diff --git a/Makefile b/Makefile deleted file mode 100644 index 3d2484c..0000000 --- a/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -all: move pandoc rmd2md reducepdf - -vignettes: - cd inst/stuff;\ -Rscript -e 'library(knitr); knit("rinatVignette.Rmd")' - -move: - cp inst/stuff/rinat* vignettes - -pandoc: - cd vignettes;\ -pandoc -H margins.sty rinatVignette.md -o rinatVignette.pdf --highlight-style=tango;\ -pandoc -H margins.sty rinatVignette.md -o rinatVignette.html --highlight-style=tango - -rmd2md: - cd vignettes;\ -cp rinatVignette.md rinatVignette.Rmd;\ - -reducepdf: - Rscript -e 'tools::compactPDF("vignettes/rinatVignette.pdf", gs_quality = "ebook")';\ diff --git a/NEWS.md b/NEWS.md index e69de29..9d0313d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -0,0 +1,18 @@ +rinat 0.1.5 +========== + +## BUG FIXES + +* Fixed bug where an error occurred when >20K records were requested and code now throws a warning to not hammer the API + +* Fixed warning thrown when building vignettes on Linux systems + +* Fixed bug where example code parameter names were different than actual parameter names + +## NEW FEATURES + +* Added NEWS file. + +* Added a full suite of tests + +* Added new vignette that builds with markdown and not hacky prebuilt PDF \ No newline at end of file diff --git a/R/get_inat_obs_user.R b/R/get_inat_obs_user.R index 3f92115..ee377a9 100644 --- a/R/get_inat_obs_user.R +++ b/R/get_inat_obs_user.R @@ -6,7 +6,7 @@ #' @return a list with full details on a given record #' @examples \dontrun{ #' m_obs <- get_inat_obs(query="Monarch Butterfly") -#' get_inat_obs_user(as.character(m_obs$User.login[1])) +#' get_inat_obs_user(as.character(m_obs$user_login[1])) #' } #' @import httr jsonlite #' @export diff --git a/README.Rmd b/README.Rmd index 58b1952..4a204e7 100644 --- a/README.Rmd +++ b/README.Rmd @@ -7,6 +7,10 @@ output: md_document [![Build Status](https://api.travis-ci.org/ropensci/rinat.png)](https://travis-ci.org/ropensci/rinat) [![Build status](https://ci.appveyor.com/api/projects/status/gv7s9um107bep4na/branch/master)](https://ci.appveyor.com/project/sckott/rinat/branch/master) [![codecov.io](https://codecov.io/github/ropensci/rinat/coverage.svg?branch=master)](https://codecov.io/github/ropensci/rinat?branch=master) +[![Downloads](http://cranlogs.r-pkg.org/badges/rinat +](http://cranlogs.r-pkg.org/badges/rinat) + + ## Quickstart guide diff --git a/README.md b/README.md index 35696a8..c6c6149 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,7 @@ -[![Build -Status](https://api.travis-ci.org/ropensci/rinat.png)](https://travis-ci.org/ropensci/rinat) -[![Build -status](https://ci.appveyor.com/api/projects/status/gv7s9um107bep4na/branch/master)](https://ci.appveyor.com/project/sckott/rinat/branch/master) +[![Build Status](https://api.travis-ci.org/ropensci/rinat.png)](https://travis-ci.org/ropensci/rinat) +[![Build status](https://ci.appveyor.com/api/projects/status/gv7s9um107bep4na/branch/master)](https://ci.appveyor.com/project/sckott/rinat/branch/master) [![codecov.io](https://codecov.io/github/ropensci/rinat/coverage.svg?branch=master)](https://codecov.io/github/ropensci/rinat?branch=master) +[![Downloads](http://cranlogs.r-pkg.org/badges/rinat](http://cranlogs.r-pkg.org/badges/rinat) Quickstart guide ---------------- @@ -38,9 +37,9 @@ vernal pool. We can then see all the species names found. vp_obs <- get_inat_obs(query = "vernal pool") head(vp_obs$species_guess) - ## [1] "Great Blue Skimmer" "Wood Frog" - ## [3] "" "" - ## [5] "Vernal