- matrix(c(NA, 1, NA, 1, 1, 1, NA, 1, NA), nrow = 3, ncol = 3) +window_lsm(landscape, window = window_circular, what = c("lsm_l_pr", "lsm_l_joinent")) } } @@ -69,7 +72,7 @@ earth observation and geoinformation, 44, 205-216. McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following -website: \url{http://www.umass.edu/landeco/research/fragstats/fragstats.html} +website: \url{https://www.umass.edu/landeco/} } \seealso{ \code{\link{list_lsm}} \cr diff --git a/vignettes/articles/comparing_tools.Rmd b/vignettes/articles/comparing_tools.Rmd index 57657d0b4..7cae00b98 100644 --- a/vignettes/articles/comparing_tools.Rmd +++ b/vignettes/articles/comparing_tools.Rmd @@ -1,15 +1,21 @@ --- title: "Differences FRAGSTATS|landscapemetrics|SDMTools" date: "`r Sys.Date()`" -output: - github_document: - html_preview: false +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Differences FRAGSTATS|landscapemetrics|SDMTools} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +editor_options: + chunk_output_type: console --- + ```{r load_libraries_hidden, message = FALSE, warning = FALSE, include = FALSE} library(landscapemetrics) -library(patchwork) library(raster) -library(tidyverse) + +library(dplyr) +library(purrr) ``` # Comparison with FRAGSTATS @@ -38,8 +44,8 @@ cv <- function(x) { # CV calculated from patch values of FRAGSTATS fragstats_calculated <- fragstats_patch_landscape %>% - group_by(TYPE) %>% - summarise(cv = cv(AREA)) %>% + dplyr::group_by(TYPE) %>% + dplyr::summarise(cv = cv(AREA)) %>% purrr::set_names("class", "fragstats_calculated") # Output of FRAGSTATS @@ -52,13 +58,11 @@ landscapemetrics_output <- lsm_c_area_cv(landscape) %>% dplyr::select(class, value) %>% purrr::set_names("class", "landscapemetrics") -fragstats <- full_join(x = fragstats_output, - y = fragstats_calculated, - by = "class") +fragstats <- dplyr::full_join(x = fragstats_output, y = fragstats_calculated, + by = "class") -cv_full <- full_join(x = fragstats, - y = landscapemetrics_output, - by = "class") +cv_full <- dplyr::full_join(x = fragstats, y = landscapemetrics_output, + by = "class") ``` @@ -75,8 +79,8 @@ As for the *cv*, the results for the *sd* are similiar. The result calculated fr ```{r} # SD calculated from patch values of FRAGSTATS fragstats_calculated <- fragstats_patch_landscape %>% - group_by(TYPE) %>% - summarise(sd = sd(AREA)) %>% + dplyr::group_by(TYPE) %>% + dplyr::summarise(sd = sd(AREA)) %>% purrr::set_names("class", "fragstats_calculated") @@ -90,13 +94,11 @@ landscapemetrics_output <- lsm_c_area_sd(landscape) %>% dplyr::select(class, value) %>% purrr::set_names("class", "landscapemetrics") -fragstats <- full_join(x = fragstats_output, - y = fragstats_calculated, - by = "class") +fragstats <- dplyr::full_join(x = fragstats_output, y = fragstats_calculated, + by = "class") -sd_full <- full_join(x = fragstats, - y = landscapemetrics_output, - by = "class") +sd_full <- dplyr::full_join(x = fragstats, y = landscapemetrics_output, + by = "class") ``` @@ -137,14 +139,12 @@ landscapemetrics_gyrate <- lsm_p_gyrate(landscape) %>% dplyr::select(id, value) %>% purrr::set_names("id", "landscapemetrics_gyrate") -fragstats <- full_join(x = fragstats_area, - y = fragstats_gyrate, - by = "id") %>% +fragstats <- dplyr::full_join(x = fragstats_area, y = fragstats_gyrate, + by = "id") %>% dplyr::filter(fragstats_area == 0.0001) -landscapemetrics <- full_join(x = landscapemetrics_area, - y = landscapemetrics_gyrate, - by = "id") %>% +landscapemetrics <- dplyr::full_join(x = landscapemetrics_area, + y = landscapemetrics_gyrate, by = "id") %>% dplyr::filter(landscapemetrics_area == 0.0001) ``` @@ -188,9 +188,9 @@ We implemented PARA as documented in the FRAGSTATS manual using square meters. N fragstats <- fragstats_patch_landscape %>% dplyr::select(PID, AREA, PERIM, PARA) %>% purrr::set_names("id", "area", "perim", "para") %>% - mutate(para_calculated_ha = perim / area, - para_calculated_m = perim / (area * 10000)) %>% - arrange(area) + dplyr::mutate(para_calculated_ha = perim / area, + para_calculated_m = perim / (area * 10000)) %>% + dplyr::arrange(area) # Output