Merge pull request #22 from mapme-initiative/20-reconsider-using-dot-…

…in-front-of-asset-ids

rename .assetid to assetid

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mapme.biodiversity
 Title: Efficient Monitoring of Global Biodiversity Portfolios
-Version: 0.0.1
+Version: 0.1.0
 Authors@R: c(
     person("Darius A.", "Görgen", , "darius2402@web.de", role = c("aut", "cre")),
     person("Om Prakash", "Bhandari", role = "aut")

NEWS.md

@@ -1,5 +1,27 @@
+# mapme.biodiversity (development version)
+
+## Breaking changes
+
+## New features
+
+## Internal
+
+# mapme.biodiversity 0.1.0
+
+## Breaking changes
+* renamed '.assetid' to 'assetid' (#22)
+
+## New features
+* None
+
+## Internal
+* ensured that tests and examples adhere to CRAN policies of
+only writing to the temporal directory (#22)
+
 # mapme.biodiversity 0.0.1
 
+## Initial release
+
 * Added a `NEWS.md` file to track changes to the package.
 * initial supported resources are:
   - ecoregions
@@ -45,6 +67,8 @@
 * on MacOS, the s2 engine for spherical geometric vector operations is disabled and
   lwgeom is used instead.
 
-* Introduced absolute URLS in userguide.Rmd pointing to the online documentation (#58)
-* \value tags added to all exported functions explaining what is the output/sideffect (#58)
+## Internal
+
+* Introduced absolute URLS in userguide.Rmd pointing to the online documentation (#59)
+* \value tags added to all exported functions explaining what is the output/sideffect (#59)
 * using requireNamespace() instead of installed.packages() to check if packages listed in SUGGEST are loadable (#58)

R/calc_accessibility.R

@@ -23,12 +23,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2022,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_biome.R

@@ -14,12 +14,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2001,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_chirpsprec.R

@@ -28,12 +28,20 @@
 #' if(Sys.getenv("NOT_CRAN") == "true"){
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2010,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     cores = 1,
 #'     verbose = FALSE
 #'   ) %>%

R/calc_drought_indicator.R

@@ -23,12 +23,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2022,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_elevation.R

@@ -22,12 +22,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2000:2020,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_emissions.R

@@ -23,12 +23,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2016:2017,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_gmw.R

@@ -14,14 +14,22 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "shell_beach_protected_area_41057_B.gpkg",
 #'   package = "mapme.biodiversity"
 #' ) %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = c(1996, 2016),
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_landcover.R

@@ -16,12 +16,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2016:2017,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_popcount.R

@@ -25,12 +25,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2000:2010,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_soilproperties.R

@@ -26,12 +26,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2022,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_teow.R

@@ -14,12 +14,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2001,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_treecover.R

@@ -21,12 +21,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2016:2017,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_treeloss.R

@@ -23,12 +23,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2016:2017,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_tri.R

@@ -35,12 +35,20 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2000:2020,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE

R/calc_wcprec.R

@@ -22,12 +22,21 @@
 #' @examples
 #' library(sf)
 #' library(mapme.biodiversity)
+#'
+#' temp_loc <- file.path(tempdir(), "mapme.biodiversity")
+#' if(!file.exists(temp_loc)){
+#' dir.create(temp_loc)
+#' resource_dir <- system.file("res", package = "mapme.biodiversity")
+#' file.copy(resource_dir, temp_loc, recursive = TRUE)
+#' }
+#'
+#'
 #' (aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg", package = "mapme.biodiversity") %>%
 #'   read_sf() %>%
 #'   init_portfolio(
 #'     years = 2018,
-#'     outdir = system.file("res", package = "mapme.biodiversity"),
-#'     tmpdir = system.file("tmp", package = "mapme.biodiversity"),
+#'     outdir = file.path(temp_loc, "res"),
+#'     tmpdir = tempdir(),
 #'     add_resources = FALSE,
 #'     cores = 1,
 #'     verbose = FALSE