version 1.3.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: GIFT
 Type: Package
 Title: Access to the Global Inventory of Floras and Traits (GIFT)
-Version: 1.3.1
+Version: 1.3.2
 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: 2024-01-08 21:09:07 UTC; Pierre
+Packaged: 2024-02-27 10:03:00 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: 2024-01-09 02:10:02 UTC
+Date/Publication: 2024-02-27 10:50:02 UTC

MD5

@@ -1,13 +1,13 @@
-99d54072f7d8c5314608da661765a5f0 *DESCRIPTION
+4ca1d828d77d703ad79549b03188bc60 *DESCRIPTION
 729d122d2d4c333f243fca6bda30cc11 *NAMESPACE
-0150e571b883de95e476bcabda1cd1ad *NEWS.md
+aa907f4abefb5e0310c56c7d217692e4 *NEWS.md
 fc6db48a95772ef9331f9f853b2e02b6 *R/GIFT_checklists.R
 3e084469221739db88f54b53d0b2ff83 *R/GIFT_checklists_conditional.R
 fe6ad55fa563781dcf685145e0af019c *R/GIFT_checklists_raw.R
 b522a4a0d4d59621d9c0be39dbe8955d *R/GIFT_coverage.R
 4fea0753771dc4f0c997c12dd53c69bf *R/GIFT_env.R
-13cd89cd641aeb1ffd0a7fb687de2f31 *R/GIFT_env_meta_misc.R
-fa70b408864df69f710a0fc86e9316ff *R/GIFT_env_meta_raster.R
+a2f464840a6df704404c7af0c464735f *R/GIFT_env_meta_misc.R
+30a51f5980426ac4bf473a2365dfb154 *R/GIFT_env_meta_raster.R
 aa24fd4e3c07223294d80ce819548fed *R/GIFT_lists.R
 3301682c59ed182c588efba783ed8ca6 *R/GIFT_no_overlap.R
 ad2853f0dfcd1bdf04dcbb6b0a33463a *R/GIFT_overlap.R
@@ -16,7 +16,7 @@ ad2853f0dfcd1bdf04dcbb6b0a33463a *R/GIFT_overlap.R
 a578c86815fd892e4b5519216d69b47e *R/GIFT_regions.R
 b68aeab9cff5d84484beb7fa1a46ad79 *R/GIFT_richness.R
 aaa158337b77d9c2c60638968c45da91 *R/GIFT_shapes.R
-fb043c8989791684e5e4936256f4304d *R/GIFT_spatial.R
+97bc0c2e332b1c0b5a7d0c1105918518 *R/GIFT_spatial.R
 5ceb4be1793fcee0e2077db9c173206e *R/GIFT_species.R
 08f25cc9b845e392bc6bc95d44a63df6 *R/GIFT_species_distribution.R
 2187b7db11480523a1b7366c15f8b53a *R/GIFT_species_lookup.R
@@ -27,23 +27,23 @@ fb043c8989791684e5e4936256f4304d *R/GIFT_spatial.R
 3eafc139ba28c47616fa6a087e5dae1c *R/GIFT_traits_raw.R
 fe8315d3934a893e50ec63bba96bbfe6 *R/GIFT_traits_tax.R
 1240e335ae592a6b79af6980dadb8db5 *R/GIFT_versions.R
-15b0f4988b97e672bb8411d89181cc6c *R/check_functions.R
+2d06d22014c1015436d76d29f0bc3d53 *R/check_functions.R
 d478f4e0b13f11f6059e82ac27aa0243 *R/figures_vignette.R
 1319b7ae28fb531c98be7d5f79be1eac *R/function_dependency.R
 629d794dd2bd4c7dc67f5acd3fb332e4 *R/pkg_check.R
 f81eaa1c946a8cb8766652b8c9886f4f *R/western_mediterranean.R
 19c9307ec04bb183020abab0d34c6805 *README.md
 70b52af4591ea58d1130d15fdd60aa60 *build/vignette.rds
 61fca6d5bfe61d0cdb98a388172528e5 *data/western_mediterranean.rda