of landscapemetrics area_landscapmetrics <- lsm_p_area(landscape) %>% @@ -208,11 +208,10 @@ para_landscapemetrics <- lsm_p_para(landscape) %>% landscapemetrics <- dplyr::full_join(x = area_landscapmetrics, y = perim_landscapmetrics, by = "id") %>% - full_join(para_landscapemetrics, - by = "id") %>% - mutate(para_calculated_ha = perim / area, - para_calculated_m = perim / (area * 10000)) %>% - arrange(area) + dplyr::full_join(para_landscapemetrics, by = "id") %>% + dplyr::mutate(para_calculated_ha = perim / area, + para_calculated_m = perim / (area * 10000)) %>% + dplyr::arrange(area) ``` @@ -253,8 +252,7 @@ circle_landscapmetrics <- lsm_p_circle(landscape) %>% dplyr::select(id, value) %>% purrr::set_names("id_lsm", "circle_lsm") -landscapemetrics <- dplyr::full_join(x = area_landscapmetrics, - y = circle_landscapmetrics, +landscapemetrics <- dplyr::full_join(x = area_landscapmetrics, y = circle_landscapmetrics, by = "id_lsm") %>% dplyr::filter(area_lsm == 0.0001) ``` @@ -282,25 +280,22 @@ mat[4, 4:10] <- 1 ras <- raster::raster(mat, xmn = 0, xmx = 13, ymn = 0, ymx = 13) # get circumscribing circle -circle_lsm <- landscapemetrics::get_circumscribingcircle(ras) +circle_lsm <- get_circumscribingcircle(ras) # construct circle using diameter / 2 -circle_lsm <- landscapemetrics::construct_buffer(coords = matrix(c(circle_lsm$center_x, - circle_lsm$center_y), - nrow = 1, ncol = 2), - shape = "circle", - size = circle_lsm$value / 2, - return_sp = FALSE) +circle_lsm <- construct_buffer(coords = matrix(c(circle_lsm$center_x, + circle_lsm$center_y), + nrow = 1, ncol = 2), + shape = "circle", size = circle_lsm$value / 2, + return_sp = FALSE) # calculate max distance between corner points of cells circle_max_dist <- dist(matrix(data = c(3, 10, 7, 4), byrow = TRUE, nrow = 2, ncol = 2)) # construct circle using diamter /2 -circle_max_dist <- landscapemetrics::construct_buffer(coords = matrix(c(6.5, 7.5), - nrow = 1, ncol = 2), - shape = "circle", - size = circle_max_dist / 2, - return_sp = FALSE) +circle_max_dist <- construct_buffer(coords = matrix(c(6.5, 7.5), nrow = 1, ncol = 2), + shape = "circle", size = circle_max_dist / 2, + return_sp = FALSE) # plot results plot(ras, col = "#D5B528", legend = FALSE) @@ -319,7 +314,7 @@ polygon(circle_max_dist, border = "#922418", lwd = 2.5) # red circle To get all availabel metrics on e.g. patch level with `SDMTools`, you have to make a binary landscape for every class in your landscape, perform connected components labelling on it and then calculate the patch metrics. ```{r} -library(SDMTools) +library(SDMTools) # remotes::install_version("SDMTools", version = "1.1-221.2") # binarize every class in the landscape and calculate patch metrics sdmtools_result <- lapply(raster::unique(landscape), FUN = function(x){ @@ -351,7 +346,7 @@ knitr::kable(bind_rows(sdmtools_result)) ## References -- McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: http://www.umass.edu/landeco/research/fragstats/fragstats.html +- McGarigal, K., SA Cushman, and E Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: https://www.umass.edu/landeco/ - Jeremy VanDerWal, Lorena Falconi, Stephanie Januchowski, Luke Shoo and Collin Storlie (2014). SDMTools: Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises. R package version 1.1-221. https://CRAN.R-project.org/package=SDMTools diff --git a/vignettes/articles/general-background.Rmd b/vignettes/articles/general_background.Rmd similarity index 96% rename from vignettes/articles/general-background.Rmd rename to vignettes/articles/general_background.Rmd index 8aeb91853..6a26db086 100644 --- a/vignettes/articles/general-background.Rmd +++ b/vignettes/articles/general_background.Rmd @@ -1,9 +1,13 @@ --- title: "General background" date: "`r Sys.Date()`" -output: - github_document: - html_preview: false +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{General background} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +editor_options: + chunk_output_type: console --- ```{r, echo = FALSE} @@ -62,6 +66,6 @@ Those were the main reasons we implemented `landscapemetrics`, however, we want - Baker, W.L. and Cai, Y. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. Landscape Ecology 7(4):291-302. -- McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: +- McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: - VanDerWal, J., Falconi, L., Januchowski, S., Shoo, L., and Storlie, C. 2014. SDMTools: Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises. R package version 1.1-221. diff --git a/vignettes/articles/guide_moving_window.Rmd b/vignettes/articles/guide_moving_window.Rmd index 6d58c06e9..3ce96a3f8 100644 --- a/vignettes/articles/guide_moving_window.Rmd +++ b/vignettes/articles/guide_moving_window.Rmd @@ -2,6 +2,12 @@ title: "Moving window" date: "`r Sys.Date()`" output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Moving window} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +editor_options: + chunk_output_type: console --- Results of a landscape analysis are scale dependent (Šímová 2012). One approach to deal with this is by using a moving window (Hagen-Zanker 2016). For each focal cell in the landscape, a matrix is used to specify the neighborhood and the metric value of this local neighborhood is assigned to each focal cell (Fletcher 2018). Thereby, the windows are allowed to overlap (McGarigal et al. 2012). The result of a moving window analysis is a raster with an identical extent as the input, however, each cell now describes the neighborhood in regard to the variability of the chosen metric (Hagen-Zanker 2016). Of course, the selection of the matrix size largely influences the scale of the result (Hagen-Zanker 2016). @@ -13,6 +19,8 @@ We provide the function `window_lsm()` in **landscapemetrics** to analyse an inp ```{r packages, message = FALSE} library(landscapemetrics) library(raster) + +library(ggplot2) ``` First, we need to specify the local neighborhood matrix. This matrix must have sides defined as odd numbers, in which the focal cell is always the center cell. Because we want to weight all cells identically, all values need to be 1 (for more details, see `?raster::focal()`). @@ -34,25 +42,21 @@ To be type-stable, the result will be a nested list. The first level includes a ```{r plot-result, echo = FALSE, fig.align = "center"} result_stack <- raster::stack(landscape, result[[1]]$lsm_l_pr) -ggplot2::ggplot(data = raster::as.data.frame(landscape, xy = TRUE)) + - ggplot2::geom_raster(ggplot2::aes(x = x, y = y, fill = factor(clumps))) + - ggplot2::scale_fill_viridis_d(name = "Landscape class") + - ggplot2::coord_equal() + - ggplot2::theme(axis.line = ggplot2::element_blank(), - axis.ticks = ggplot2::element_blank(), - axis.text = ggplot2::element_blank(), - axis.title = ggplot2::element_blank(), - legend.position = "bottom") - -ggplot2::ggplot(data = raster::as.data.frame(result[[1]]$lsm_l_pr, xy = TRUE)) + - ggplot2::geom_raster(ggplot2::aes(x = x, y = y, fill = factor(layer))) + - ggplot2::scale_fill_viridis_d(name = "Number of classes", option = "C") + - ggplot2::coord_equal() + - ggplot2::theme(axis.line = ggplot2::element_blank(), - axis.ticks = ggplot2::element_blank(), - axis.text = ggplot2::element_blank(), - axis.title = ggplot2::element_blank(), - legend.position = "bottom") +ggplot(data = raster::as.data.frame(landscape, xy = TRUE)) + + geom_raster(aes(x = x, y = y, fill = factor(clumps))) + + scale_fill_viridis_d(name = "Landscape class") + + coord_equal() + + theme(axis.line = element_blank(), axis.ticks = element_blank(), + axis.text = element_blank(), axis.title = element_blank(), + legend.position = "bottom") + +ggplot(data = raster::as.data.frame(result[[1]]$lsm_l_pr, xy = TRUE)) + + geom_raster(ggplot2::aes(x = x, y = y, fill = factor(layer))) + + scale_fill_viridis_d(name = "Number of classes", option = "C") + + coord_equal() + + theme(axis.line = element_blank(), axis.ticks = element_blank(), + axis.text = element_blank(), axis.title = element_blank(), + legend.position = "bottom") ``` In the future, we also plan to allow class level metrics, however, patch metrics are not meaningful (McGarigal 2012) and will not be included in the future. @@ -63,6 +67,6 @@ In the