Merge remote-tracking branch 'origin/development' into development

ianmseddy · Nov 15, 2018 · 54c4145 · 54c4145
2 parents eeaf530 + 80c619e
commit 54c4145
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Showing 3 changed files with 16 additions and 16 deletions.
diff --git a/Boreal_LBMRDataPrep.R b/Boreal_LBMRDataPrep.R
@@ -453,7 +453,7 @@ Save <- function(sim) {
                             targetFile = asPath(basename(biomassMapFilename)),
                             archive = asPath(c("kNN-StructureBiomass.tar",
                                                "NFI_MODIS250m_kNN_Structure_Biomass_TotalLiveAboveGround_v0.zip")),
-                            #url = extractURL("biomassMap"),
+                            url = extractURL("biomassMap"),
                             destinationPath = dPath,
                             studyArea = sim$shpStudyArea,
                             rasterToMatch = sim$rasterToMatch,

diff --git a/R/initialCommunityProducer.R b/R/initialCommunityProducer.R
@@ -1,13 +1,13 @@
 initialCommunityProducer <- function(speciesLayers, speciesPresence, studyArea, rstStudyArea) {
-  specieslayerInStudyArea <- crop(speciesLayers, studyArea)
+  specieslayerInStudyArea <- crop(speciesLayers, studyArea)  ## TODO: Ceres: this is probably no longer necessary
   #if(isTRUE(tryCatch(getCluster(), error=function(x) TRUE, silent=TRUE))) beginCluster()
-  specieslayerInStudyArea <- specieslayerInStudyArea * rstStudyArea
-  names(specieslayerInStudyArea) <- names(speciesLayers)
+  specieslayerInStudyArea <- specieslayerInStudyArea * rstStudyArea  ## TODO: Ceres: this is probably no longer necessary
+  names(specieslayerInStudyArea) <- names(speciesLayers)  ## TODO: Ceres: this is probably no longer necessary
 
   #specieslayerInStudyArea <- specieslayerInStudyArea*(!is.na(rstStudyArea))
   # specieslayerInStudyArea <- suppressWarnings(fastMask(specieslayerInStudyArea, #                                                  studyArea))
-  speciesNames <- names(specieslayerInStudyArea)[which(maxValue(specieslayerInStudyArea) >= speciesPresence)]
-  specieslayerBySpecies <- raster::subset(specieslayerInStudyArea, speciesNames[1])
+  speciesNames <- names(specieslayerInStudyArea)[which(maxValue(specieslayerInStudyArea) >= speciesPresence)]   ## TODO: Ceres: this is probably no longer necessary
+  specieslayerBySpecies <- raster::subset(specieslayerInStudyArea, speciesNames[1])    ## TODO: Ceres: this is probably no longer necessary
   specieslayerBySpecies[which(is.na(specieslayerBySpecies[]) & specieslayerBySpecies[] <= 5)] <- 0    ##  Ceres: this is weird, shouldn't this be OR?
   # specieslayerBySpecies[Which(is.na(specieslayerBySpecies) & specieslayerBySpecies<=5,
   #                             cells = TRUE)] <- 0 # 5% or less presence removed

diff --git a/R/loadkNNSpeciesLayers.R b/R/loadkNNSpeciesLayers.R
@@ -2,7 +2,7 @@
 ## Function to load kNN species layers from online data repository
 ## ------------------------------------------------------------------
 
-## dataPath: directory to data folder
+## dPath: directory to data folder
 ## rasterToMatch: passed to prepInputs
 ## studyArea: passed to prepInputs
 ## species is either a character vector of species names to download,
@@ -12,7 +12,7 @@
 ##    Defaults to 1
 ## url: is the source url for the data, passed to prepInputs.
 
-loadkNNSpeciesLayers <- function(dataPath, rasterToMatch, studyArea,
+loadkNNSpeciesLayers <- function(dPath, rasterToMatch, studyArea,
                                  speciesList = NULL, thresh = 1, url, cachePath, ...) {
 
 
@@ -38,20 +38,20 @@ loadkNNSpeciesLayers <- function(dataPath, rasterToMatch, studyArea,
 
   species1 <- Cache(loadFun, url = url, spp = speciesList, #[, "speciesNamesRaw"],
                     #loadFun,
-                    dataPath = dataPath,
+                    dPath = dPath,
                     suffix = suffix,
                     studyArea = studyArea, rasterToMatch = rasterToMatch,
                     userTags = "kNN_SppLoad")
   # species1 <- Cache(lapply, seq_len(NROW(speciesList)),
   #                   spp = speciesList, #[, "speciesNamesRaw"],
-  #                   loadFun, url = url, dataPath = dataPath,
+  #                   loadFun, url = url, dPath = dPath,
   #                   suffix = suffix,
   #                   studyArea = studyArea, rasterToMatch = rasterToMatch,
   #                   userTags = "kNN_SppLoad")
 
   ## get all kNN species
   if (FALSE) { #TODO This no longer does all species }
-    allSpp <- Cache(untar, tarfile = file.path(dataPath, "kNN-Species.tar"), list = TRUE)
+    allSpp <- Cache(untar, tarfile = file.path(dPath, "kNN-Species.tar"), list = TRUE)
     allSpp <- allSpp %>%
       grep(".zip", ., value = TRUE) %>%
       sub("_v0.zip", "", .) %>%
@@ -83,7 +83,7 @@ loadkNNSpeciesLayers <- function(dataPath, rasterToMatch, studyArea,
       sumSpecies <- spp2sum[[i]]
       newLayerName <- names(spp2sum)[i]
 
-      fname <- .suffix(file.path(dataPath, paste0("KNN", newLayerName, ".tif")), suffix)
+      fname <- .suffix(file.path(dPath, paste0("KNN", newLayerName, ".tif")), suffix)
       a <- Cache(sumRastersBySpecies,
                  speciesLayers = species1[sumSpecies],
                  newLayerName = newLayerName,
@@ -135,7 +135,7 @@ sumRastersBySpecies <- function(speciesLayers, layersToSum,
   ras_out # Work around for Cache
 }
 
-loadFun <- function(speciesListIndex, spp, suffix, url, dataPath,
+loadFun <- function(speciesListIndex, spp, suffix, url, dPath,
                     studyArea, rasterToMatch) {
 
   if (is.null(spp)) {
@@ -173,7 +173,7 @@ loadFun <- function(speciesListIndex, spp, suffix, url, dataPath,
       targetFile = targetFile,
       url = url,
       archive = archive,
-      destinationPath = asPath(dataPath),
+      destinationPath = asPath(dPath),
       fun = "raster::raster")#,
       #studyArea = studyArea,
       #rasterToMatch = rasterToMatch,
@@ -203,7 +203,7 @@ loadFun <- function(speciesListIndex, spp, suffix, url, dataPath,
   species1 <- Map(targetFile = targetFiles, archive = archives,
                   filename2 = postProcessedFilenames,
                   MoreArgs = list(url = url,
-                                  destinationPath = asPath(dataPath),
+                                  destinationPath = asPath(dPath),
                                   fun = "raster::raster",
                                   studyArea = studyArea,
                                   rasterToMatch = rasterToMatch,
@@ -216,7 +216,7 @@ loadFun <- function(speciesListIndex, spp, suffix, url, dataPath,
   #   targetFile = targetFile,
   #   url = url,
   #   archive = archive,
-  #   destinationPath = asPath(dataPath),
+  #   destinationPath = asPath(dPath),
   #   fun = "raster::raster",
   #   studyArea = studyArea,
   #   rasterToMatch = rasterToMatch,