version 1.3.1

cran · Jan 9, 2024 · 711d71b · 711d71b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: GIFT
 Type: Package
 Title: Access to the Global Inventory of Floras and Traits (GIFT)
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: c(
   person("Pierre", "Denelle", email = "pierre.denelle@gmail.com",
     role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5037-2281")),
@@ -31,9 +31,9 @@ URL: https://github.com/BioGeoMacro/GIFT,
 BugReports: https://github.com/BioGeoMacro/GIFT/issues
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2023-11-20 13:54:36 UTC; Pierre
+Packaged: 2024-01-08 21:09:07 UTC; Pierre
 Author: Pierre Denelle [aut, cre] (<https://orcid.org/0000-0001-5037-2281>),
   Patrick Weigelt [aut] (<https://orcid.org/0000-0002-2485-3708>)
 Maintainer: Pierre Denelle <pierre.denelle@gmail.com>
 Repository: CRAN
-Date/Publication: 2023-11-20 17:10:02 UTC
+Date/Publication: 2024-01-09 02:10:02 UTC
diff --git a/MD5 b/MD5
@@ -1,75 +1,75 @@
-3032d9fab196955f356024aaea43aff9 *DESCRIPTION
+99d54072f7d8c5314608da661765a5f0 *DESCRIPTION
 729d122d2d4c333f243fca6bda30cc11 *NAMESPACE
-22b56b0adfd5cb5d30615f740fbed91e *NEWS.md
-ed6e623d58bf2b212c97daf68ad0e911 *R/GIFT_checklists.R
-c478ee9c3c501f040332ac69de4e8003 *R/GIFT_checklists_conditional.R
-c91230493b331edff70eafeb66a7572a *R/GIFT_checklists_raw.R
-226a28624c878e2c592a915427e4607d *R/GIFT_coverage.R
-a0a03aecc7e9898876a293aba215af11 *R/GIFT_env.R
-fa6cd60c0b29c1b9fb0d2c38e1d09572 *R/GIFT_env_meta_misc.R
-34ca2731c64fa4b3a0fc96b302be1f51 *R/GIFT_env_meta_raster.R
-cb05c80e71cf46fa4a1a439a1a13a417 *R/GIFT_lists.R
-bbebc379b4b54c1fbfb6ff828c5e0faa *R/GIFT_no_overlap.R
-1fbc280c9c02cbbc1455385c1493c32a *R/GIFT_overlap.R
-bda2857e91aa8ca3da3e52e3c51037d5 *R/GIFT_phylogeny.R
-bd0ae0b565d379f79556a9aca63828ef *R/GIFT_references.R
-1b379ab8a3f1b59a0a6f273b570010ec *R/GIFT_regions.R
-86bce900f23f3511a93fd52203c586b0 *R/GIFT_richness.R
-4d82ef14939ba384bf9d5ba6083c90a6 *R/GIFT_shapes.R
-ad0ceef593fcc2ddfaea91b129975c86 *R/GIFT_spatial.R
-bb9391d69a1cde063cd741e9e17107cb *R/GIFT_species.R
-4535d69b1a8cbff8e23286a2cd671413 *R/GIFT_species_distribution.R
-53193c5e022b791dedd9c6a83d106ddb *R/GIFT_species_lookup.R
-7448041c2d9288e28619164f8744e5e1 *R/GIFT_taxgroup.R
-74d812cf4e5525120cb50cbf89cfed46 *R/GIFT_taxonomy.R
-8075d68e4d4ef590d1d45934e5787e0c *R/GIFT_traits.R
-497c8d786d3182ff5be3db2915d5a122 *R/GIFT_traits_meta.R
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-fea0a1f5fa3c69c45eca9e0aedeeabcf *R/GIFT_traits_tax.R
-24b4c08b10e170d6b6b6850f0adc59d5 *R/GIFT_versions.R
+0150e571b883de95e476bcabda1cd1ad *NEWS.md
+fc6db48a95772ef9331f9f853b2e02b6 *R/GIFT_checklists.R
+3e084469221739db88f54b53d0b2ff83 *R/GIFT_checklists_conditional.R