Pool Fairy Shrimp" "Fairy Shrimp" + ## [1] "Eastern Hemlock" "" + ## [3] "Longtail Tadpole Shrimp" "Great Blue Skimmer" + ## [5] "Wood Frog" "" *Taxon query* To return only records for a specific species or taxonomic group, use the taxon option. @@ -90,22 +89,22 @@ search. head(get_inat_obs_id(m_obs$id[1])) ## $id - ## [1] 5196678 + ## [1] 5209229 ## ## $observed_on - ## [1] "2017-02-28" + ## [1] "2016-12-12" ## ## $description - ## [1] "One seen in the distance flying by." + ## NULL ## ## $latitude - ## [1] "-43.646084" + ## [1] "-42.9071542023" ## ## $longitude - ## [1] "172.467806" + ## [1] "172.6419067383" ## ## $map_scale - ## [1] 15 + ## NULL *Get all observations by user* @@ -116,27 +115,27 @@ quite large (easily into the 1000's) m_obs <- get_inat_obs(query = "Monarch Butterfly") head(get_inat_obs_user(as.character(m_obs$user_login[1]), maxresults = 20))[,1:5] - ## scientific_name datetime - ## 1 Buddleja davidii 2017-02-28 16:58:00 +1300 - ## 2 Trifolium repens 2017-02-28 16:58:00 +1300 - ## 3 Danaus plexippus 2017-02-28 16:58:00 +1300 - ## 4 Vanessa itea 2017-02-28 15:14:00 +1300 - ## 5 Urtica ferox 2017-02-28 15:14:00 +1300 - ## 6 Muehlenbeckia complexa 2017-02-28 15:14:00 +1300 - ## description - ## 1 The butterfly bush was just about finished flowering. We didn't see butterflies on it other than a couple of visits by cabbage white butterflies. - ## 2 The only possible butterfly host plant we could find at this site. The clover, like the rest of the lawn, was very dry. Clover flowers can be fed on by southern blue butterfly caterpillars. - ## 3 One seen in the distance flying by. - ## 4 We found three admiral pupae on the planted Urtica ferox plus one dead late instar larva. One pupa was mature so we collected it and it eclosed into an adult yellow admiral later the same afternoon. Our identification of the pupae is based on that. - ## 5 One of the potential host plants for butterflies found in the garden outside the Landscape Architecture building. Admiral butterfly caterpillars can feed on these nettles. - ## 6 One of the potential host plants for butterflies found in the garden outside the Landscape Architecture building. Coppers can feed on these. - ## place_guess latitude - ## 1 Lincoln University, New Zealand -43.64608 - ## 2 Lincoln University, New Zealand -43.64608 - ## 3 Lincoln University, New Zealand -43.64608 - ## 4 Lincoln University, New Zealand -43.64469 - ## 5 Lincoln University, New Zealand -43.64469 - ## 6 Lincoln University, New Zealand -43.64469 + ## scientific_name datetime + ## 1 Vanessa itea 2016-12-12 12:33:00 +1300 + ## 2 Danaus plexippus 2016-12-12 12:30:00 +1300 + ## 3 Danaus plexippus 2016-12-12 11:53:00 +1300 + ## 4 Danaus plexippus 2016-12-12 11:52:00 +1300 + ## 5 Danaus plexippus 2016-12-12 11:41:00 +1300 + ## 6 Danaus plexippus 2016-12-12 11:43:00 +1300 + ## description + ## 1 + ## 2 + ## 3 + ## 4 + ## 5 + ## 6 This Monarch appears to have slightly deformed wings. + ## place_guess latitude + ## 1 Hawarden, New Zealand -42.90615 + ## 2 Hawarden, New Zealand -42.90715 + ## 3 Hawarden, New Zealand -42.91621 + ## 4 Hawarden, New Zealand -42.90816 + ## 5 Hawarden, New Zealand -42.91319 + ## 6 NA *Stats by taxa* @@ -147,7 +146,7 @@ place ID (numeric ID), or user ID (string) counts <- get_inat_taxon_stats(date = "2010-06-14") print(counts$total) - ## [1] 119 + ## [1] 120 print(counts$species_counts[1:5,]) @@ -156,13 +155,13 @@ place ID (numeric ID), or user ID (string) ## 2 2 17008 Sayornis phoebe species 10 ## 3 2 52589 