## This runs on the condor node to do all habitat calcs
install.packages("ncdf4_1.4.zip", lib='./rLibs', repos=NULL)
install.packages("rGLM_0.1.5.tar.gz", lib='./rLibs', repos=NULL, type='source')
install.packages('rLakeAnalyzer_1.0.zip', lib='./rLibs', repos=NULL)
install.packages('stringr_0.6.2.zip', lib='./rLibs', repos=NULL)
source('chained.GLM.lib.R')
library('ncdf4')
library('rGLM')
library('rLakeAnalyzer')
library('stringr')
info = read.table('run.info.tsv', header=TRUE, sep='\t')
wtr = get.wtr.chained.prefix('.')
write.table(wtr, 'output.wtr', sep='\t', col.names=TRUE, row.names=FALSE)
plotGLM <- function(GLM,figName="glmPlot",folder="./",cLim=c(0,30)){
# saves GLM plot to directory
elevs <- getElevGLM(GLM)
lvls <- seq(cLim[1],cLim[2])
figW <- 8
figH <- 3.5
lM <- .95
bM <- .55
rM <- .15
tM <- 0.25
fRes <- 300
fontN <- 11
xL <- c(as.numeric(min(GLM$DateTime)),as.numeric(max(GLM$DateTime)))
yL <- c(min(elevs,na.rm=TRUE),max(elevs,na.rm=TRUE))
cMap <- rev(rainbow(length(lvls),s=1,v=1,start=0,end=4/6))
vals <- data.matrix(GLM)
output = paste(folder,figName,".png", sep = "")
png(output, width=figW, height=figH, units="in",res=fRes)
par(mai=c(bM,lM,rM,tM),usr=c(xL[1],xL[2],yL[1],yL[2]))
wtr <- vals[,2:(length(elevs)+1)]
filled.contour(x=GLM$DateTime,y=elevs,z=wtr,col = cMap,
levels=lvls,xaxs = "i",plot.title = title(ylab = "Elevation from bottom (m)"),
xlim=xL, ylim=yL, xaxp = c(xL[1],xL[2],50))
dev.off()
}
plotGLM(wtr)
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