-081787ac72ba5c66614abfc75b5e347a *inst/doc/GIFT.R
-8be63e6c331ade1fa9f44e2961f4fca6 *inst/doc/GIFT.Rmd
-91772ccf46b231dcbe547d26acdd9b25 *inst/doc/GIFT.html
+811f3a2d555320864a7d2572bb5418e3 *inst/doc/GIFT.R
+154941e82866de24a353960550ce6cc4 *inst/doc/GIFT.Rmd
+c729c1bda2db59b5aa0b89b3e8d5ec33 *inst/doc/GIFT.html
 5489dd8c667ea2cad5a0626bb7647b35 *inst/doc/GIFT_API.R
 b884898c064d14ff0753b1a5d30e736a *inst/doc/GIFT_API.Rmd
-24b27d914b50fa1a80a365dcce52df25 *inst/doc/GIFT_API.html
+6e58d085cf0f58244e258bdecb077fdd *inst/doc/GIFT_API.html
 2f19840804d66320978e314b7027d353 *inst/doc/GIFT_advanced_users.R
 e02f1f602be481afddae7962126eb813 *inst/doc/GIFT_advanced_users.Rmd
-f013a7a026cd96954bf2bc98ac788ea6 *inst/doc/GIFT_advanced_users.html
+785b4d2c43fd3fa4079ec251537ce09b *inst/doc/GIFT_advanced_users.html
 8d69b7ea88ecb2c6a423ac04603a598a *man/GIFT_checklists.Rd
 dcbe04400d4eb025d35ebf5ff16f071c *man/GIFT_checklists_conditional.Rd
 91188371b273d0a5cbe632f32314593a *man/GIFT_checklists_raw.Rd
@@ -59,7 +59,7 @@ f9e6455e87b01c0c8bcc046c0696806d *man/GIFT_no_overlap.Rd
 094c397ed3ea3d70659091eb5a324fb4 *man/GIFT_regions.Rd
 49b7f0c02144d26cdbf0fe15380fc55f *man/GIFT_richness.Rd
 8a7b6898e2c9a9e9aa5d02fa3362899d *man/GIFT_shapes.Rd
-644c831df365092073468a8b28210e28 *man/GIFT_spatial.Rd
+60f5f8d5a674ab9538612c298fd30dd2 *man/GIFT_spatial.Rd
 327243489a95d20acda89f3aef56d96c *man/GIFT_species.Rd
 e9b15687d62b977497694f3505ea5e1a *man/GIFT_species_distribution.Rd
 15226ca28dafe17fd91a5adf50d2c699 *man/GIFT_species_lookup.Rd
@@ -120,6 +120,6 @@ eea57da0e5771d4b67e0b9112b03436c *tests/testthat/test-GIFT_species_distribution.
 6fff45280cfcc80aba5e4cce313aef6b *tests/testthat/test-GIFT_traits_raw.R
 c096c4ac48a58f5f738a75be41bce8d1 *tests/testthat/test-GIFT_traits_tax.R
 28acd92149932c19c840426112697ca7 *tests/testthat/test-GIFT_versions.R
-8be63e6c331ade1fa9f44e2961f4fca6 *vignettes/GIFT.Rmd
+154941e82866de24a353960550ce6cc4 *vignettes/GIFT.Rmd
 b884898c064d14ff0753b1a5d30e736a *vignettes/GIFT_API.Rmd
 e02f1f602be481afddae7962126eb813 *vignettes/GIFT_advanced_users.Rmd

NEWS.md

@@ -1,5 +1,15 @@
 # GIFT
 
+# GIFT 1.3.2
+## Minor changes
+
+* Better description of entity_ID argument in GIFT_spatial
+* Example added in GIFT_spatial
+* Main vignette: detail added regarding the version of GIFT used for the
+species distribution, packages edited in the beginning
+* Function check_query() added in the check_functions and implemented in
+GITT_env_meta_raster() and GIFT_env_meta_misc()
+
 # GIFT 1.3.1
 ## Minor changes
 

