process new ecocode

scripts/analysis/lmer.all.no.log.output.R

@@ -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,

scripts/analysis/results.fig.R

@@ -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')
 

scripts/analysis/test.jags.R

@@ -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')
 }