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 15b0f4988b97e672bb8411d89181cc6c *R/check_functions.R
 d478f4e0b13f11f6059e82ac27aa0243 *R/figures_vignette.R
 1319b7ae28fb531c98be7d5f79be1eac *R/function_dependency.R
 629d794dd2bd4c7dc67f5acd3fb332e4 *R/pkg_check.R
 f81eaa1c946a8cb8766652b8c9886f4f *R/western_mediterranean.R
-ba43d69127ed1c855c33ab8ba4691c05 *README.md
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 70b52af4591ea58d1130d15fdd60aa60 *build/vignette.rds
 61fca6d5bfe61d0cdb98a388172528e5 *data/western_mediterranean.rda
 081787ac72ba5c66614abfc75b5e347a *inst/doc/GIFT.R
 8be63e6c331ade1fa9f44e2961f4fca6 *inst/doc/GIFT.Rmd
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 5489dd8c667ea2cad5a0626bb7647b35 *inst/doc/GIFT_API.R
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 2f19840804d66320978e314b7027d353 *inst/doc/GIFT_advanced_users.R
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-703249016abf3cc950ffeaeaa226d921 *man/GIFT_versions.Rd
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+1a10fa93231034084a89f4d59fab6251 *man/GIFT_lists.Rd
+f9e6455e87b01c0c8bcc046c0696806d *man/GIFT_no_overlap.Rd
+83239d37eff32826e8a3230429b737f2 *man/GIFT_overlap.Rd
+5ac71c0d117d533c85a0d816c1c3c7a1 *man/GIFT_phylogeny.Rd
+391dbfefff82258da2581f5266a7e5cb *man/GIFT_references.Rd
+094c397ed3ea3d70659091eb5a324fb4 *man/GIFT_regions.Rd
+49b7f0c02144d26cdbf0fe15380fc55f *man/GIFT_richness.Rd
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+644c831df365092073468a8b28210e28 *man/GIFT_spatial.Rd
+327243489a95d20acda89f3aef56d96c *man/GIFT_species.Rd
+e9b15687d62b977497694f3505ea5e1a *man/GIFT_species_distribution.Rd
+15226ca28dafe17fd91a5adf50d2c699 *man/GIFT_species_lookup.Rd
+01d1f42aafa6c0530f328fa1f0341054 *man/GIFT_taxgroup.Rd
+5ebfba6c5cda78442cace991a90b9bac *man/GIFT_taxonomy.Rd
+ed31b0211c142eeba6d98c78a7ceae49 *man/GIFT_traits.Rd
+d2eeea1082953a35372986787267020e *man/GIFT_traits_meta.Rd
+3edab38747e445ae493b11d1d7cce049 *man/GIFT_traits_raw.Rd
+1c9bfeac498243fe5e49b7c7a11c8379 *man/GIFT_traits_tax.Rd
+3c3584b2962f1496be60f824a54c387f *man/GIFT_versions.Rd
 4b598cc3e7187c2d719debb95bf8f50f *man/figures/Aisen_Chile_GMBA_overlap.png
 bb1f47ee559f993560ede6c796d45f1b *man/figures/GIFT.png
 a8ac941d66ec17fed4e374a0b77a9d5d *man/figures/GIFT_complete_floristic.svg
@@ -122,4 +122,4 @@ c096c4ac48a58f5f738a75be41bce8d1 *tests/testthat/test-GIFT_traits_tax.R
 28acd92149932c19c840426112697ca7 *tests/testthat/test-GIFT_versions.R
 8be63e6c331ade1fa9f44e2961f4fca6 *vignettes/GIFT.Rmd
 b884898c064d14ff0753b1a5d30e736a *vignettes/GIFT_API.Rmd
-f9263cdbcf525932dd1b40a4dc56fc65 *vignettes/GIFT_advanced_users.Rmd
+e02f1f602be481afddae7962126eb813 *vignettes/GIFT_advanced_users.Rmd
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,11 @@
 # GIFT
 
