Added bash wrapper to main script. Fix bug which prevented the GBIF_*...

Added bash wrapper to main script. Fix bug which prevented the GBIF_* environmental variabled from being used.

R/downloadOccupancyData.R

@@ -42,8 +42,8 @@
 #' @export
 #'
 downloadOccupancyData <- function(speciesIDs, outFolder = paste(tempdir(), "occData", sep = "/"),
-	yearLimits = c(1960, Inf), GBIFUsername = Sys.getenv("GBIFUser", unset = NA),
-	GBIFPassword = Sys.getenv("GBIFPass", unset = NA), GBIFEmail = Sys.getenv("GBIFEmail", unset = NA),
+	yearLimits = c(1960, Inf), GBIFUsername = Sys.getenv("GBIF_USER", unset = NA),
+	GBIFPassword = Sys.getenv("GBIF_PWD", unset = NA), GBIFEmail = Sys.getenv("GBIF_EMAIL", unset = NA),
 	GBIFAttemptTime = 1800, maxGBIFTime = 14400, templateGrid=NULL) {
 	### 1.1 ==== Sanity check the function inputs ====
 	# Set the GBIF projection information
@@ -126,11 +126,12 @@ downloadOccupancyData <- function(speciesIDs, outFolder = paste(tempdir(), "occD
 	
 	### 1.2 ==== Create GBIF credentials ====
 	# Sanity check the GBIF username and password
+  
 	gbifCredentials <- tryCatch(c(
 		as.character(GBIFUsername),
 		as.character(GBIFPassword),
 		as.character(GBIFEmail)), error = function(err) {
-		stop(paste("invalid entry for the GBIF credentials:", err, sep = " "))
+      stop(paste("invalid entry for the GBIF credentials:", err, sep = " "))
 	})
 	if(length(gbifCredentials) != 3) {
 		stop("invalid entry for the GBIF credentials: username, password, and email must have a length of 1")

R/writeDistributionModelOutput.R

@@ -38,7 +38,7 @@ writeDistributionModelOutput <- function(fullOutputLoc, speciesInfo, climateData
     modelPredictions <- as.data.frame(savedModelOutput$spatialPredictions)
     curResponseCurve <- savedModelOutput$responsePredictions
     inlaLogMessages <- savedModelOutput$modelObject$logfile
-    inlaModelSummary <- summary(savedModelOutput$modelObject$logfile) 
+    inlaModelSummary <- summary(savedModelOutput$modelObject) 
     rm(savedModelOutput)
         
 		# Create response curve plots
@@ -88,10 +88,14 @@ writeDistributionModelOutput <- function(fullOutputLoc, speciesInfo, climateData
     modelPredictionsGrob <- ggplot(modelPredictions, aes(x=meanClimatePred, y=meanSpatialPred)) +
       geom_point(alpha=0.33, size=0.25) +
       geom_rangeframe() +
+      geom_abline(intercept = INLA::inla.link.logit(0.1), slope =-1, size=0.25, color='#f7fcb9') +
+      geom_abline(intercept = INLA::inla.link.logit(0.5), slope =-1, size=0.25, color='#addd8e') +
+      geom_abline(intercept = INLA::inla.link.logit(0.9), slope =-1, size=0.25, color='#31a354') +
       theme_tufte()
-    svg(paste(fullOutputLocSp,"/", "diagnostics_effectdepend", ".svg", sep = ""), width = 5, height = 5)
-    grid.draw(modelPredictionsGrob)
-    dev.off()
+    ggsave(paste( fullOutputLocSp,"/", "diagnostics_effectdepend", ".png", sep = ""),width = 5, height = 5)
+    # svg(paste(fullOutputLocSp,"/", "diagnostics_effectdepend", ".svg", sep = ""), width = 5, height = 5)
+    #grid.draw(modelPredictionsGrob)
+    #dev.off()
 
     sink(paste(fullOutputLocSp, "inla_logfile.txt", sep="/"))
     print(inlaLogMessages)

artsappsdm

+#!/bin/sh
+
+ARTSAPP_HOME=/local/home/artsapp
+
+source ${ARTSAPP_HOME}/.gbifpass
+
+Rscript $ARTSAPP_HOME/scripts/artsappsdm.R $*
+
+
+

scripts/artsappsdm.R

@@ -8,8 +8,11 @@ library(readr)
 ## Configuration
 ##
 
-
-ARTSAPP_HOME = "/local/home/artsapp"
+if(Sys.getenv("ARTSAPP_HOME")!="") {
+  ARTSAPP_HOME=Sys.getenv("ARTSAPP_HOME")
+} else {
+  ARTSAPP_HOME=normalizePath(getwd())
+}
 
 CACHE_LOC = paste(ARTSAPP_HOME, "data/norge/occurrences.cache", sep="/")
 OUTPUT_LOC = paste(ARTSAPP_HOME, "output", sep="/")
@@ -181,10 +184,6 @@ runDownload   <- function() {
     speciesOccRaw <- downloadOccupancyData(taxaMissing,
                                            tempDirectory,
                                            yearLimits,
-                                           gbifLoginCredentials$username,
-                                           gbifLoginCredentials$password,
-                                           gbifLoginCredentials$email,
-                                           gbifAttemptTime, gbifMaxTime,
                                            templateGrid=extentGrid)
     
     writeOccurrences(speciesOccRaw,CACHE_LOC)