rm browser

ianmseddy · Oct 22, 2018 · 084cc90 · 084cc90
1 parent 6b63623
commit 084cc90
Showing 1 changed file with 25 additions and 27 deletions.
diff --git a/R/loadkNNSpeciesLayers.R b/R/loadkNNSpeciesLayers.R
@@ -35,15 +35,13 @@ loadkNNSpeciesLayers <- function(dataPath, rasterToMatch, studyArea,
   })
   kNNnames <- sapply(kNNnames, function(x) paste(x, collapse = "_"))
   speciesList[, 1] <- kNNnames
-  
+
   species1 <- Cache(loadFun, url = url, spp = speciesList, #[, "speciesNamesRaw"],
                     #loadFun,
                     dataPath = dataPath,
                     suffix = suffix,
                     studyArea = studyArea, rasterToMatch = rasterToMatch,
                     userTags = "kNN_SppLoad")
-  browser()
-
   # species1 <- Cache(lapply, seq_len(NROW(speciesList)),
   #                   spp = speciesList, #[, "speciesNamesRaw"],
   #                   loadFun, url = url, dataPath = dataPath,
@@ -58,8 +56,8 @@ loadkNNSpeciesLayers <- function(dataPath, rasterToMatch, studyArea,
       grep(".zip", ., value = TRUE) %>%
       sub("_v0.zip", "", .) %>%
       sub(".*Species_", "", .)
-    
-    
+
+
     ## check for missing species
     if(any(!speciesList[,1] %in% allSpp)) {
       warning("Some species not present in kNN database.
@@ -141,25 +139,25 @@ loadFun <- function(speciesListIndex, spp, suffix, url, dataPath,
                     studyArea, rasterToMatch) {
 