R/GIFT_env_meta_misc.R

@@ -49,6 +49,9 @@ GIFT_env_meta_misc <- function(
     GIFT_version <- check_gift_version(GIFT_version)
 
     # Return the miscellaneous environmental information as a data frame
+    check_query(paste0(
+      api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
+      ".php?query=env_misc"))
     tmp <- jsonlite::read_json(paste0(
       api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
       ".php?query=env_misc"), simplifyVector = TRUE)
@@ -58,6 +61,9 @@ GIFT_env_meta_misc <- function(
     tmp$citavi_ID <- substr(tmp$citavi_ID, 1, (nchar(tmp$citavi_ID)-1))
 
     # Merging complete reference names
+    check_query(paste0(
+      api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
+      ".php?query=references_citavi"))
     refs <- jsonlite::read_json(paste0(
       api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
       ".php?query=references_citavi"), simplifyVector = TRUE)

R/GIFT_env_meta_raster.R

@@ -53,6 +53,9 @@ GIFT_env_meta_raster <- function(
     GIFT_version <- check_gift_version(GIFT_version)
 
     # Return the raster environmental information
+    check_query(paste0(
+      api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
+      ".php?query=env_raster"))
     tmp <- jsonlite::read_json(paste0(
       api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
       ".php?query=env_raster"), simplifyVector = TRUE)
@@ -61,6 +64,9 @@ GIFT_env_meta_raster <- function(
     tmp$citavi_ID <- gsub("^.*\\#", "", tmp$citavi_ID)
     tmp$citavi_ID <- substr(tmp$citavi_ID, 1, (nchar(tmp$citavi_ID)-1))
 
+    check_query(paste0(
+      api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
+      ".php?query=references_citavi"))
     refs <- jsonlite::read_json(paste0(
       api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
       ".php?query=references_citavi"), simplifyVector = TRUE)

R/GIFT_spatial.R

@@ -16,7 +16,9 @@
 #' `extent_intersect` means that every polygon from GIFT for which the extent
 #' intersects the provided shape/coordinates will be retrieved.
 #' 
-#' @param entity_ID List of entity_ID to retrieve.
+#' @param entity_ID Constrain the list of regions to be received by a
+#' predefined set of entity_IDs. E.g. this list could come from
+#' GIFT_checklists_conditional().
 #' 
 #' @template GIFT_version_api
 #' 
@@ -39,22 +41,31 @@
 #'
 #' @examples
 #' \donttest{
+#' # With a shapefile
 #' data("western_mediterranean")
 #' ex <- GIFT_spatial(shp = western_mediterranean, overlap = "centroid_inside")
 #' 
+#' # With a shapefile coming from GIFT
+#' spain <- GIFT_shapes(entity_ID = 10071)
+#' ex_spain <- GIFT_spatial(shp = spain)
+#' 
+#' # With a point 
 #' custom_point <- cbind(9.9, 51)
 #' ex2 <- GIFT_spatial(coordinates = custom_point,
 #' overlap = "extent_intersect")
 #' 
+#' # With an extent
 #' custom_extent <- cbind(c(-13, -18), c(27.5, 29.3))
 #' ex3 <- GIFT_spatial(coordinates = custom_extent,
 #' overlap = "extent_intersect")
 #' 
+#' # With a custom polygon
 #' custom_polygon <- cbind(c(-18, -16.9, -13, -13, -18, -18),
 #' c(29.3, 33, 29.3, 27.5, 27.5, 29.3))
 #' ex4 <- GIFT_spatial(coordinates = custom_polygon,
 #' overlap = "extent_intersect")
 #' 
+#' #With a linestring
 #' custom_linestring <- rbind(c(9.9, 51), c(2.35, 48.9))
 #' custom_linestring <- sf::st_as_sf(as.data.frame(custom_linestring),
 #' coords = c("V1", "V2"))

