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‎.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$
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Makefile

‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata

‎DESCRIPTION

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Package: PACKAGE
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Title: Organising Projects
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Version: 2020.5.25
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Authors@R: c(
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person(c("Richard","Aubrey"), "White", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6747-1726")),
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person(given = "Folkehelseinstituttet", role = c("cph"))
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)
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Description: A system to help you organize projects. Most analyses have three (or more) main sections: code, results, and data, each with different requirements (version control/sharing/encryption). You provide folder locations and 'org' helps you take care of the details.
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Depends: R (>= 3.3.0)
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License: MIT + file LICENSE
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URL: https://docs.sykdomspulsen.no/PACKAGE, https://github.com/sykdomspulsen-org/PACKAGE
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BugReports: https://github.com/sykdomspulsen-org/PACKAGE/issues
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Encoding: UTF-8
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LazyData: true
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Imports: data.table,
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magrittr,
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ggplot2
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Suggests: testthat,
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knitr,
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rmarkdown,
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rstudioapi,
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glue
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RoxygenNote: 7.1.1
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VignetteBuilder: knitr

‎LICENSE

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YEAR: 2021
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COPYRIGHT HOLDER: Folkehelseinstituttet

‎Makefile

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# h/t to @jimhester and @yihui for this parse block:
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# https://github.com/yihui/knitr/blob/dc5ead7bcfc0ebd2789fe99c527c7d91afb3de4a/Makefile#L1-L4
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# Note the portability change as suggested in the manual:
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# https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-portable-packages
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export PKGNAME=`sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION`
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export PKGVERS=`sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION`
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export DATETIME=`date +%Y-%m-%d\ %H:%M:%S`
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export DATETIMEUTC=`date -u +%Y-%m-%d\ %H:%M:%S`
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export DATE=`date +%Y.%-m.%-d`
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#export PWD=$(abspath $(lastword $(MAKEFILE_LIST)))
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all: build
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.ONESHELL:
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fix_description_version:
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sed -i "s/^Version: .*/Version: $(DATE)/" DESCRIPTION
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sed -i '/Date\/Publication:/d' DESCRIPTION # delete if exists
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echo "Date/Publication: $(DATETIMEUTC) UTC" >> DESCRIPTION #append to bottom
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sudo chmod -R 777 ..
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.ONESHELL:
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build_data:
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sudo podman run --rm --privileged \
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-v $(shell pwd):/rpkg \
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docker.io/fhix/rfhiverse:latest /bin/bash -c \
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'Rscript -e "devtools::load_all(\"/rpkg/\"); gen_data_all(\"/rpkg/data\")"'
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sudo chmod -R 777 ..
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.ONESHELL:
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build_package:
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sudo rm -rf ../built
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mkdir ../built
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sudo podman run --rm --privileged \
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-v $(shell pwd):/rpkg \
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-v $(shell pwd)/../built:/built \
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docker.io/fhix/rfhiverse:latest /bin/bash -c \
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' \
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cd /; \
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R CMD build /rpkg; \
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cp *.tar.gz /built/; \
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'
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sudo chown -R go ../built
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sudo chmod -R 777 ..
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.ONESHELL:
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check_package:
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sudo podman run --rm --privileged \
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-v $(shell pwd):/rpkg \
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-v $(shell pwd)/../built:/built \
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docker.io/fhix/rfhiverse:latest /bin/bash -c \
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' \
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R CMD check --no-manual /built/*.tar.gz; \
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mv *.Rcheck /built/; \
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'
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sudo chmod -R 777 ..
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if grep -Fq "WARNING" ../built/*.Rcheck/00check.log
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then
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# code if found
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exit 1
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else
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# code if not found
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echo "NO WARNINGs"
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fi
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if grep -Fq "ERROR" ../built/*.Rcheck/00check.log
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then
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# code if found
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exit 1
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else
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# code if not found
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echo "NO ERRORs"
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fi
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.ONESHELL:
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drat:
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git -C .. clone [email protected]:folkehelseinstituttet/drat.git --branch gh-pages
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sudo podman run --rm --privileged \
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-v $(shell pwd):/rpkg \
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-v $(shell pwd)/../built:/built \
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-v $(shell pwd)/../drat:/drat \
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docker.io/fhix/rfhiverse:latest /bin/bash -c 'Rscript -e "drat::insertPackage(fs::dir_ls(\"/built/\", regexp=\".tar.gz\$\"), repodir = \"/drat\")"'
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sed -i "/## News/a - **$(PKGNAME) $(PKGVERS)** (linux) inserted at $(DATETIME)" ../drat/README.md
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sed -i '1001,\\\$ d' ../drat/README.md # only keep first 1000 lines of readme
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git config --global user.email "[email protected]"
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git config --global user.name "sykdomspulsen"
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git -C ../drat add -A
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git -C ../drat commit -am "gocd $(PKGNAME) $(PKGVERS)" #Committing the changes
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git -C ../drat push -f origin gh-pages #pushes to master branch
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sudo chmod -R 777 ..
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.ONESHELL:
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pkgdown:
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sudo podman run --rm --privileged \
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-v $(shell pwd):/rpkg \
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-v $(shell pwd)/../built:/built \
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-v $(shell pwd)/../drat:/drat \
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docker.io/fhix/rfhiverse:latest /bin/bash -c 'Rscript -e "devtools::install(\"/rpkg\", dependencies = TRUE, upgrade = FALSE); pkgdown::build_site(\"/rpkg\")"'
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git add .
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git commit -am "Pkgdown built"
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git subtree split --prefix docs -b gh-pages # create a local gh-pages branch containing the splitted output folder
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git push -f origin gh-pages:gh-pages # force the push of the gh-pages branch to the remote gh-pages branch at origin
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git branch -D gh-pages # delete the local gh-pages because you will need it: ref
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sudo chmod -R 777 ..
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.ONESHELL:
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drat_prune_history:
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cd /tmp
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git clone "[email protected]:folkehelseinstituttet/drat.git"
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cd drat
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git config user.name "Sykdomspulsen"
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git config user.email "[email protected]"
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git config push.default simple
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git checkout gh-pages
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git checkout --orphan latest_branch
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git add -A
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git commit -am "Cleaning history" #Committing the changes
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git branch -D gh-pages #Deleting master branch
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git branch -m gh-pages #renaming branch as master
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git -C /tmp/drat push -f origin gh-pages #pushes to master branch

‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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import(data.table)
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import(ggplot2)
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importFrom(magrittr,"%>%")

‎NEWS.md

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# PACKAGE 2020.2.17
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- Package is created

‎R/3_onAttach.R

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#' @import data.table ggplot2
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#' @importFrom magrittr %>%
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.onAttach <- function(libname, pkgname) {
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packageStartupMessage(paste0(
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"PACKAGE ",
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# utils::packageDescription("PACKAGE")$Version,
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"\n",
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"https://docs.sykdomspulsen.no/PACKAGE"
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))
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}

‎README.md

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# PACKAGE <a href="https://docs.sykdomspulsen.no/PACKAGE"><img src="man/figures/logo.png" align="right" width="120" /></a>
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## Overview
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[PACKAGE](https://docs.sykdomspulsen.no/PACKAGE) is a system to help you organize projects. Most analyses have three (or more) main sections: code, results, and data, each with different requirements (version control/sharing/encryption). You provide folder locations and 'org' helps you take care of the details.
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Read the introduction vignette [here](http://docs.sykdomspulsen.no/PACKAGE/articles/PACKAGE.html) or run `help(package="PACKAGE")`.
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## splverse
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<a href="https://docs.sykdomspulsen.no/packages"><img src="https://docs.sykdomspulsen.no/packages/splverse.png" align="right" width="120" /></a>
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The [splverse](https://docs.sykdomspulsen.no/packages) is a set of R packages developed to help solve problems that frequently occur when performing infectious disease surveillance.
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If you want to install the dev versions (or access packages that haven't been released on CRAN), run `usethis::edit_r_profile()` to edit your `.Rprofile`.
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Then write in:
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```
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options(
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repos = structure(c(
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FHI = "https://folkehelseinstituttet.github.io/drat/",
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CRAN = "https://cran.rstudio.com"
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))
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)
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```
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Save the file and restart R.
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You can now install [splverse](https://docs.sykdomspulsen.no/packages) packages from the FHI registry.
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```
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install.packages("PACKAGE")
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```
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‎_pkgdown.yml

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url: https://docs.sykdomspulsen.no/PACKAGE
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template:
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bootstrap: 5
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bslib:
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primary: "#0054AD"
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border-radius: 0.5rem
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btn-border-radius: 0.25rem

‎cran-comments.md

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## Resubmission
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This is a resubmission. In this version I have:
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- Omitted all redundancies like "R Functions" in my title
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- Added more details about my package in my Description text
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- Fixed unexecutable code in man/InitialiseProject.Rd
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## Test environments
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* local Debian 9.5 install, R 3.5.2
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* ubuntu 14.04 (on travis-ci), R 3.5.2
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* win-builder (devel and release)
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## R CMD check results
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0 errors | 0 warnings
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Notes:
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* checking CRAN incoming feasibility ... NOTE
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Maintainer: 'Richard White <[email protected]>'
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New submission
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## Downstream dependencies
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none

‎license.md

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# MIT License
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Copyright (c) 2021 Folkehelseinstituttet
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎man/figures/logo.png

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‎project.Rproj

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Version: 1.0
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RestoreWorkspace: No
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SaveWorkspace: No
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source
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PackageRoxygenize: rd,collate,namespace

‎vignettes/PACKAGE.Rmd

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---
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title: "Introduction to PACKAGE"
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author: "Richard White"
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date: "2020-02-17"
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{Introduction to PACKAGE}
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteEncoding{UTF-8}
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---
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```{r setup, include = FALSE}
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knitr::opts_chunk$set(
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collapse = TRUE,
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comment = "#>"
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)
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```
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## Concept

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