Merge branch 'main' into inherit-parsing-issues

inbo · Nov 9, 2023 · 931059b · 931059b
2 parents 4927224 + 166e246
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: camtraptor
 Title: Read, Explore and Visualize Camera Trap Data Packages
-Version: 0.20.2
+Version: 0.21.0
 Authors@R: c(
     person("Damiano", "Oldoni", email = "[email protected]",
            role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3445-7562")),
@@ -22,7 +22,7 @@ Authors@R: c(
            role = "fnd", comment = "https://lifewatch.be")
   )
 Description: Read, explore and visualize Camera Trap Data Packages (Camtrap DP).
-    'Camtrap DP' (<https://tdwg.github.io/camtrap-dp/>) is a community developed 
+    'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a community developed 
     data exchange format for this type of data. With camtraptor you can read and 
     filter data, create overviews of observed species, relative abundance or 
     effort, and plot these data on a map.

diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,8 @@
+# camtraptor 0.21.0
+
+- `read_camtrap_dp()` supports Camtrap DP 1.0 (upcoming Agouti export format) 
+  in favour of Camtrap DP 1.0-rc.1 (#284).
+  To avoid breaking changes to users, it will down-convert Camtrap DP 1.0 to
+  0.1.6 which is currently used as internal data model for camtraptor.
+- `get_custom_effort()` now calculates per calendar month/week (#219).
+- `write_dwc()` has an updated mapping for dwc_audubon.csv (#274).
diff --git a/R/calc_animal_pos.R b/R/calc_animal_pos.R
@@ -51,8 +51,11 @@ calc_animal_pos <- function(animal_pos,
   assertthat::assert_that(
     length(not_found_cols) == 0,
     msg = glue::glue(
-      "Columns `{not_found_cols}` not found in `animal_pos`.",
-      .transformer = collapse_transformer(sep = "`, `", last = "` and `")
+      "Columns ",
+      glue::glue_collapse(
+        glue::backtick(not_found_cols), sep = ", ", last = " and "
+      ),
+      " not found in `animal_pos`."
     )
   )
 

diff --git a/R/check_package.R b/R/check_package.R
@@ -52,8 +52,8 @@ check_package <- function(package = NULL,
   assertthat::assert_that(
     length(tables_absent) == 0,
     msg = glue::glue(
-      "Can't find {length(tables_absent)} elements in data package: {tables_absent*}",
-      .transformer = collapse_transformer(sep = ", ", last = " and ")
+      "Can't find {length(tables_absent)} elements in data package: ",
+      glue::glue_collapse(tables_absent, sep = ", ", last = " and ")
     )
   )
   if (media) {

diff --git a/R/data.R b/R/data.R
@@ -1,6 +1,6 @@
 #' Sample of Camtrap DP formatted data
 #'
-#' A sample [Camera Trap Data Package](https://tdwg.github.io/camtrap-dp) as
+#' A sample [Camera Trap Data Package](https://camtrap-dp.tdwg.org) as
 #' read by [read_camtrap_dp()].
 #' The source data are derived from the [Camtrap DP example dataset](
 #' https://github.com/tdwg/camtrap-dp/tree/ad0278ef86ef518dacfb306c598dce97667cfb81/example)

diff --git a/R/get_n_individuals.R b/R/get_n_individuals.R
@@ -87,9 +87,8 @@ get_n_individuals <- function(package = NULL,
       if (length(species) > 1) {
         ignored_species <- species[!species == "all"]
         warning(glue::glue(
-          "Value `all` found in `species`.",
-          "All other values are ignored: {ignored_species*}.",
-          .transformer = collapse_transformer(sep = ", ", last = " and ")
+          "Value `all` found in `species`. All other values are ignored: ",
+          glue::glue_collapse(ignored_species, sep = ", ", last = " and ")
         ))
       }
       species <- get_species(package)$scientificName

