map.surface = function( ip=NULL, plotvar, pyears, vclass, log.transf=F, ... ) {
# ip is the first parameter passed in the parallel mode
if (exists( "libs", p)) RLibrary( p$libs )
if (is.null(ip)) ip = 1:length(pyears)
outdir = file.path( project.datadirectory("bio.snowcrab"), "R", "habitat", "maps" )
dir.create(path=outdir, recursive=T, showWarnings=F)
if ( plotvar %in% c("habitat", "habitat.sim") ) {
dr = c( 0, 1)
}
if ( plotvar %in% c("abundance", "abundance.sim") ) {
xx = snowcrab.db("set.biologicals")[, "R0.mass" ]
dr = range( xx, na.rm=T )
if (log.transf) {
er = range( xx[ which(xx >0)])
dr = log10(er)
}
}
datarange = seq( dr[1] , dr[2], length.out=100 )
cols = color.code( "seis", datarange )
for (iy in ip) {
y = pyears[iy]
fn = paste( plotvar, y, vclass, sep=".")
print ( file.path(outdir,fn) )
PS = predictive.simulations( DS="PS", vclass=vclass, pyears=y )
if (log.transf) {
PS[, plotvar ] = log10( PS[, plotvar ] )
}
map( PS[, c("plon", "plat", plotvar)], xyz.coords="planar", cfa.regions=T, depthcontours=T, annot=y,
fn=fn, loc=outdir, at=datarange, col.regions=cols, corners=planar.corners) # planar.corners defined in load.environment.r
}
return( "Complete" )
}
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