Coenonympha pamphilus species 10 ## 4 2 55908 Lepus timidus species 10 - ## 5 2 58484 Thymelicus lineola species 10 + ## 5 2 56057 Leucanthemum vulgare species 10 ## taxon.default_name.id taxon.default_name.name ## 1 91278 Glanville Fritillary ## 2 20369 Eastern Phoebe ## 3 114753 Small Heath ## 4 88688 Mountain Hare - ## 5 455733 Essex Skipper + ## 5 89055 Ox-eye Daisy ## taxon.default_name.is_valid taxon.default_name.lexicon ## 1 TRUE English ## 2 TRUE English @@ -170,34 +169,34 @@ place ID (numeric ID), or user ID (string) ## 4 TRUE English ## 5 TRUE English ## taxon.default_name.taxon_id taxon.default_name.created_at - ## 1 57495 2010-03-16T20:57:02.000-10:00 - ## 2 17008 2008-03-12T17:33:20.000-10:00 - ## 3 52589 2011-05-05T09:50:31.000-10:00 - ## 4 55908 2010-02-11T06:05:42.000-10:00 - ## 5 58484 2013-06-15T03:09:14.435-10:00 + ## 1 57495 2010-03-17T07:57:02.000+01:00 + ## 2 17008 2008-03-13T04:33:20.000+01:00 + ## 3 52589 2011-05-05T21:50:31.000+02:00 + ## 4 55908 2010-02-11T17:05:42.000+01:00 + ## 5 56057 2010-02-16T22:05:51.000+01:00 ## taxon.default_name.updated_at taxon.default_name.position - ## 1 2010-03-16T20:57:02.000-10:00 0 - ## 2 2008-03-12T17:33:20.000-10:00 0 - ## 3 2011-05-05T09:50:31.000-10:00 0 - ## 4 2010-02-11T06:05:42.000-10:00 0 - ## 5 2016-09-16T04:07:20.465-10:00 6 - ## taxon.image_url - ## 1 https://farm6.staticflickr.com/5206/5309980832_01c907d2f9_s.jpg - ## 2 https://farm6.staticflickr.com/5009/5346970195_d0eac9966b_s.jpg - ## 3 https://farm5.staticflickr.com/4005/4624300321_d1a46ff97e_s.jpg - ## 4 https://farm6.staticflickr.com/5483/11718223795_b05531bbf6_s.jpg - ## 5 https://farm1.staticflickr.com/72/186298101_13518924fe_s.jpg + ## 1 2010-03-17T07:57:02.000+01:00 0 + ## 2 2008-03-13T04:33:20.000+01:00 0 + ## 3 2011-05-05T21:50:31.000+02:00 0 + ## 4 2010-02-11T17:05:42.000+01:00 0 + ## 5 2017-01-05T00:57:29.655+01:00 0 + ## taxon.image_url + ## 1 https://farm6.staticflickr.com/5206/5309980832_01c907d2f9_s.jpg + ## 2 https://farm6.staticflickr.com/5009/5346970195_d0eac9966b_s.jpg + ## 3 https://farm5.staticflickr.com/4005/4624300321_d1a46ff97e_s.jpg + ## 4 https://farm6.staticflickr.com/5483/11718223795_b05531bbf6_s.jpg + ## 5 https://static.inaturalist.org/photos/10419/square.jpg?1444278709 ## taxon.iconic_taxon_name taxon.conservation_status_name ## 1 Insecta ## 2 Aves least_concern ## 3 Insecta ## 4 Mammalia least_concern - ## 5 Insecta + ## 5 Plantae print(counts$rank_counts) ## $species - ## [1] 101 + ## [1] 102 ## ## $genus ## [1] 8 @@ -227,7 +226,7 @@ observation count. counts <- get_inat_user_stats(date = "2010-06-14") print(counts$total) - ## [1] 60 + ## [1] 61 print(counts$most_observations[1:10,]) @@ -293,14 +292,14 @@ observation count. print(place_counts$most_observations[1:10,]) ## count user.id user.login user.name - ## 1 18170 12158 erikamitchell Erika Mitchell + ## 1 18329 12158 erikamitchell Erika Mitchell ## 2 15800 2179 charlie Charlie Hohn ## 3 8046 12610 susanelliott Susan Elliott ## 4 5924 12036 zaccota Zac Cota - ## 5 4387 11792 kylejones Kyle Jones - ## 6 4317 12045 larry522 Larry Clarfeld + ## 5 4388 11792 kylejones Kyle Jones + ## 6 4324 12045 larry522 Larry Clarfeld ## 7 4308 317 kpmcfarland Kent McFarland - ## 8 3833 28921 rwp84 roy pilcher + ## 8 3835 28921 rwp84 roy pilcher ## 9 3065 18303 marvelliott Marv Elliott ## 10 2761 12049 gaudettelaura Laura Gaudette ## user.user_icon_url @@ -318,16 +317,16 @@ observation count. print(place_counts$most_species[1:10,]) ## count user.id user.login user.name - ## 1 