Update geo_filt.R

R/geo_filt.R

@@ -1,14 +1,33 @@
+#' Excludes occurrence points within a given geographic distance
+#'
+#' @inheritParams setup_sdmdata
+#' @param min_distance Numeric. Minimum distance between points in the unit of
+#' the predictor raster (most likely degrees). This value will be used to create a raster
+#' with a \code{min_distance} resolution, from which the redundant occurences
+#' will be excluded. 
+#' @return Data frame of the occurrence points thinned to have the minimum
+#' distance indicated in \code{min_distance} between them
+#' @author Diogo S. B. Rocha
+#' @references Varela, S., Anderson, R. P., García-Valdés, R., &
+#' Fernández-González, F. (2014). Environmental filters reduce the effects of
+#' sampling bias and improve predictions of ecological niche models.
+#' Ecography, 37(11), 1084-1091. doi:10.1111/j.1600-0587.2013.00441.x
+#' @seealso \code{\link[dismo]{gridSample}}
+#' @seealso \pkg{spThin}
+#'
+#' @importFrom dismo gridSample
 geo_filt <- function(occurrences,
                      lon = "lon",
                      lat = "lat",
-                     min_distance = 10) {
+                     min_distance = 1) {
+
     res <- min_distance
     r <- raster::raster(extent(range(occurrences[, lon]),
                                range(occurrences[, lat])) + res)
     res(r) <- res
     pts <- dismo::gridSample(occurrences, r, n = 1)
     message(paste0(dim(pts)[1],
                " Points remaining after the geographic filter of ",
-               min_distance, "km", "\n"))
+               min_distance, "degrees", "\n"))
     return(pts)
 }