future, we also plan to allow class level metrics, however, patch metrics - Hagen-Zanker, A. 2016. A computational framework for generalized moving windows and its application to landscape pattern analysis. International journal of applied earth observation and geoinformation, 44, 205-216. -- McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: +- McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: - Šímová, P., & Gdulová, K. 2012. Landscape indices behavior: A review of scale effects. Applied Geography, 34, 385–394. diff --git a/vignettes/articles/guide_sample_lsm.Rmd b/vignettes/articles/guide_sample_lsm.Rmd index 045537c76..aea412aef 100644 --- a/vignettes/articles/guide_sample_lsm.Rmd +++ b/vignettes/articles/guide_sample_lsm.Rmd @@ -2,12 +2,20 @@ title: "Sampling around points of interest" date: "`r Sys.Date()`" output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Sampling around points of interest} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +editor_options: + chunk_output_type: console --- ```{r packages, message = FALSE} -library(ggplot2) library(landscapemetrics) library(raster) +library(sp) + +library(ggplot2) ``` **landscapemetrics** provides several functions to sample metrics *at* or *around* sample points. On possible application for this feature could be a study in which the study organism only encounters the landscape within a local neighborhood of sample points. For most functions, sample points can be provided as a 2-column matrix(x- and y-coordinate), SpatialPoints and SpatialLines ([**sp**](https://cran.r-project.org/web/packages/sp/index.html); Roger et al. 2013) and even [**sf**](https://cran.r-project.org/web/packages/sf/index.html) objects (Pebesma 2018) are supported. For some functions, also SpatialPolygons (i.e. sample plots) can be provided. @@ -36,20 +44,17 @@ sample_lines `extract_lsm()` returns the metrics of all patches in which a sample point is located. However, since this only makes sense for individual patches, it's only possible to extract patch-level metrics. ```{r, echo = FALSE, fig.align = "center"} -ggplot2::ggplot(data = raster::as.data.frame(landscape, xy = TRUE)) + - ggplot2::geom_raster(ggplot2::aes(x = x, y = y, fill = factor(clumps))) + - ggplot2::geom_point(data = data.frame(x = points[, 1], y = points[, 2]), - ggplot2::aes(x = x, y = y), pch = 19, size = 1.5) + - ggplot2::geom_path(data = data.frame(x = c(x1, x2), - y = c(y1, y2), id = c(1, 1, 1, 1, 2, 2)), - ggplot2::aes(x = x, y = y, group = id), size = 1) + - ggplot2::scale_fill_viridis_d(name = "Landscape class") + - ggplot2::coord_equal() + - ggplot2::theme(axis.line = ggplot2::element_blank(), - axis.ticks = ggplot2::element_blank(), - axis.text = ggplot2::element_blank(), - axis.title = ggplot2::element_blank(), - legend.position = "bottom") +ggplot(data = raster::as.data.frame(landscape, xy = TRUE)) + + geom_raster(aes(x = x, y = y, fill = factor(clumps))) + + geom_point(data = data.frame(x = points[, 1], y = points[, 2]), + aes(x = x, y = y), pch = 19, size = 1.5) + + geom_path(data = data.frame(x = c(x1, x2), y = c(y1, y2), id = c(1, 1, 1, 1, 2, 2)), + aes(x = x, y = y, group = id), size = 1) + + scale_fill_viridis_d(name = "Landscape class") + + coord_equal() + + theme(axis.line = element_blank(), axis.ticks = element_blank(), + axis.text = element_blank(), axis.title = element_blank(), + legend.position = "bottom") ``` Now, it's straightforward to extract e.g. the patch area of all patches in which a sample point is located. Similar to all functions calculating several landscape metrics, the selected metrics can be specified by various arguments (see `list_lsm()` for more details). The resulting tibble includes one extra column (compared to `calculate_lsm()`), indicating the ID of the sample points. @@ -80,21 +85,18 @@ sample_plots <- data.frame(construct_buffer(coords = points, size = 10, return_sp = FALSE)) -ggplot2::ggplot(data = raster::as.data.frame(landscape, xy = TRUE)) + - ggplot2::geom_raster(ggplot2::aes(x = x, y = y, fill = factor(clumps))) + - ggplot2::geom_polygon(data = sample_plots, ggplot2::aes(x = sample_plots[, 1], - y = sample_plots[, 2], - group = sample_plots[, 3]), - col = "black", fill = NA) + - ggplot2::geom_point(data = data.frame(x = points[, 1], y = points[, 2]), - ggplot2::aes(x = x, y = y), pch = 19, size = 1.5) + - ggplot2::scale_fill_viridis_d(name = "Landscape class") + - ggplot2::coord_equal() + - ggplot2::theme(axis.line = ggplot2::element_blank(), - axis.ticks = ggplot2::element_blank(), - axis.text = ggplot2::element_blank(), - axis.title = ggplot2::element_blank(), - legend.position = "bottom") +ggplot(data = raster::as.data.frame(landscape, xy = TRUE)) + + geom_raster(ggplot2::aes(x = x, y = y, fill = factor(clumps))) + + geom_polygon(data = sample_plots, aes(x = sample_plots[, 1], y = sample_plots[, 2], + group = sample_plots[, 3]), + col = "black", fill = NA) + + geom_point(data = data.frame(x = points[, 1], y = points[, 2]), + aes(x = x, y = y), pch = 19, size = 1.5) + + scale_fill_viridis_d(name = "Landscape class") + + coord_equal() + + theme(axis.line = element_blank(), axis.ticks = element_blank(), + axis.text = element_blank(), axis.title = element_blank(), + legend.position = "bottom") ``` ```{r, collapse = TRUE} diff --git a/vignettes/articles/landscape_distribution_statistics.Rmd b/vignettes/articles/landscape_distribution_statistics.Rmd index 6c983d3d6..45b003bdc 100644 --- a/vignettes/articles/landscape_distribution_statistics.Rmd +++ b/vignettes/articles/landscape_distribution_statistics.Rmd @@ -2,6 +2,12 @@ title: "Landscape distribution statistics" date: "`r Sys.Date()`" output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Landscape distribution statistics} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +editor_options: + chunk_output_type: console --- Landscape distribution statistics summarise the properties of all patches belonging to the same class *i* or of all patches in the landscape together (McGarigal et al. 2012). @@ -13,6 +19,7 @@ Even though they are not implemented in **landscapemetrics**, R allows to calcul ```{r packages, message = FALSE} library(landscapemetrics) library(raster) + library(dplyr) ``` @@ -49,8 +56,8 @@ To calculate the area-weighted mean on landscape-level, comment out the `dplyr:: ```{r mean_b} # calculate weighted mean -metric_wght_mean <- left_join(x = metric_patch, y = area_patch, - by = c("layer", "level", "class", "id")) %>% +metric_wght_mean <- dplyr::left_join(x = metric_patch, y = area_patch, + by = c("layer", "level", "class", "id")) %>% dplyr::mutate(value.w = value.x * value.y) %>% dplyr::group_by(class) %>% dplyr::summarise(value.am = sum(value.w) / sum(value.y)) @@ -94,4 +101,4 @@ metric_md_l ### References -- McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: +- McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: diff --git a/vignettes/articles/new_metrics.Rmd b/vignettes/articles/new_metrics.Rmd index d3061826d..966ccce43 100644 --- a/vignettes/articles/new_metrics.Rmd +++ b/vignettes/articles/new_metrics.Rmd @@ -1,9 +1,13 @@ --- -title: "New Metrics outside FRAGSTATS" +title: "New metrics outside FRAGSTATS" date: "`r Sys.Date()`" -output: - github_document: - html_preview: false +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{New metrics outside FRAGSTATS} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +editor_options: + chunk_output_type: console --- ```{r setup, include = FALSE} diff --git a/vignettes/articles/publication_record.Rmd b/vignettes/articles/publication_record.Rmd index 172f130e7..a9b1d9daa 100644 --- a/vignettes/articles/publication_record.Rmd +++ b/vignettes/articles/publication_record.Rmd @@ -1,9 +1,11 @@ --- title: Publication record date: "`r Sys.Date()`" -output: - github_document: - html_preview: false +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Publication record} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} --- We are always happy to hear from you if you used `landscapemetrics` for a publication. You can either just drop us an e-mail or [file an issue on GitHub](https://github.com/r-spatialecology/landscapemetrics/issues/new/). diff --git a/vignettes/articles/utility.Rmd