remove pfocal

LandSciTech · Jun 23, 2023 · 5603c66 · 5603c66
1 parent 5797c61
commit 5603c66
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Showing 3 changed files with 53 additions and 51 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -53,10 +53,7 @@ Suggests:
     rmarkdown,
     viridis,
     tmap,
-    bench,
-    pfocal
-Remotes: LandSciTech/pfocal
-Additional_repositories: https://LandSciTech.github.io/drat
+    bench
 VignetteBuilder: knitr
 Depends: R (>= 2.10)
 Collate: 

diff --git a/R/getDistFromSource.R b/R/getDistFromSource.R
@@ -37,8 +37,9 @@
 #'   of the CRS.
 #' @param kwidth Integer, for the "pfocal" and "terra" methods the width of the
 #' moving window. For the "pfocal2" method the aggregation factor.
-#' @param method Character, the method to use, one of "terra", "pfocal" or
-#'   "pfocal2". See below for details.
+#' @param method Character, the method to use, currently only "terra" supported
+# #' one of "terra", "pfocal" or
+# #'   "pfocal2". See below for details.
 #'
 #' @return A SpatRaster
 #' @export
@@ -75,38 +76,40 @@ getDistFromSource <- function(src, maxDist, kwidth = 3, method = "terra") {
     src <- terra::rast(src)
   }
   if(method == "pfocal2"){
-    if(!rlang::is_installed("pfocal")){
-      stop("The pfocal2 method requires the pfocal package. ",
-           "It can be installed with remotes::install_github('LandSciTech/pfocal')",
-           call. = FALSE)
-    }
-    src <- src > 0
-
-    # aggregate based on kwidth in a way that matches the moving window version
-    if(kwidth > 1){
-      src <- terra::aggregate(src, kwidth, fun = "max", na.rm = TRUE)
-    }
-    # convert maxDist to ncells
-    maxDist <- maxDist/terra::res(src)[1]
-
-    # make kernal for distance from center
-    kn <- pfocal::euclidean_distance_kernel(maxDist)
-    kn <- kn*terra::res(src)[1]
-
-
-    src2 <- terra::mask(src, src, maskvalues = 0, updatevalue = NA)
-    dist_src <- pfocal::pfocal(terra::as.matrix(src2, wide = TRUE), kernel = kn, edge_value = NA, na.rm = TRUE,
-                               reduce_function = "min")
-    dist_src <- terra::rast(src, vals = dist_src)
-    # min when all NA is Inf so need to convert to NA
-    dist_src <- terra::mask(dist_src, dist_src > (maxDist * terra::res(src2)[1]),
-                            maskvalues = 1, updatevalue = NA)
-
-    if(kwidth > 1){
-      dist_src <- terra::disagg(dist_src, fact = kwidth, method = "bilinear")
-    }
-
-    return(dist_src)
+    stop("method pfocal2 is only available with the development version of roads.", 
+         call. = FALSE)
+    # if(!rlang::is_installed("pfocal")){
+    #   stop("The pfocal2 method requires the pfocal package. ",
+    #        "It can be installed with remotes::install_github('LandSciTech/pfocal')",
+    #        call. = FALSE)
+    # }
+    # src <- src > 0
+    # 
+    # # aggregate based on kwidth in a way that matches the moving window version
+    # if(kwidth > 1){
+    #   src <- terra::aggregate(src, kwidth, fun = "max", na.rm = TRUE)
+    # }
+    # # convert maxDist to ncells
+    # maxDist <- maxDist/terra::res(src)[1]
+    # 
+    # # make kernal for distance from center
+    # kn <- pfocal::euclidean_distance_kernel(maxDist)
+    # kn <- kn*terra::res(src)[1]
+    # 
+    # 
+    # src2 <- terra::mask(src, src, maskvalues = 0, updatevalue = NA)
+    # dist_src <- pfocal::pfocal(terra::as.matrix(src2, wide = TRUE), kernel = kn, edge_value = NA, na.rm = TRUE,
+    #                            reduce_function = "min")
+    # dist_src <- terra::rast(src, vals = dist_src)
+    # # min when all NA is Inf so need to convert to NA
+    # dist_src <- terra::mask(dist_src, dist_src > (maxDist * terra::res(src2)[1]),
+    #                         maskvalues = 1, updatevalue = NA)
+    # 
+    # if(kwidth > 1){
+    #   dist_src <- terra::disagg(dist_src, fact = kwidth, method = "bilinear")
+    # }
+    # 
+    # return(dist_src)
   }
   src <- src > 0
   if (dissag) {
@@ -127,15 +130,17 @@ getDistFromSource <- function(src, maxDist, kwidth = 3, method = "terra") {
       ssD2 <- terra::focal(cPop, w = mm, fun = "sum", na.rm = TRUE)
       # ssD2 <- terra::init(cPop, fun = ssO2)
     } else if(method == "pfocal"){
-      if(!rlang::is_installed("pfocal")){
-        stop("The pfocal method requires the pfocal package. ",
-             "It can be installed with remotes::install_github('LandSciTech/pfocal')",
-             call. = FALSE)
-      }
-      ssO2 <- pfocal::pfocal(as.matrix(cPop, wide = TRUE), mm, reduce_function = "SUM",
-                             transform_function = "MULTIPLY")
-      ssD2 <- cPop
-      terra::values(ssD2) <- ssO2
+      stop("method pfocal is only available with the development version of roads.", 
+           call. = FALSE)
+      # if(!rlang::is_installed("pfocal")){
+      #   stop("The pfocal method requires the pfocal package. ",
+      #        "It can be installed with remotes::install_github('LandSciTech/pfocal')",
+      #        call. = FALSE)
+      # }
+      # ssO2 <- pfocal::pfocal(as.matrix(cPop, wide = TRUE), mm, reduce_function = "SUM",
+      #                        transform_function = "MULTIPLY")
+      # ssD2 <- cPop
+      # terra::values(ssD2) <- ssO2
     }
     # Add back 0s for existing roads
     ssD2 <- terra::mask(ssD2, dd, inverse = TRUE, updatevalue = 0)

diff --git a/tests/testthat/test-getDistFromSource.R b/tests/testthat/test-getDistFromSource.R
@@ -18,10 +18,10 @@ test_that("distance to roads has expected values", {
   maxDist <- 5
   fastRough <- getDistFromSource(src, maxDist, kwidth = 1)
   wideCircle <- getDistFromSource(src, maxDist, kwidth = 5)
-  if(requireNamespace("pfocal", quietly = TRUE)){
-    slowFine <- getDistFromSource(src, maxDist, kwidth = 1, method = "pfocal2")
-    smootherCircle <- getDistFromSource(src, maxDist, kwidth = 5, method = "pfocal2")
-  }
+  # if(requireNamespace("pfocal", quietly = TRUE)){
+  #   slowFine <- getDistFromSource(src, maxDist, kwidth = 1, method = "pfocal2")
+  #   smootherCircle <- getDistFromSource(src, maxDist, kwidth = 5, method = "pfocal2")
+  # }
 
   if(interactive()){
     res <- c(fastRough, slowFine, wideCircle, smootherCircle)