+# GIFT 1.3.1
+## Minor changes
+
+* Better message in GIFT_env with missing raster/misc
+* Citation updated in all functions and Readme
+
 # GIFT 1.3.0
 
 * Better handling of functions when the Internet or the GIFT server are down

diff --git a/R/GIFT_checklists.R b/R/GIFT_checklists.R
@@ -136,6 +136,11 @@
 #' want to consider regions classified as `suit_geo`.
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_checklists_conditional.R b/R/GIFT_checklists_conditional.R
@@ -76,6 +76,11 @@
 #' \emph{taxon_name} - Name of the group of taxa available.
 #' 
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_checklists_raw.R b/R/GIFT_checklists_raw.R
@@ -25,8 +25,7 @@
 #' 
 #' @param taxonomy `NULL` by default. If not, it has to be the taxonomy table
 #' (see [GIFT::GIFT_taxonomy()]). Used internally in [GIFT::GIFT_checklists()]
-#' to avoid downloading the taxonomy table many times.
-#' 
+#' to avoid downloading the taxonomy table many times.#' 
 #' 
 #' 
 #' @template GIFT_version_api
@@ -70,6 +69,11 @@
 #' \emph{cons_status} - Conservation status of the species
 #' 
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_coverage.R b/R/GIFT_coverage.R
@@ -48,6 +48,11 @@
 #' geographic region.
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_env.R b/R/GIFT_env.R
@@ -44,6 +44,11 @@
 #' The other columns relate to the environmental variables the user asked for.
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623
@@ -97,7 +102,9 @@ GIFT_env <- function(
          length(miscellaneous)){
         message(paste0(
           "The following miscellaneous variable(s) are not available in GIFT: ",
-          miscellaneous[!(miscellaneous %in% gift_env_meta_misc$variable)]))
+          paste0(miscellaneous[!(miscellaneous %in%
+                                   gift_env_meta_misc$variable)],
+                 collapse = ", ")))
 
         miscellaneous <- miscellaneous[(miscellaneous %in%
                                           gift_env_meta_misc$variable)]
@@ -119,7 +126,9 @@ GIFT_env <- function(
          length(rasterlayer)){
         message(paste0(
           "The following raster layer(s) are not available in GIFT: ",
-          rasterlayer[!(rasterlayer %in% gift_env_meta_raster$layer_name)]))
+          paste0(rasterlayer[!(rasterlayer %in%
+                                 gift_env_meta_raster$layer_name)],
+                 collapse = ", ")))
 
         rasterlayer <- rasterlayer[(rasterlayer %in%
                                       gift_env_meta_raster$layer_name)]

diff --git a/R/GIFT_env_meta_misc.R b/R/GIFT_env_meta_misc.R
@@ -18,6 +18,11 @@
 #' \emph{ref_long} - Full reference to cite when using an environmental layer.
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_env_meta_raster.R b/R/GIFT_env_meta_raster.R
@@ -21,6 +21,11 @@
 #' \emph{ref_long} - Full reference to cite when using an environmental layer
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_lists.R b/R/GIFT_lists.R
@@ -22,6 +22,11 @@
 #' \emph{entity_unit} give additional details about the polygon.
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_no_overlap.R b/R/GIFT_no_overlap.R
@@ -27,6 +27,11 @@
 #' non-overlapping.
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_overlap.R b/R/GIFT_overlap.R
@@ -22,6 +22,11 @@
 #' \emph{overlap21} - The other way around
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_phylogeny.R b/R/GIFT_phylogeny.R
@@ -31,6 +31,11 @@
 #' \emph{rgt} - Right border of a given taxon in the Newick sequence\cr
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_references.R b/R/GIFT_references.R
@@ -28,6 +28,11 @@
 #' \emph{proc_date} - When the source was processed
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_regions.R b/R/GIFT_regions.R
@@ -19,6 +19,11 @@
 #' \emph{country} - Whether the polygon is a country
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_richness.R b/R/GIFT_richness.R
@@ -23,6 +23,11 @@
 #' occurrences of species which go back to infraspecific taxa. 
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_shapes.R b/R/GIFT_shapes.R
@@ -26,6 +26,11 @@
 #' \emph{geometry} - Geometry column from sf
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623

diff --git a/R/GIFT_spatial.R b/R/GIFT_spatial.R
@@ -26,6 +26,11 @@
 #'  the different polygons of GIFT.
 #'
 #' @references
+#'      Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
+#'      access the Global Inventory of Floras and Traits. Methods in Ecology
+#'      and Evolution, 14, 2738-2748.
+#'      https://doi.org/10.1111/2041-210X.14213
+#' 
 #'      Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 #'      Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 #'      https://doi.org/10.1111/jbi.13623