fixe bugs in new subsampling per plot

R/analysis/lmer.run.R

@@ -116,7 +116,7 @@ resample.plot.by.var <- function(df, var.sample, sample.size){
     df2 <- add.sampling.prob.by.var.sample(df, var.sample)
     mean.prob.per.plot <- tapply(df2[['prob.sample']], df2[['plot']], mean,
                                  na.rm =TRUE)
-    rm(df2,df1)
+    rm(df2)
     df1 <- data.frame(plot = names(mean.prob.per.plot),
                       prob.sample = as.numeric(mean.prob.per.plot))
     num.sample.plot <- sample(1:nrow(df1), size = sample.size,
@@ -141,7 +141,6 @@ load.data.for.lmer <- function(trait, cat.TF,
   df <- readRDS(file = file.path(base.dir,paste('data', trait, type,'rds',
                                               sep = '.')))
   df$sp.name[is.na(df$sp.name)] <-  'missing.sp'
-  browser()
   if(!is.na(select.biome.)) {
     df <-  df[df$biomes == select.biome., ]
     }

R/analysis/stan.run.R

@@ -14,7 +14,7 @@ model.files.stan.Tf.1 <-
 
 
 fun.generate.init <-  function(init.fun, list, N_chains){
- inits <- lapply(1:N_chains,init.fun,list)
+ inits <- lapply(1:N_chains, init.fun, list)
  return(inits)
 }
 
@@ -131,7 +131,7 @@ run.stan <- function (model.file, trait, init.TF,
 
 #========================================================================
 fun.load.stan <- function(trait,fname , cat.TF, sample.size, var.sample,
-                          sample.vec.TF, select.biome, select.set){
+                          sample.vec.TF, select.biome = NA, select.set = NA){
   df.lmer <- load.data.for.lmer(trait,fname = fname, cat.TF = cat.TF,
                                 sample.size. = sample.size,
                                 var.sample. = var.sample,

launch.cluster/launch_all_jags_init.bash

-#!/bin/bash
-# Georges Kunstler 14/05/2014
-# read one variable
-export LD_LIBRARY_PATH=/usr/lib64/R/library
-
-mkdir -p trait.workshop
-
-iter=50000
-warmup=5000
-thin=50
-# test parameter
-nbargs=$#
-echo "number of arguments="$nbargs
-if [ $nbargs -ne 1 ]
-then
-  echo "need one and only one argument"
-  echo " usage :"
-  echo " ./launch_all_lmer.sh  sample.size"
-  exit 100
-fi
-
-
-samplesize=$1
-# 
-for trait in "'SLA'" "'Wood.density'" "'Max.height'" "'Seed.mass'" "'Leaf.N'"; do
-
-  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(c(model.files.jags.Tf.1), run.jags,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id',iter = $iter, warmup = $warmup, chains = 3, thin = $thin, init.TF = TRUE);print('done')\"" > trait.workshop/speciesjags${trait}.sh
-	qsub trait.workshop/speciesjags${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "jags${trait}" -q opt32G -j oe
-
-
-
-done
-

launch.cluster/launch_all_stan.init.bash

@@ -23,7 +23,7 @@ samplesize=$1
 # "'Wood.density'" "'Max.height'"
 for trait in "'SLA'" ; do
 
-  	echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1[3], run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = TRUE);print('done')\"" > trait.workshop/speciesstanA1${trait}.sh
+  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = TRUE);print('done')\"" > trait.workshop/speciesstanA1${trait}.sh
 	qsub trait.workshop/speciesstanA1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
 
 

launch.cluster/launch_all_stan_init_local.bash

-#!/bin/bash
-# Georges Kunstler 14/05/2014
-# read one variable
-export LD_LIBRARY_PATH=/usr/lib64/R/library
-
-mkdir -p trait.workshop
-
-# test parameter
-nbargs=$#
-echo "number of arguments="$nbargs
-if [ $nbargs -ne 1 ]
-then
-  echo "need one and only one argument"
-  echo " usage :"
-  echo " ./launch_all_lmer.sh  sample.size"
-  exit 100
-fi
-
-
-samplesize=$1
-
-for trait in "'Wood.density'"; do
-
-Rscript -e "source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1[3], run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id', init.TF = TRUE);print('done')"
-
-done
-