Merge pull request #371 from sjevelazco/occfilt_geo

new argument in occfilt_geo
sjevelazco · Mar 13, 2024 · ee82c89 · ee82c89
2 parents 6be53e3 + 5af7e80
commit ee82c89
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Showing 8 changed files with 61 additions and 31 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# flexsdm 1.3.5
+
+-   occfilt_geo has a new argument "rep" to control number o repetition to filter occurrences
+
 # flexsdm 1.3.4
 
 -   rgeos was removed from dependencies [#356](https://github.com/sjevelazco/flexsdm/pull/356)

diff --git a/R/occfilt_geo.R b/R/occfilt_geo.R
@@ -23,6 +23,7 @@
 #' }
 #' @param prj character. Projection string (PROJ4) for occurrences. Not necessary if
 #' the projection used is WGS84 ("+proj=longlat +datum=WGS84"). Default "+proj=longlat +datum=WGS84"
+#' @param reps integer. Number of times to repeat the thinning process. Default 20
 #'
 #' @return
 #' A tibble object with data filtered geographically
@@ -127,7 +128,7 @@
 #'
 #' @seealso \code{\link{occfilt_env}}
 #'
-occfilt_geo <- function(data, x, y, env_layer, method, prj = "+proj=longlat +datum=WGS84") {
+occfilt_geo <- function(data, x, y, env_layer, method, prj = "+proj=longlat +datum=WGS84", reps = 20) {
   da <- data0 <- data
   rm(data)
   da <- da[c(x, y)]
@@ -223,7 +224,7 @@ occfilt_geo <- function(data, x, y, env_layer, method, prj = "+proj=longlat +dat
           long.col = x,
           spec.col = ".spp",
           thin.par = d,
-          reps = 20,
+          reps = reps,
           write.files = FALSE,
           locs.thinned.list.return = TRUE,
           write.log.file = FALSE
@@ -263,7 +264,7 @@ occfilt_geo <- function(data, x, y, env_layer, method, prj = "+proj=longlat +dat
           long.col = x,
           spec.col = ".spp",
           thin.par = distance,
-          reps = 20,
+          reps = reps,
           write.files = FALSE,
           locs.thinned.list.return = TRUE,
           write.log.file = FALSE
@@ -294,7 +295,7 @@ occfilt_geo <- function(data, x, y, env_layer, method, prj = "+proj=longlat +dat
           long.col = x,
           spec.col = ".spp",
           thin.par = as.numeric(method["d"]),
-          reps = 20,
+          reps = reps,
           write.files = FALSE,
           locs.thinned.list.return = TRUE,
           write.log.file = FALSE

diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -8,7 +8,7 @@ articles:
   v04_Red_fir_example: v04_Red_fir_example.html
   v05_Rare_species_example: v05_Rare_species_example.html
   v06_Extrapolation_example: v06_Extrapolation_example.html
-last_built: 2024-01-16T20:03Z
+last_built: 2024-03-13T13:14Z
 urls:
   reference: https://sjevelazco.github.io/flexsdm/reference
   article: https://sjevelazco.github.io/flexsdm/articles

diff --git a/docs/reference/env_outliers.html b/docs/reference/env_outliers.html