lulc drops

GAM pipeline analytics/Iceberg Dispersal.R

@@ -9,7 +9,7 @@ library(tidyverse)
 
 
 buffer2 <- function(r, dist) {
-  projR <- projectRaster(euras, crs=CRS("+proj=moll +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs"))
+  projR <- projectRaster(r, crs=CRS("+proj=moll +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs"))
   projRb <- raster::buffer(projR, dist)
   projRb <- projectRaster(projRb, crs=CRS("+proj=longlat +datum=WGS84"))
   projRb[!is.na(projRb)] <- 1

SDM pipeline analytics/lulcdrops.R

@@ -0,0 +1,88 @@
+library(ncdf4)
+library(raster)
+setwd("D:/ICEBERG")
+
+ncin <- nc_open("states.nc")
+
+get <- function(varname) {
+  soilm_array <- ncvar_get(ncin,varname,start=c(1,1,1166))
+  slice <- raster(t(soilm_array))
+  raster::extent(slice) <- c(-180,180,-90,90)
+  return(slice)
+}
+
+lutypes <- names(ncin$var)[1:12]
+
+landuse2017 <- stack(lapply(lutypes,get))
+names(landuse2017) <- lutypes
+landuse2017 <- (landuse2017>0)
+plot(landuse2017)
+
+###################################
+
+#IUCN grabber: run back half of iucn habitat
+#####################
+
+# 1. read in the list of species we're including
+setwd('C:/Users/cjcar/Dropbox/ViralChatter')
+spname <- gsub('_',' ',read.csv('FinalSpeciesList.csv')[,2])
+
+# 2. read in their habitat types document
+
+iucndat <- read.csv('Land cover data/IucnHabitatData.csv')
+LUHdat<-as.list(rep(NA,length(spname))) 
+convcodes <- read.csv('Land cover data/IUCN_LUH_conversion_table.csv')
+
+for (i in 1:length(LUHdat)){
+
+  #get iucn habitat codes for the species  
+  iucncodes<-iucndat[iucndat$name %in% spname[i],"code"]
+
+  if(length(iucncodes)==0) {
+    LUHdat[[i]]<-NULL
+    names(LUHdat)[[i]]<-as.character(spname[i])
+    next
+  }
+  #get matching LUH land use types  
+  LUH<-unique(convcodes$LUH[match(as.numeric(as.character(iucncodes)),convcodes$IUCN_hab)])
+
+  # when there is no match make LUH = NA
+  # A single NA value means the species lives only in IUCN categories that have no 
+  # mapping to LUH data (e.g., caves or ocean habitats)
+  suppressWarnings(if (is.na(LUH) & length(LUH)==1) {
+    LUHdat[[i]]<-NA
+    names(LUHdat)[[i]]<-as.character(spname[i])
+    next
+  })
+  # when there is a match    
+  LUHvector<-unlist(strsplit(as.character(LUH),".", fixed=TRUE))
+
+  LUHdat[[i]]<-LUHvector
+  names(LUHdat)[[i]]<-as.character(spname[i])
+}
+
+########################################################
+
+# 3. create a for loop
+
+noL.auto <- c()
+drop.marine <- c()
+
+#length(spname)
+for (i in 1:length(spname)) {
+  spnamei <- spname[i]
+  wdir <- paste('D:/ICEBERG/RawENMs/PPM/BinaryMaps/',
+                gsub(' ','_',spnamei),sep='')
+
+  if(length(list.files(wdir))==0) { next } else {
+    LUHi <- LUHdat[spnamei]
+    if (all(is.na(LUHi))) { 
+      noL.auto <- c(noL.auto, spnamei)
+    } else { 
+      LUHi[[1]] <- LUHi[[1]][!is.na(LUHi[[1]])]
+      if (all(LUHi[[1]]=='MARINE')) {
+            drop.marine <- c(drop.marine,spnamei)
+      } 
+    }
+  }
+}