Merge branch 'main' into 79-new-function-install-depricated-package

inbo · Oct 11, 2024 · 5dc78fc · 5dc78fc
2 parents 84f6ff0 + 26a9dd7
commit 5dc78fc
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diff --git a/.github/ISSUE_TEMPLATE/nieuwe-functie-aanmaken.md b/.github/ISSUE_TEMPLATE/nieuwe-functie-aanmaken.md
@@ -13,7 +13,8 @@ assignees: ''
 - [ ] list of the expected functionality
 
 ## Checklist
-- [ ] maak een nieuw R-bestand 
+- [ ] maak een nieuw R-bestand
+- [ ] vermijd `library("package")` en `require("package")` gebruik `package::function()` *of als het echt niet anders gaat `requirenamespace("package")`*
 - [ ] sla het R bestand op onder `./R` met filenaam is gelijk aan functienaam
 - [ ] voorzie een functie titel met `#'` op regel 1 van je script
 - [ ] voorzie een auteur met `#' @author`
@@ -26,9 +27,6 @@ assignees: ''
 - [ ] voer `roxygen2::roxygenise()` uit in de console
 - [ ] voer `devtools::check()` uit in de console
 - [ ] los eventuele errors, warnings en notes<sup>1</sup> op
-- [ ] increment versie dmv `usethis::use_version(which = "minor")`<sup>2</sup>
 - [ ] maak een pull request met @soriadelva of @SanderDevisscher en eventueel andere relevante gebruikers als reviewer.
 
 *<sup>1</sup>in de mate van het mogelijke*
-
-*<sup>2</sup>als je meer dan 5 functies en/of datasets in één pull request veranderd hebt gebruik: `usethis::use_version(which = "major")`*
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: fistools
 Title: Tools & data used for wildlife management & invasive species in Flanders
-Version: 1.2.8
+Version: 1.2.11
 Authors@R: c(
     person(given = "Sander", middle = "", family = "Devisscher", "sander.devisscher@inbo.be", 
       role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2015-5731")),
@@ -37,5 +37,4 @@ Imports:
     sp (>= 2.1.4),
     mapview (>= 2.11.2),
     osmdata (>= 0.2.5),
-    readr (>= 2.1.5),
-    RCurl (>= 1.98.1.16)
+    readr (>= 2.1.5)
diff --git a/NAMESPACE b/NAMESPACE
@@ -16,6 +16,7 @@ export(install_depricated)
 export(install_sp)
 export(label_converter)
 export(label_selecter)
+export(rename_ct_files)
 importClassesFrom(sp,CRS)
 importFrom(magrittr,"%>%")
 importFrom(sp,CRS)

diff --git a/R/CRS_extracter.R b/R/CRS_extracter.R
@@ -45,9 +45,9 @@
 CRS_extracter <- function(CRS,
                           EPSG = TRUE){
 
-  install_sp()
+  fistools::install_sp()
 
-  Lib_CRS <- lib_crs
+  Lib_CRS <- fistools::lib_crs
 
   if(grepl("wgs", CRS, ignore.case = TRUE)){
     CRS <- "WGS"

diff --git a/R/rename_ct_files.R b/R/rename_ct_files.R
@@ -0,0 +1,52 @@
+#' Rename camera trap files for upload in Agouti
+#'
+#' @author: Lynn Pallemaerts and Someone Before Her
+#'
+#' @description Function that rename camera trap files (i.e. photos) by
+#' appending folder name (e.g. 1000RECX) to file name (e.g. IMG0001) to create
+#' all unique file names across a deployment. Needed for deployments with more
+#' than 9999 pictures, so they can be uploaded in Agouti. This is a copy of the
+#' old `rename_file_names()` in the old `fis-projecten` (archived).
+#'
+#' @param foldername DCIM folder to be treated
+#' @param extensions file extensions to be rename. Default is jpg, jpeg, bmp and png
+#'
+#' @returns renamed picture files in the original folder
+#'
+#' @examples
+#' \dontrun{
+#' tempzip <- tempfile(fileext = ".zip")
+#' fistools::download_gdrive_if_missing(gfileID = "1-84hbKouLKGwnLgBSRaQO1BnfogoFZWz",
+#'                                      destfile = tempzip,
+#'                                      email = Sys.getenv("email"),
+#'                                      update_always = TRUE)
+#'
+#' foldername <- paste0(tempdir(), "/test_case_renaming")
+#' unzip(tempzip,
+#'       exdir = tempdir())
+#' rename_ct_files(foldername)
+#' browseURL(foldername)
+#' unlink(foldername,
+#'        recursive = TRUE)
+#'}
+#'
+#' @export
+
+rename_ct_files <- function(foldername,
+                            extensions = c("jpg", "png", "jpeg", "bmp")) {
+
+  # list all the files in the subfolders and prepare new file names
+  images <- dir(foldername, recursive = TRUE,  full.names = FALSE) %>%
+    as.data.frame(stringsAsFactors = FALSE) %>%
+    dplyr::select(filename = ".") %>%
+    dplyr::filter(grepl(paste0(extensions, collapse = "|"), tolower(filename))) %>%
+    dplyr::mutate(subfolder = dirname(filename)) %>%
+    dplyr::mutate(foldername = foldername) %>%
+    dplyr::mutate(new_filename = gsub("/", "_", filename)) %>%
+    dplyr::mutate(full_filename = as.character(file.path(foldername, filename))) %>%
+    dplyr::mutate(full_new_filename = as.character(file.path(foldername, subfolder, new_filename)))
+
+  # execute file renaming
+  file.rename(images$full_filename, images$full_new_filename)
+
+}
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
 pandoc: 2.9.2.1
-pkgdown: 2.1.0
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-09-04T17:33Z
+last_built: 2024-10-10T13:48Z
diff --git a/docs/reference/CRS_extracter.html b/docs/reference/CRS_extracter.html
diff --git a/docs/reference/UUID_List.html b/docs/reference/UUID_List.html
diff --git a/docs/reference/apply_grtsdb.html b/docs/reference/apply_grtsdb.html
diff --git a/docs/reference/boswachterijen.html b/docs/reference/boswachterijen.html
diff --git a/docs/reference/calculate_polygon_centroid.html b/docs/reference/calculate_polygon_centroid.html
diff --git a/docs/reference/check.html b/docs/reference/check.html
diff --git a/docs/reference/cleanup_sqlite.html b/docs/reference/cleanup_sqlite.html
diff --git a/docs/reference/col_content_compare.html b/docs/reference/col_content_compare.html