R/check_functions.R

@@ -474,6 +474,53 @@ check_overlap_threshold <- function(overlap_threshold) {
   }
 }
 
+# Checking manual queries
+#
+# Authors: Pierre Denelle
+#
+# Stop if api argument does not have the right format
+#
+# Args:
+#   api a character
+#
+# Returns:
+#   nothing, shows an error message
+
+# Run the API and see if we get 'no query selected'
+check_query <- function(api) {
+  if(length(api) != 1 || !is.character(api)){
+    stop("api must be a character string indicating which API to use.")
+  }
+
+  # First check: internet connection
+  if(!curl::has_internet()) {
+    message("No internet connection found.")
+    return(NULL)
+  }
+
+  # Second check: web API available
+  req <- httr2::request(api)
+  resp <- httr2::req_error(req, is_error = function(resp) FALSE)
+
+  # test for non-existing APIs
+  tryCatch(expr = httr2::req_perform(resp),
+           error = function(expr) {
+             message(
+               "Either the API is wrongly specified or the server is down.")
+             return(NULL)
+           })
+
+  # If the server was found, check for status
+  resp_status <- httr2::resp_status_desc(httr2::req_perform(resp))
+  if(resp_status == "Unauthorized"){
+    message("A password is needed for this restricted API.")
+    return(NULL)
+  } else if(resp_status != "OK"){
+    message("Either the API is wrongly specified or the server is down.")
+    return(NULL)
+  }
+}
+
 # Checking ref_excluded argument
 #
 # Authors: Pierre Denelle

inst/doc/GIFT.R

@@ -15,6 +15,7 @@ suppressPackageStartupMessages({
     library("rnaturalearthdata")
     library("tidyr")
     library("ape")
+    library("patchwork")
   })
 })
 
@@ -27,11 +28,14 @@ knitr::include_graphics("../man/figures/GIFT.png")
 ## ----echo=TRUE, eval=FALSE----------------------------------------------------
 #  library("GIFT")
 #  library("dplyr")
+#  library("knitr")
+#  library("kableExtra")
 #  library("ggplot2")
 #  library("sf")
 #  library("rnaturalearth")
 #  library("rnaturalearthdata")
 #  library("tidyr")
+#  library("ape")
 #  library("patchwork")
 
 ## ----echo = TRUE, eval = FALSE------------------------------------------------
@@ -236,7 +240,8 @@ kable(anemone_lookup, "html") %>%
 
 ## -----------------------------------------------------------------------------
 anemone_distr <- GIFT_species_distribution(
-  genus = "Anemone", epithet = "nemorosa", aggregation = TRUE)
+  genus = "Anemone", epithet = "nemorosa", aggregation = TRUE,
+  GIFT_version = "2.2")
 
 anemone_statuses <- anemone_distr %>%
   mutate(native = ifelse(native == 1, "native", "non-native"),

inst/doc/GIFT.Rmd

@@ -35,6 +35,7 @@ suppressPackageStartupMessages({
     library("rnaturalearthdata")
     library("tidyr")
     library("ape")
+    library("patchwork")
   })
 })
 
@@ -69,11 +70,14 @@ The following R packages are required to build this vignette:
 ```{r, echo=TRUE, eval=FALSE}
 library("GIFT")
 library("dplyr")
+library("knitr")
+library("kableExtra")
 library("ggplot2")
 library("sf")
 library("rnaturalearth")
 library("rnaturalearthdata")
 library("tidyr")
+library("ape")
 library("patchwork")
 ```
 
@@ -529,7 +533,8 @@ more details.
 
 ```{r}
 anemone_distr <- GIFT_species_distribution(
-  genus = "Anemone", epithet = "nemorosa", aggregation = TRUE)
+  genus = "Anemone", epithet = "nemorosa", aggregation = TRUE,
+  GIFT_version = "2.2")
 
 anemone_statuses <- anemone_distr %>%
   mutate(native = ifelse(native == 1, "native", "non-native"),