diff --git a/R/get_n_obs.R b/R/get_n_obs.R
@@ -84,9 +84,8 @@ get_n_obs <- function(package = NULL,
       if (length(species) > 1) {
         ignored_species <- species[!species == "all"]
         warning(glue::glue(
-          "Value `all` found in `species`.",
-          "All other values are ignored: {ignored_species*}.",
-          .transformer = collapse_transformer(sep = ", ", last = " and ")
+          "Value `all` found in `species`. All other values are ignored: ",
+          glue::glue_collapse(ignored_species, sep = ", ", last = " and ")
         ))
       }
       species <- get_species(package)$scientificName

diff --git a/R/get_prefixes.R b/R/get_prefixes.R
@@ -3,7 +3,7 @@
 #' Stores prefixes for info shown while hovering over a deployment with the
 #' mouse.
 #' List fields in deployments as in
-#' <https://tdwg.github.io/camtrap-dp/data/#deployments>.
+#' <https://camtrap-dp.tdwg.org/data/#deployments>.
 #'
 #' Returns a data.frame of all prefixes with the following columns:
 #' - `info`: Deployment info.

diff --git a/R/map_dep.R b/R/map_dep.R
@@ -57,7 +57,7 @@
 #'   - `latitude`
 #'   - `longitude`
 #'
-#'   See the [Deployment](https://tdwg.github.io/camtrap-dp/data/#deployments)
+#'   See the [Deployment](https://camtrap-dp.tdwg.org/data/#deployments)
 #'   section of Camtrap DP for the full list of columns you can use.
 #' @param palette The palette name or the colour function that values will be
 #'   mapped to.
@@ -545,8 +545,8 @@ map_dep <- function(package = NULL,
     if (n_not_found_cols > 0) {
       warning(glue::glue(
         "Can't find {n_not_found_cols} columns defined in `hover_columns` in ",
-        "deployments: {not_found_cols*}",
-        .transformer = collapse_transformer(sep = ", ", last = " and ")
+        "deployments: ",
+        glue::glue_collapse(not_found_col, sep = ", ", last = " and ")
       ))
     }
   }

diff --git a/R/read_camtrap_dp.R b/R/read_camtrap_dp.R
@@ -1,7 +1,7 @@
 #' Read a Camtrap DP
 #'
 #' Reads files from a [Camera Trap Data Package](
-#' https://tdwg.github.io/camtrap-dp) into memory.
+#' https://camtrap-dp.tdwg.org) into memory.
 #' All datetime information is automatically transformed to Coordinated
 #' Universal Time (UTC).
 #' Vernacular names found in the metadata (`package$taxonomic`) are added to the
@@ -80,12 +80,12 @@ read_camtrap_dp <- function(file = NULL,
   package <- frictionless::read_package(file)
 
   # supported versions
-  supported_versions <- c("0.1.6", "1.0-rc.1")
+  supported_versions <- c("0.1.6", "1.0")
 
   # get package version
   profile <- package$profile
-  if (profile == "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0-rc.1/camtrap-dp-profile.json") {
-    version <- "1.0-rc.1"
+  if (profile == "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/camtrap-dp-profile.json") {
+    version <- "1.0"
   } else {
     if (profile == "https://raw.githubusercontent.com/tdwg/camtrap-dp/0.1.6/camtrap-dp-profile.json") {
       version <- "0.1.6"
@@ -97,13 +97,10 @@ read_camtrap_dp <- function(file = NULL,
   # check version is supported
   assertthat::assert_that(
     version %in% supported_versions,
-    msg = paste0(
-      glue::glue("Version {version} "), 
-      "is not supported. Supported versions: ",
-      glue::glue_collapse(glue::glue("{supported_versions}"), 
-                              sep = " ", 
-                              last = " and "),
-      ".")
+    msg = glue::glue(
+      "Version `{version}` is not supported. Supported versions: ",
+      glue::glue_collapse(supported_versions, sep = " ", last = " and ")
+    )
   )
 
   # get resource names
@@ -152,7 +149,7 @@ read_camtrap_dp <- function(file = NULL,
   package <- add_taxonomic_info(package)
 
