Merge branch 'main' of https://github.com/inbo/mbag-bodem

LICENSE.md

@@ -1,6 +1,4 @@
-## creative commons
-
-# Attribution 4.0 International
+# Creative Commons Attribution 4.0 International
 
 Creative Commons Corporation (“Creative Commons”) is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses and related information available on an “as-is” basis. Creative Commons gives no warranties regarding its licenses, any material licensed under their terms and conditions, or any related information. Creative Commons disclaims all liability for damages resulting from their use to the fullest extent possible.
 

checklist.yml

@@ -18,3 +18,5 @@ spelling:
   other:
     en-GB:
       - source/r/geocomputations.R
+      - source/rmarkdown/analyses_diversity/test_breakaway_diversity.Rmd
+      - source/rmarkdown/compositional_analysis/test_rademu.Rmd

inst/en_gb.dic

@@ -0,0 +1,6 @@
+β
+Akker
+Mangiola
+modelmisspecification
+poisson
+sccomp

inst/nl_be.dic

@@ -1,36 +1,92 @@
+'by
 +/-
 -SNE
 .Rdata
+.txt
+18S
+18s
+@example
+AICc
 Achaeta
+Aitchinson
 Annelida
+Beta
 Cmon
+Dicranocentrus
+Entomobryidae
+Folsomia
+GRTS
+HPC
 Henlea
+Isotomidae
+Isotomurus
 Lumbricus
 MBAG
 Marionina
+Megalothorax
+Names
 OTU
 OTUs
 Ordinaties
+Protaphorura
 Rarefaction
+Scientific
+WestEurope
+archaea
+arthropoda
+ascomycota
+basidiomycota
+be
 beta-binomiaal
 bimodaliteit
 bodembiodiversiteit
 bodemkoolstofmeetnet
+bodemstaal
+bodemstaalnamelocaties
+can
 centered-log-ratio
+chytridiomycota
+collembola
+collineaire
 counts
 covariaat
 covariaten
 credibiliteitsinterval
 csv
+design'
 design-variabelen
+diversity
 eDNA
+from
+fysico-chemische
+fysicochemische
 gepaardheid
 intercept
 macro-invertebraten
+meso-
 metabarcoding
+metazoa
+mollusca
 multivariaat
+names
 natuurgrasland
+natuurgraslanden
+nematoda
+nematodenstalen
+nolint
+nulwaarnemingen
+ordinatieruimte
+ordinaties
 phyloseq
 phylum
+platyhelminthes
+presence
+randomisatieprocedure
 rarefaction
+rarefy
+read
 reads
+result
+sub-sampled
+tardigrada
+which

source/r/check_presence.R

@@ -1,5 +1,5 @@
 #' Deze functie gaat na of een soort volgens GBIF voorkomt in een gekozen set
-#' van landen
+#' van landen # nolint start
 #'
 #' Default zijn West-Europese landen ingesteld: België, Frankrijk, Duitsland,
 #' Luxemburg, Nederland, Zwitserland, Oostenrijk
@@ -10,7 +10,7 @@
 #'
 #' @example
 #' result_WestEurope <- check_presence_from_file()
-#' print(result_WestEurope)
+#' print(result_WestEurope) # nolint end
 check_presence <- function(
     input = NULL,
     countries = c("BE", "FR", "DE", "LU", "NL", "CH", "AT")) {
@@ -35,20 +35,23 @@ check_presence <- function(
   for (country in countries) {
     # Function to check occurrence data and handle errors
     check_occurrence <- function(name) {
-      data <- tryCatch({
-        rgbif::occ_data(
-          scientificName = name,
-          country = country,  # Specify one country at a time
-          limit = 1
-        )
-      }, error = function(e) {
-        return(list(error = TRUE))
-      })
+      data <- tryCatch(
+        {
+          rgbif::occ_data(
+            scientificName = name,
+            country = country, # Specify one country at a time
+            limit = 1
+          )
+        },
+        error = function(e) {
+          return(list(error = TRUE))
+        }
+      )
 
       if (inherits(data, "error") || is.null(data$data)) {
-        return(FALSE)  # Occurrence data is not present or error occurred
+        return(FALSE) # Occurrence data is not present or error occurred
       } else {
-        return(TRUE)   # Occurrence data is present
+        return(TRUE) # Occurrence data is present
       }
     }
 

source/r/geocomputations.R

@@ -10,11 +10,13 @@
 #'
 #' @examples
 point_to_gridcell <- function(
-  xy,
-  cell_width_m = 500,
-  point_position = c("center", "lowerleft", "upperleft", "lowerright",
-                     "upperright"),
-  crs = 31370) {
+    xy,
+    cell_width_m = 500,
+    point_position = c(
+      "center", "lowerleft", "upperleft", "lowerright",
+      "upperright"
+    ),
+    crs = 31370) {
   point_position <- match.arg(point_position)
 
   if (point_position != "center") stop(point_position, " not yet implemented")
@@ -24,13 +26,15 @@ point_to_gridcell <- function(
   xy <- sf::st_geometry(xy)
 