   if (is.null(spp)) {
-    knownSp <- c("Abie_Ama", "Abie_Bal", "Abie_Gra", "Abie_Las", "Abie_Spp", 
-                 "Acer_Cir", "Acer_Mac", "Acer_Neg", "Acer_Pen", "Acer_Rub", "Acer_Sac", 
-                 "Acer_Sah", "Acer_Spi", "Acer_Spp", "Alnu_Inc_Rug", "Alnu_Inc_Ten", 
-                 "Alnu_Inc", "Alnu_Rub", "Alnu_Spp", "Arbu_Men", "Asim_Tri", "Betu_All", 
-                 "Betu_Pap", "Betu_Pop", "Betu_Spp", "Carp_Car", "Cary_Cor", "Cast_Den", 
-                 "Cham_Noo", "Crat_Spp", "Fagu_Gra", "Frax_Ame", "Frax_Nig", "Frax_Pen_Sub", 
-                 "Frax_Pen", "Frax_Spp", "Generic_BroadLeaf_Spp", "Generic_NeedleLeaf_Spp", 
-                 "Gled_Tri", "Jugl_Cin", "Jugl_Nig", "Juni_Vir", "Lari_Kae", "Lari_Lar", 
-                 "Lari_Lya", "Lari_Occ", "Lari_Spp", "Malu_Fus", "Malu_Spp", "Ostr_Vir", 
-                 "Pice_Abi", "Pice_Eng_Gla", "Pice_Eng", "Pice_Gla", "Pice_Mar", 
-                 "Pice_Rub", "Pice_Sit", "Pice_Spp", "Pinu_Alb", "Pinu_Ban", "Pinu_Con_Lat", 
-                 "Pinu_Con", "Pinu_Fle", "Pinu_Mon", "Pinu_Pon", "Pinu_Res", "Pinu_Rig", 
-                 "Pinu_Spp", "Pinu_Str", "Pinu_Syl", "Plat_Occ", "Popu_Bal", "Popu_Del", 
-                 "Popu_Gra", "Popu_Spp", "Popu_Tre", "Popu_Tri", "Prun_Pen", "Prun_Ser", 
-                 "Prun_Vir", "Pseu_Men_Gla", "Pseu_Men_Men", "Pseu_Men", "Quer_Alb", 
-                 "Quer_Bic", "Quer_Gar", "Quer_Mac", "Quer_Rub", "Robi_Pse", "Sali_Beb", 
-                 "Sali_Nig", "Sali_Spp", "Sass_Alb", "Sorb_Ame", "Sorb_Dec", "Sorb_Spp", 
-                 "Thuj_Occ", "Thuj_Pli", "Thuj_Spp", "Tili_Ame", "Tsug_Can", "Tsug_Het", 
-                 "Tsug_Mer_Het", "Tsug_Mer", "Tsug_Spp", "Ulmu_Ame", "Ulmu_Rub", 
+    knownSp <- c("Abie_Ama", "Abie_Bal", "Abie_Gra", "Abie_Las", "Abie_Spp",
+                 "Acer_Cir", "Acer_Mac", "Acer_Neg", "Acer_Pen", "Acer_Rub", "Acer_Sac",
+                 "Acer_Sah", "Acer_Spi", "Acer_Spp", "Alnu_Inc_Rug", "Alnu_Inc_Ten",
+                 "Alnu_Inc", "Alnu_Rub", "Alnu_Spp", "Arbu_Men", "Asim_Tri", "Betu_All",
+                 "Betu_Pap", "Betu_Pop", "Betu_Spp", "Carp_Car", "Cary_Cor", "Cast_Den",
+                 "Cham_Noo", "Crat_Spp", "Fagu_Gra", "Frax_Ame", "Frax_Nig", "Frax_Pen_Sub",
+                 "Frax_Pen", "Frax_Spp", "Generic_BroadLeaf_Spp", "Generic_NeedleLeaf_Spp",
+                 "Gled_Tri", "Jugl_Cin", "Jugl_Nig", "Juni_Vir", "Lari_Kae", "Lari_Lar",
+                 "Lari_Lya", "Lari_Occ", "Lari_Spp", "Malu_Fus", "Malu_Spp", "Ostr_Vir",
+                 "Pice_Abi", "Pice_Eng_Gla", "Pice_Eng", "Pice_Gla", "Pice_Mar",
+                 "Pice_Rub", "Pice_Sit", "Pice_Spp", "Pinu_Alb", "Pinu_Ban", "Pinu_Con_Lat",
+                 "Pinu_Con", "Pinu_Fle", "Pinu_Mon", "Pinu_Pon", "Pinu_Res", "Pinu_Rig",
+                 "Pinu_Spp", "Pinu_Str", "Pinu_Syl", "Plat_Occ", "Popu_Bal", "Popu_Del",
+                 "Popu_Gra", "Popu_Spp", "Popu_Tre", "Popu_Tri", "Prun_Pen", "Prun_Ser",
+                 "Prun_Vir", "Pseu_Men_Gla", "Pseu_Men_Men", "Pseu_Men", "Quer_Alb",
+                 "Quer_Bic", "Quer_Gar", "Quer_Mac", "Quer_Rub", "Robi_Pse", "Sali_Beb",
+                 "Sali_Nig", "Sali_Spp", "Sass_Alb", "Sorb_Ame", "Sorb_Dec", "Sorb_Spp",
+                 "Thuj_Occ", "Thuj_Pli", "Thuj_Spp", "Tili_Ame", "Tsug_Can", "Tsug_Het",
+                 "Tsug_Mer_Het", "Tsug_Mer", "Tsug_Spp", "Ulmu_Ame", "Ulmu_Rub",
                  "Ulmu_Spp", "Ulmu_Tho")
     stop("This loadFun has not been tested for all species. Please specify the actual species desired by name",
          " Known species are:\n", paste(knownSp, collapse = "\n"))
@@ -169,7 +167,7 @@ loadFun <- function(speciesListIndex, spp, suffix, url, dataPath,
   if (is.null(spp)) {
       ## set to NULL so prepInputs extracts all of them
     targetFile <- NULL
-    
+
     # just get tar file, no crop/reproject etc. Too many
     tarFile <- prepInputs(
       targetFile = targetFile,
@@ -200,7 +198,7 @@ loadFun <- function(speciesListIndex, spp, suffix, url, dataPath,
   } else stop("species must be a character vector or a two-column matrix")
 
   postProcessedFilenames <- .suffix(targetFiles, suffix = suffix)
-  
+
 
   species1 <- Map(targetFile = targetFiles, archive = archives,
                   filename2 = postProcessedFilenames,
@@ -213,7 +211,7 @@ loadFun <- function(speciesListIndex, spp, suffix, url, dataPath,
                                   datatype = "INT2U"
                   ),
                   prepInputs)
-  
+
   # species1 <- prepInputs(
   #   targetFile = targetFile,
   #   url = url,