diff --git a/CITATION.cff b/CITATION.cff index fbc0478..7951bf2 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -34,6 +34,18 @@ authors: name-particle: de email: garidel@cerege.fr orcid: https://orcid.org/0000-0001-8983-9571 +preferred-citation: + type: manual + title: 'forcis: An R client to access the FORCIS database' + authors: + - name: Casajus Nicolas + - name: Greco Mattia + - name: Chaabane Sonia + - name: Giraud Xavier + - name: de Garidel-Thoron Thibault + year: '2024' + notes: R package version 0.1.0.9000 + url: https://frbcesab.github.io/forcis repository-code: https://github.com/FRBCesab/forcis url: https://frbcesab.github.io/forcis contact: @@ -42,6 +54,62 @@ contact: email: nicolas.casajus@fondationbiodiversite.fr orcid: https://orcid.org/0000-0002-5537-5294 references: +- type: article + title: 'The FORCIS database: A global census of planktonic Foraminifera from ocean + waters' + authors: + - name: Chaabane Sonia + - name: De Garidel-Thoron Thibault + - name: Giraud Xavier + - name: Schiebel Ralf + - name: Beaugrand Gregory + - name: Brummer Geert-Jan + - name: Casajus Nicolas + - name: Greco Mattia + - name: Grigoratou Maria + - name: Howa Hélène + - name: Jonkers Lukas + - name: Kucera Michal + - name: Kuroyanagi Azumi + - name: Meilland Julie + - name: Monteiro Fanny + - name: Mortyn Graham + - name: Almogi-Labin Ahuva + - name: Asahi Hirofumi + - name: Avnaim-Katav Simona + - name: Bassinot Franck + - name: Davis Catherine V. + - name: Field David B. + - name: Hernández-Almeida Iván + - name: Herut Barak + - name: Hosie Graham + - name: Howard Will + - name: Jentzen Anna + - name: Johns David G. + - name: Keigwin Lloyd + - name: Kitchener John + - name: Kohfeld Karen E. + - name: Lessa Douglas V. O. + - name: Manno Clara + - name: Marchant Margarita + - name: Ofstad Siri + - name: Ortiz Joseph D. + - name: Post Alexandra + - name: Rigual-Hernandez Andres + - name: Rillo Marina C. + - name: Robinson Karen + - name: Sagawa Takuya + - name: Sierro Francisco + - name: Takahashi Kunio T. + - name: Torfstein Adi + - name: Venancio Igor + - name: Yamasaki Makoto + - name: Ziveri Patrizia + journal: Scientific Data + volume: '10' + doi: 10.1038/s41597-023-02264-2 + year: '2023' + start: '354' - type: software title: 'R: A Language and Environment for Statistical Computing' notes: Depends @@ -293,6 +361,31 @@ references: year: '2024' doi: 10.32614/CRAN.package.testthat version: '>= 3.0.0' +- type: software + title: vdiffr + abstract: 'vdiffr: Visual Regression Testing and Graphical Diffing' + notes: Suggests + url: https://vdiffr.r-lib.org/ + repository: https://CRAN.R-project.org/package=vdiffr + authors: + - family-names: Henry + given-names: Lionel + email: lionel@posit.co + - family-names: Pedersen + given-names: Thomas Lin + email: thomas.pedersen@posit.co + orcid: https://orcid.org/0000-0002-5147-4711 + - family-names: Luciani + given-names: T Jake + email: jake@apache.org + - family-names: Decorde + given-names: Matthieu + email: matthieu.decorde@ens-lyon.fr + - family-names: Lise + given-names: Vaudor + email: lise.vaudor@ens-lyon.fr + year: '2024' + doi: 10.32614/CRAN.package.vdiffr - type: software title: withr abstract: 'withr: Run Code ''With'' Temporarily Modified Global State' diff --git a/DESCRIPTION b/DESCRIPTION index 040d3cb..25522e6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -62,5 +62,6 @@ Suggests: knitr, rmarkdown, testthat (>= 3.0.0), + vdiffr, withr Config/testthat/edition: 3 diff --git a/codemeta.json b/codemeta.json index 8661653..9b559ca 100644 --- a/codemeta.json +++ b/codemeta.json @@ -133,6 +133,18 @@ }, "sameAs": "https://CRAN.R-project.org/package=testthat" }, + { + "@type": "SoftwareApplication", + "identifier": "vdiffr", + "name": "vdiffr", + "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=vdiffr" + }, { "@type": "SoftwareApplication", "identifier": "withr", @@ -244,7 +256,7 @@ }, "SystemRequirements": null }, - "fileSize": "2716.372KB", + "fileSize": "3718.985KB", "citation": [ { "@type": "SoftwareSourceCode", diff --git a/tests/testthat/_snaps/geom_basemap/plot-with-basemap.svg b/tests/testthat/_snaps/geom_basemap/plot-with-basemap.svg new file mode 100644 index 0000000..f399300 --- /dev/null +++ b/tests/testthat/_snaps/geom_basemap/plot-with-basemap.svg @@ -0,0 +1,350 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Plot with basemap + + diff --git a/tests/testthat/_snaps/ggmap_data/map-data.svg b/tests/testthat/_snaps/ggmap_data/map-data.svg new file mode 100644 index 0000000..e31fb4b --- /dev/null +++ b/tests/testthat/_snaps/ggmap_data/map-data.svg @@ -0,0 +1,351 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Map data + + diff --git a/tests/testthat/_snaps/plot_record_by_depth/plot-record-by-depth.svg b/tests/testthat/_snaps/plot_record_by_depth/plot-record-by-depth.svg new file mode 100644 index 0000000..b463496 --- /dev/null +++ b/tests/testthat/_snaps/plot_record_by_depth/plot-record-by-depth.svg @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + +from 100m-300m +from first 100m + + + + + + + + +0.0 +0.5 +1.0 +1.5 +2.0 +Number of FORCIS samples +Sampling interval +Plot record by depth + + diff --git a/tests/testthat/_snaps/plot_record_by_month/plot-record-by-month.svg b/tests/testthat/_snaps/plot_record_by_month/plot-record-by-month.svg new file mode 100644 index 0000000..82a3799 --- /dev/null +++ b/tests/testthat/_snaps/plot_record_by_month/plot-record-by-month.svg @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.0 +0.5 +1.0 +1.5 +2.0 + + + + + + + + + + + + + + + + + + + +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +NA +Month +Number of FORCIS samples +Plot record by month + + diff --git a/tests/testthat/_snaps/plot_record_by_season/plot-record-by-season.svg b/tests/testthat/_snaps/plot_record_by_season/plot-record-by-season.svg new file mode 100644 index 0000000..e62ed9b --- /dev/null +++ b/tests/testthat/_snaps/plot_record_by_season/plot-record-by-season.svg @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +1 +2 +3 + + + + + + + + + + +Fall +Winter +Spring +Summer +Unknown +Season +Number of FORCIS samples +Plot record by season + + diff --git a/tests/testthat/_snaps/plot_record_by_year/plot-net-record-by-year.svg b/tests/testthat/_snaps/plot_record_by_year/plot-net-record-by-year.svg new file mode 100644 index 0000000..0ca0162 --- /dev/null +++ b/tests/testthat/_snaps/plot_record_by_year/plot-net-record-by-year.svg @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + + + + + + + + +2000 +2005 +2010 +2015 +2020 +2025 +Year +Number of FORCIS samples +Plot net record by year + + diff --git a/tests/testthat/_snaps/plot_record_by_year/plot-record-by-year.svg b/tests/testthat/_snaps/plot_record_by_year/plot-record-by-year.svg new file mode 100644 index 0000000..680dac7 --- /dev/null +++ b/tests/testthat/_snaps/plot_record_by_year/plot-record-by-year.svg @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + + + + + + + + +2000 +2005 +2010 +2015 +2020 +2025 +Year +Number of FORCIS samples +Plot record by year + + diff --git a/tests/testthat/_snaps/plot_record_by_year/plot-trap-record-by-year.svg b/tests/testthat/_snaps/plot_record_by_year/plot-trap-record-by-year.svg new file mode 100644 index 0000000..c30541d --- /dev/null +++ b/tests/testthat/_snaps/plot_record_by_year/plot-trap-record-by-year.svg @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + + + + + + + + +2000 +2005 +2010 +2015 +2020 +2025 +Year +Number of FORCIS samples +Plot trap record by year + + diff --git a/tests/testthat/test-geom_basemap.R b/tests/testthat/test-geom_basemap.R index 048795d..935522c 100644 --- a/tests/testthat/test-geom_basemap.R +++ b/tests/testthat/test-geom_basemap.R @@ -16,4 +16,8 @@ test_that("Test geom_basemap() for success", { } expect_true("element_blank" %in% class(geom[[5]][[1]])) + + expect_silent({ gg <- ggplot2::ggplot() + geom_basemap() }) + + vdiffr::expect_doppelganger("Plot with basemap", gg) }) diff --git a/tests/testthat/test-ggmap_data.R b/tests/testthat/test-ggmap_data.R index f84c169..4aec442 100644 --- a/tests/testthat/test-ggmap_data.R +++ b/tests/testthat/test-ggmap_data.R @@ -12,4 +12,6 @@ test_that("Test ggmap_data() for success", { expect_true("gg" %in% class(gg)) expect_true("ggplot" %in% class(gg)) + + vdiffr::expect_doppelganger("Map data", gg) }) diff --git a/tests/testthat/test-plot_record_by_depth.R b/tests/testthat/test-plot_record_by_depth.R index 783964e..f6aac47 100644 --- a/tests/testthat/test-plot_record_by_depth.R +++ b/tests/testthat/test-plot_record_by_depth.R @@ -27,4 +27,6 @@ test_that("Test plot_record_by_depth() for success", { expect_true("gg" %in% class(gg)) expect_true("ggplot" %in% class(gg)) + + vdiffr::expect_doppelganger("Plot record by depth", gg) }) diff --git a/tests/testthat/test-plot_record_by_month.R b/tests/testthat/test-plot_record_by_month.R index eec7eb0..e27bc5a 100644 --- a/tests/testthat/test-plot_record_by_month.R +++ b/tests/testthat/test-plot_record_by_month.R @@ -26,5 +26,7 @@ test_that("Test plot_record_by_month() for success", { expect_true("gg" %in% class(gg)) expect_true("ggplot" %in% class(gg)) + + vdiffr::expect_doppelganger("Plot record by month", gg) }) diff --git a/tests/testthat/test-plot_record_by_season.R b/tests/testthat/test-plot_record_by_season.R index be4017b..9416ac7 100644 --- a/tests/testthat/test-plot_record_by_season.R +++ b/tests/testthat/test-plot_record_by_season.R @@ -28,4 +28,6 @@ test_that("Test plot_record_by_season() for success", { expect_true("gg" %in% class(gg)) expect_true("ggplot" %in% class(gg)) + + vdiffr::expect_doppelganger("Plot record by season", gg) }) diff --git a/tests/testthat/test-plot_record_by_year.R b/tests/testthat/test-plot_record_by_year.R index 8732520..5595bad 100644 --- a/tests/testthat/test-plot_record_by_year.R +++ b/tests/testthat/test-plot_record_by_year.R @@ -1,16 +1,16 @@ ## Data for tests ---- -df_net <- data.frame("data_type" = rep("Net", 6), +df_net <- data.frame("data_type" = rep("Net", 5), "profile_date_time" = c("01/02/1999", "01/03/2020", "01/03/2022", "01/04/2023", - "01/07/2024", NA), - "sample_id" = c(1, 1, 2, 3, 3, 3)) + "01/07/2024"), + "sample_id" = c(1, 1, 2, 3, 3)) -df_trap <- data.frame("data_type" = rep("Sediment trap", 6), +df_trap <- data.frame("data_type" = rep("Sediment trap", 5), "sample_date_time_start" = c("01/02/1999", "01/03/2020", "01/03/2022", "01/04/2023", - "01/07/2024", NA), - "sample_id" = c(1, 1, 2, 3, 3, 3)) + "01/07/2024"), + "sample_id" = c(1, 1, 2, 3, 3)) ## plot_record_by_year() ---- @@ -22,8 +22,12 @@ test_that("Test plot_record_by_year() for success", { expect_true("gg" %in% class(gg)) expect_true("ggplot" %in% class(gg)) + vdiffr::expect_doppelganger("Plot net record by year", gg) + expect_silent({ gg <- plot_record_by_year(df_trap) }) expect_true("gg" %in% class(gg)) expect_true("ggplot" %in% class(gg)) + + vdiffr::expect_doppelganger("Plot trap record by year", gg) })