   # convert to 0.1.6
-  if (version == "1.0-rc.1") {
+  if (version == "1.0") {
     package <- convert_to_0.1.6(package, version, media = media)
   }
 

diff --git a/R/read_wi.R b/R/read_wi.R
@@ -7,7 +7,7 @@
 #' [private](https://www.wildlifeinsights.org/get-started/download/private)
 #' download.
 #' The function transforms data and metadata to a [Camera Trap Data Package](
-#' https://tdwg.github.io/camtrap-dp) which can be written to file with
+#' https://camtrap-dp.tdwg.org) which can be written to file with
 #' [frictionless::write_package()].
 #'
 #' **The function has only been tested on image-based projects.**
@@ -61,7 +61,7 @@ read_wi <- function(directory = ".") {
   # Create package
   package <- frictionless::create_package() # Also sets profile, resources
 
-  # Set metadata properties, see https://tdwg.github.io/camtrap-dp/metadata
+  # Set metadata properties, see https://camtrap-dp.tdwg.org/metadata
   package$name <- basename(directory) # Unique name if unchanged from WI export zip
   package$id <- wi_project$ark_id # (e.g. http://n2t.net/ark:/63614/w12001317)
   package$created <- lubridate::format_ISO8601(lubridate::now())
@@ -229,7 +229,7 @@ read_wi <- function(directory = ".") {
     # packageID = ""
   )
 
-  # Create deployments, see https://tdwg.github.io/camtrap-dp/data/#deployments
+  # Create deployments, see https://camtrap-dp.tdwg.org/data/#deployments
   deployments <-
     wi_deployments %>%
     dplyr::left_join(wi_cameras, by = c("project_id", "camera_id")) %>%
@@ -298,7 +298,7 @@ read_wi <- function(directory = ".") {
       `_id` = NA_character_
     )
 
-  # Create media, see https://tdwg.github.io/camtrap-dp/data/#media
+  # Create media, see https://camtrap-dp.tdwg.org/data/#media
   media <-
     wi_images %>%
     dplyr::distinct(.data$location, .keep_all = TRUE) %>%
@@ -317,7 +317,7 @@ read_wi <- function(directory = ".") {
       `_id` = NA_character_
     )
 
-  # Create observations, see https://tdwg.github.io/camtrap-dp/data/#observations
+  # Create observations, see https://camtrap-dp.tdwg.org/data/#observations
   observations <-
     wi_images %>%
     dplyr::transmute(

diff --git a/R/write_dwc.R b/R/write_dwc.R
@@ -1,7 +1,7 @@
 #' Transform Camtrap DP data to Darwin Core
 #'
 #' Transforms data from a [Camera Trap Data Package](
-#' https://tdwg.github.io/camtrap-dp/) to [Darwin Core](https://dwc.tdwg.org/).
+#' https://camtrap-dp.tdwg.org) to [Darwin Core](https://dwc.tdwg.org/).
 #' The resulting CSV files can be uploaded to an [IPT](
 #' https://www.gbif.org/ipt) for publication to GBIF.
 #' A `meta.xml` file is included as well.

diff --git a/R/write_eml.R b/R/write_eml.R
@@ -1,9 +1,9 @@
 #' Transform Camtrap DP metadata to EML
 #'
 #' Transforms the metadata of a [Camera Trap Data Package](
-#' https://tdwg.github.io/camtrap-dp/) to an [EML](
-#' https://eml.ecoinformatics.org/) file that can be uploaded to a [GBIF IPT](
-#' https://www.gbif.org/ipt) for publication.
+#' https://camtrap-dp.tdwg.org) to an [EML](https://eml.ecoinformatics.org/) 
+#' file that can be uploaded to a [GBIF IPT](https://www.gbif.org/ipt) for 
+#' publication.
 #'
 #' @param package A Camtrap DP, as read by [read_camtrap_dp()].
 #' @param directory Path to local directory to write file to.