Commit f485ecf0 authored by Kunstler Georges's avatar Kunstler Georges
Browse files

process new ecocode

parent 16b13c19
This diff is collapsed.
......@@ -6,13 +6,17 @@ source("R/analysis/lmer.run.R")
## ## save list of all output for NA
format.all.output.lmer(file.name = "NA.wwf.results.nolog.all.rds",
list.file.name = 'list.lmer.out.all.NA.simple.set.rds',
models = c(model.files.lmer.Tf.0, model.files.lmer.Tf.1,
model.files.lmer.Tf.2, model.files.lmer.Tf.3),
list.file.name = 'list.lmer.out.all.NA.simple.ecocode.rds',
models = c(model.files.lmer.Tf.2),
traits = c("SLA", "Wood.density", "Max.height"))
## format.all.output.lmer(file.name = "NA.wwf.results.nolog.all.rds",
## list.file.name = 'list.lmer.out.all.NA.simple.set.rds',
## models = c(model.files.lmer.Tf.0, model.files.lmer.Tf.1,
## model.files.lmer.Tf.2, model.files.lmer.Tf.3),
## traits = c("SLA", "Wood.density", "Max.height"))
## format.all.output.lmer(file.name = "NA.wwf.results.nolog.all.rds",
## list.file.name = 'list.lmer.out.all.NA.intra.set.rds',
## models = c(model.files.lmer.Tf.intra.1,
......
......@@ -174,4 +174,21 @@ pdf('figs/figres4b.pdf', width = 8, height = 11)
fun.plot.all.param(list.all.results.set)
dev.off()
pdf('figs/figres4b.TP.pdf', width = 8, height = 11)
fun.plot.all.param(list.all.results.set, model = 'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.set.species',
MAT.MAP.TF = TRUE)
dev.off()
fun.plot.all.stabl(list.all.results.set, model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species',
MAT.MAP.TF = FALSE)
x11()
fun.plot.all.stabl(list.all.results.intra, model = 'lmer.LOGLIN.ER.AD.Tf.intra.r.set.species',
MAT.MAP.TF = FALSE, intra.TF = TRUE, data.type ='intra')
x11()
fun.plot.all.rho(list.all.results.set, model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species',
MAT.MAP.TF = FALSE)
x11()
fun.plot.all.rho(list.all.results.intra, model = 'lmer.LOGLIN.ER.AD.Tf.intra.r.set.species',
MAT.MAP.TF = FALSE, intra.TF = TRUE, data.type ='intra')
......@@ -8,7 +8,7 @@ library(runjags)
for(trait in c('SLA', 'Wood.density', 'Max.height')){
run.jags.b(model.files.jags.Tf.1[1], trait = trait,
init.TF = TRUE, var.sample = 'wwf',
sample.size = 30000, iter = 200,
sample.size = 10000, iter = 200,
warmup = 20, chains = 4,
thin = 2)
}
......@@ -16,8 +16,8 @@ for(trait in c('SLA', 'Wood.density', 'Max.height')){
for(trait in c('SLA', 'Wood.density', 'Max.height')){
run.jags.b(model.files.jags.Tf.1[1], trait = trait,
init.TF = FALSE, var.sample = 'wwf',
sample.size = 30000, iter = 2000,
warmup = 2000, chains = 3,
sample.size = 10000, iter = 10000,
warmup = 5000, chains = 2,
thin = 5, method = 'parallel')
}
......
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