1856 12158 erikamitchell Erika Mitchell + ## 1 1869 12158 erikamitchell Erika Mitchell ## 2 1833 12610 susanelliott Susan Elliott - ## 3 1676 12045 larry522 Larry Clarfeld + ## 3 1677 12045 larry522 Larry Clarfeld ## 4 1350 11792 kylejones Kyle Jones ## 5 1235 2179 charlie Charlie Hohn ## 6 1108 6624 joannerusso ## 7 1062 317 kpmcfarland Kent McFarland ## 8 998 12049 gaudettelaura Laura Gaudette ## 9 833 3847 rpayne Ron Payne - ## 10 795 28921 rwp84 roy pilcher + ## 10 793 28921 rwp84 roy pilcher ## user.user_icon_url ## 1 https://static.inaturalist.org/attachments/users/icons/12158/thumb.jpeg?1475533280 ## 2 https://static.inaturalist.org/attachments/users/icons/12610/thumb.jpg?1475533475 diff --git a/README_files/figure-markdown_strict/unnamed-chunk-14-1.png b/README_files/figure-markdown_strict/unnamed-chunk-14-1.png index eb0a5f8..b703d9a 100644 Binary files a/README_files/figure-markdown_strict/unnamed-chunk-14-1.png and b/README_files/figure-markdown_strict/unnamed-chunk-14-1.png differ diff --git a/man/get_inat_obs.Rd b/man/get_inat_obs.Rd index 1de7f85..d4ef65f 100644 --- a/man/get_inat_obs.Rd +++ b/man/get_inat_obs.Rd @@ -63,7 +63,7 @@ use case it may be advisable to use the "taxon" field instead of the query field ## Filter with by just taxon, allows higher order filtering, ## Here we can search for just stone flies (order plecoptera) - get_inat_obs(taxon="Plecoptera") + get_inat_obs(taxon_name="Plecoptera") ## get metadata (the number of results found on the server) out <- get_inat_obs(query="Monarch Butterfly", meta=TRUE) diff --git a/man/get_inat_obs_user.Rd b/man/get_inat_obs_user.Rd index b6cf22d..f8d14ad 100644 --- a/man/get_inat_obs_user.Rd +++ b/man/get_inat_obs_user.Rd @@ -20,6 +20,6 @@ Get all the observations of a specific inaturalist user \examples{ \dontrun{ m_obs <- get_inat_obs(query="Monarch Butterfly") - get_inat_obs_user(as.character(m_obs$User.login[1])) + get_inat_obs_user(as.character(m_obs$user_login[1])) } } diff --git a/man/inat_map.Rd b/man/inat_map.Rd index 27c9795..1803d11 100644 --- a/man/inat_map.Rd +++ b/man/inat_map.Rd @@ -23,7 +23,7 @@ Plot observations from iNaturalist. You have the option of automatically plotti } \examples{ \dontrun{ - m_obs <- get_inat_obs(taxon="Ambystoma maculatum") + m_obs <- get_inat_obs(taxon_name = "Ambystoma maculatum") salamander_map <- inat_map(m_obs,plot=FALSE) ### Now we can modify the returned map salamander_map + borders("state") + theme_bw() diff --git a/tests/testthat/test-all.R b/tests/testthat/test-all.R index 5bea98e..d8c8d3f 100644 --- a/tests/testthat/test-all.R +++ b/tests/testthat/test-all.R @@ -17,4 +17,30 @@ test_that("Check all search parameters", { expect_equal( dim(get_inat_obs(query="Mule Deer", bounds=bounds,maxresults = 10))[1],10) }) - \ No newline at end of file + + +test_that("Check that getting observation by ID works",{ + expect_gt(length(get_inat_obs_id(res_set$id[1])),0) + expect_equal(get_inat_obs_id(res_set$id[1])$id,res_set$id[1]) +}) + +test_that("Check that project info is retrieved",{ + expect_match(get_inat_obs_project("crows-in-vermont", type="info",raw=FALSE)$slug, "crows-in-vermont" ) +}) + +test_that("Check that getting observations by users works",{ + expect_gt(dim(get_inat_obs_user(as.character(res_set$user_login[1])))[1],0) + +}) + +test_that("Check that taxon stats works",{ + expect_gt(get_inat_taxon_stats(date="2010-06-14")$total,0) +}) + +test_that("Check that user stats works",{ + expect_gt(get_inat_user_stats(date="2010-06-14")$total,0) + +}) + + +