diff --git a/R/loadkNNSpeciesLayers.R b/R/loadkNNSpeciesLayers.R index c44be84..8be485d 100644 --- 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,