   # buffer with 1 point per quandrant
-  xy_buffer <- sf::st_buffer(x = xy,
-                             dist = cell_width_m / 2,
-                             nQuadSegs = 1)
+  xy_buffer <- sf::st_buffer(
+    x = xy,
+    dist = cell_width_m / 2,
+    nQuadSegs = 1
+  )
 
   # rotate 45 degrees around centroid
   rot <- function(a) matrix(c(cos(a), sin(a), -sin(a), cos(a)), 2, 2)
-  pl <- (xy_buffer - xy) * rot(pi/4) + xy
+  pl <- (xy_buffer - xy) * rot(pi / 4) + xy
   pl <- sf::st_sf(data.frame(xy_df, pl), crs = crs)
   return(pl)
 }
@@ -51,23 +55,24 @@ point_to_gridcell <- function(
 #'
 #' @examples
 landusemetrics_grid_cell <- function(
-  grid_cell,
-  layer,
-  grid_group_by_col = "POINT_ID",
-  layer_group_by_col = "",
-  progress = FALSE
-) {
+    grid_cell,
+    layer,
+    grid_group_by_col = "POINT_ID",
+    layer_group_by_col = "",
+    progress = FALSE) {
   require(duckdb)
-  if (inherits(layer, "SpatRaster") | inherits(layer, "RasterLayer")) {
+  require(dplyr)
+  if (inherits(layer, "SpatRaster") || inherits(layer, "RasterLayer")) {
     crs_grid <- gsub("^((.*?),\\n\\s*?){2}", "", sf::st_crs(grid_cell)$wkt)
     crs_layer <- gsub("^((.*?),\\n\\s*?){2}", "", terra::crs(layer))
     assertthat::assert_that(crs_grid == crs_layer)
 
     landcoverfraction <- function(df) {
       df %>%
-        mutate(frac_total = coverage_fraction / sum(coverage_fraction)) %>%
-        group_by(!!!syms(grid_group_by_col), value) %>%
-        summarize(freq = sum(frac_total), .groups = "drop_last")
+        mutate(frac_total = .data$coverage_fraction /
+          sum(.data$coverage_fraction)) %>%
+        group_by(!!!syms(grid_group_by_col), .data$value) %>%
+        summarize(freq = sum(.data$frac_total), .groups = "drop_last")
     }
 
     res <- exactextractr::exact_extract(
@@ -76,20 +81,20 @@ landusemetrics_grid_cell <- function(
       fun = landcoverfraction,
       summarize_df = TRUE,
       include_cols = grid_group_by_col,
-      progress = progress)
+      progress = progress
+    )
 
     return(res)
-
   }
 
   if (inherits(layer, "sf")) {
     assertthat::assert_that(sf::st_crs(grid_cell)$wkt == sf::st_crs(layer)$wkt)
 
-    int <- st_intersection(layer, grid_cell)
+    int <- sf::st_intersection(layer, grid_cell)
 
     cell_areas <- grid_cell %>%
       select(!!!syms(grid_group_by_col)) %>%
-      mutate(cell_area = sf::st_area(geometry)) %>%
+      mutate(cell_area = sf::st_area(.data$geometry)) %>%
       sf::st_drop_geometry()
 
     temparrow <- tempfile(fileext = ".parquet")
@@ -102,14 +107,15 @@ landusemetrics_grid_cell <- function(
 
     int <- arrow::open_dataset(temparrow) %>%
       arrow::to_duckdb() %>%
-      group_by(!!!syms(grid_group_by_col),
-               !!!syms(layer_group_by_col),
-               cell_area) %>%
-      summarise(area_m2 = sum(area)) %>%
-      mutate(area_prop = area_m2 / cell_area) %>%
+      group_by(
+        !!!syms(grid_group_by_col),
+        !!!syms(layer_group_by_col),
+        .data$cell_area
+      ) %>%
+      summarise(area_m2 = sum(.data$area)) %>%
+      mutate(area_prop = .data$area_m2 / .data$cell_area) %>%
       collect()
 
     return(int)
   }
 }
-