b/vignettes/articles/utility.Rmd index 75770cd78..70c124ab1 100644 --- a/vignettes/articles/utility.Rmd +++ b/vignettes/articles/utility.Rmd @@ -1,9 +1,13 @@ --- title: "Utility functions" date: "`r Sys.Date()`" -output: - github_document: - html_preview: false +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Utility functions} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +editor_options: + chunk_output_type: console --- ```{r setup, include = FALSE} @@ -16,8 +20,11 @@ knitr::opts_chunk$set( ```{r load_libraries_hidden, eval=TRUE, echo=FALSE, message=FALSE, results='hide'} library(landscapemetrics) library(raster) -library(dplyr) library(landscapetools) + +library(bench) +library(dplyr) +library(purrr) ``` ## Visualisization functions @@ -26,10 +33,8 @@ library(landscapetools) We can use the `show_landscape` function from [landscapetools](https://github.com/ropensci/landscapetools) to have look at our landscape. ```{r fig.height=12, fig.asp=0.50, fig.align='center', fig.retina = 2} -library(landscapetools) - # Plot landscape -show_landscape(landscape) +landscapetools::show_landscape(landscape) ``` This is how we typically inspect our landscape, but which also makes it quite hard to relate to the landscape metrics we are interested in. This why we show in the following how to dissect this landscape visually into the compoments, that drive the calculation of landscape metrics. @@ -39,8 +44,6 @@ This is how we typically inspect our landscape, but which also makes it quite ha To visualize patches in a landscape and encode each patch with an ID that can be used to compare a landscape metric with the actual landscape you can use the auxiliary visualisation function `show_patches()`: ```{r fig.height=12, fig.asp=0.50, fig.align='center', fig.retina = 2} -library(landscapemetrics) - # Plot landscape + landscape with labeled patches show_patches(landscape) ``` @@ -110,7 +113,6 @@ adj_raster <- function(landscape){ } # compare the two implementations -library(bench) bench::mark( get_adjacencies(landscape, neighbourhood = 4), adj_raster(landscape), @@ -134,24 +136,22 @@ min_dist <- get_nearestneighbour(patches$layer_1$class_1) # create a function that would do the same with the raster package nearest_raster_fun <- function(patches) { + np_class <- patches %>% raster::values() %>% unique() %>% na.omit() %>% length() - points_class <- patches %>% - raster::rasterToPoints() %>% - tibble::as.tibble() %>% - purrr::set_names(c("x", "y", "id")) + points_class <- raster::rasterToPoints(patches) %>% + as.data.frame() - minimum_distance <- np_class %>% - seq_len() %>% + minimum_distance <- seq_len(np_class) %>% purrr::map_dbl(function(patch_ij) { - patch_focal <- dplyr::filter(points_class, id == patch_ij) + patch_focal <- dplyr::filter(points_class, layer == patch_ij) patch_others <- - dplyr::filter(points_class, id != patch_ij) + dplyr::filter(points_class, layer != patch_ij) minimum_distance <- raster::pointDistance(patch_focal[1:2], @@ -160,14 +160,12 @@ nearest_raster_fun <- function(patches) { min() }) - tibble::tibble(id = unique(sort(points_class$id)), - distance = minimum_distance) + data.frame(id = unique(sort(points_class$layer)), distance = minimum_distance) } # compare the two implementations -library(bench) bench::mark( get_nearestneighbour(patches$layer_1$class_1)[, 2:3], nearest_raster_fun(patches$layer_1$class_1), diff --git a/vignettes/getstarted.Rmd b/vignettes/get_started.Rmd similarity index 97% rename from vignettes/getstarted.Rmd rename to vignettes/get_started.Rmd index 42d1561e0..6381f619b 100644 --- a/vignettes/getstarted.Rmd +++ b/vignettes/get_started.Rmd @@ -1,17 +1,15 @@ --- -title: "Get Started with landscapemetrics" +title: "Get started" date: "`r Sys.Date()`" -output: - rmarkdown::html_vignette: - toc: true - html_preview: false +output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Get Started} + %\VignetteIndexEntry{Get started} %\VignetteEncoding{UTF-8} %\VignetteEngine{knitr::rmarkdown} editor_options: chunk_output_type: console --- + ```{r setup, include = FALSE} knitr::opts_chunk$set( collapse = TRUE,