# NOT RUN {
library(repmis)
source_data("https://github.com/jimclarkatduke/gjam/blob/master/forestTraits.RData?raw=True")
xdata <- forestTraits$xdata
plotByTree <- gjamReZero(forestTraits$treesDeZero) # re-zero
traitTypes <- forestTraits$traitTypes
specByTrait <- forestTraits$specByTrait
tmp <- gjamSpec2Trait(pbys = plotByTree, sbyt = specByTrait,
tTypes = traitTypes)
tTypes <- tmp$traitTypes
traity <- tmp$plotByCWM
censor <- tmp$censor
formula <- as.formula(~ temp + deficit)
lo <- list(temp_gmPerSeed = 0, temp_dioecious = 0 ) # positive effect on seed size, dioecy
b <- gjamPriorTemplate(formula, xdata, ydata = traity, lo = lo)
ml <- list(ng=3000, burnin=1000, typeNames = tTypes, censor = censor, betaPrior = b)
out <- gjam(formula, xdata, ydata = traity, modelList = ml)
S <- ncol(traity)
sc <- rep('black',S)
sc[colnames(traity) <!-- %in% c('ring','drought')] <- 'blue' -->
pl <- list(specColor = sc)
gjamPlot(output = out, plotPars = pl)
# }
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