clean to git on cluster

R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.fixed.biomes.species.R

 load.model <- function () {
     list(name="lmer.LOGLIN.ER.AD.Tf.fixed.biomes.species",
          var.BLUP = 'biomes.id',
-         lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+biomes.id+Tf+Tf:biomes.id+logD+sumBn+sumBn:biomes.id+sumTfBn+sumTfBn:biomes.id+sumTnBn+sumTnBn:biomes.id+sumTnTfBn.abs+sumTnTfBn.abs:biomes.id+(1|species.id) +(logD-1|species.id) +(sumBn-1|species.id)))
+         lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+biomes.id+Tf+Tf:biomes.id+logD+sumBn+sumBn:biomes.id+sumTfBn+sumTfBn:biomes.id+sumTnBn+sumTnBn:biomes.id+sumTnTfBn.abs+sumTnTfBn.abs:biomes.id+(1|species.id) +(logD-1|species.id) +(sumBn-1|species.id)"))
 }
 

R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.fixed.species.R

 load.model <- function () {
     list(name="lmer.LOGLIN.ER.AD.Tf.fixed.species",
          var.BLUP = 'biomes.id',
-         lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+logD+sumBn+sumTfBn+sumTnBn+sumTnTfBn.abs+(1|species.id) +(logD-1|species.id) +(sumBn-1|species.id)))
+         lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+logD+sumBn+sumTfBn+sumTnBn+sumTnTfBn.abs+(1|species.id) +(logD-1|species.id) +(sumBn-1|species.id)"))
 }
 

launch.cluster/jobR32Gdir.sh

-#!/bin/sh
-# Georges Kunstler 
-# 12/08/2013
-# commande de soumission de jobs sur le cluster via qsub
-# incremente par un numero d'ordre du fichier de donnees
-# lancement ./jobJAGS.sh debut fin racineR subdir
-# ou 
-# debut est l'indice du premier fichier à traiter
-# fin est l'indice du dernier fichier à traiter
-# racineR est le début du nom du fichier R 
-# subdir est la subdirectory ou run R 
-# les fichiers à traiter seront de la forme racine.Z.R 
-#           ou Z est compris entre debut et fin
-
-
-# test d'absence de parametre
-nbargs=$#
-echo "nombre d'arguments="$nbargs
-if [ $nbargs -eq 0 ]
-then
-  echo "  il manque des parametres de lancement il en faut 4"
-  echo " usage :"
-  echo " ./jobJAGS.sh  1 5 racineR subdir"
-  exit 100
-else 
-  if [ $nbargs -lt 3 ]
-  then
-    echo " il faut 4 parametres indice de debut, indice de fin et la racine R"
-    echo " usage :"
-    echo " ./jobJAGS.sh 3 8 racineR subdir"
-    exit 100
-  fi
-fi
-
-# initialisation
-# echo "lancer "$1" jobs"
-
-JOB=R 
-REP=/data1/kunstler/workshop/
-EXP=export
-LD=LD_LIBRARY_PATH=/usr/lib64/R/library
-NAME=Rcran
-
-# boucle 
-min=$1
-max=$2
-for n in `seq $min $max`; do
-# constitution du nom du fichier de donnees
-DATA=$3$n.R
-
-cd workshop
-#ls
-echo "   $EXP $LD ; $JOB CMD BATCH  $DATA"
-echo "   $EXP $LD ; $JOB CMD BATCH  $DATA" |qsub -l nodes=1:ppn=1 -N "$NAME$n" -q opt32G -j oe
-cd /data1/kunstler/
-
-#echo " n vaut="$n
-
-done

launch.cluster/launch_all_lmer.bash

@@ -22,13 +22,13 @@ 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/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1,model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode');print('done')\"" > trait.workshop/species2${trait}.sh
+  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode');print('done')\"" > trait.workshop/species2${trait}.sh
 	qsub trait.workshop/species2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2${trait}" -q opt32G -j oe
 
-  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1,model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = NA, var.sample = NA);print('done')\"" > trait.workshop/species2T${trait}.sh
+  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = NA, var.sample = NA);print('done')\"" > trait.workshop/species2T${trait}.sh
 	qsub trait.workshop/species2T${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2T${trait}" -q opt32G -j oe
 
-  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1,  model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'sp.name');print('done')\"" > trait.workshop/species2S${trait}.sh
+  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'sp.name');print('done')\"" > trait.workshop/species2S${trait}.sh
 	qsub trait.workshop/species2S${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2S${trait}" -q opt32G -j oe
 
 done

launch.cluster/launch_all_lmer.resid.bash

-#!/bin/bash
-# Georges Kunstler 14/05/2014
-# read one variable
-export LD_LIBRARY_PATH=/usr/lib64/R/library
-
-mkdir -p trait.workshop
-
-
-
-
-# "'Seed.mass'" "'Leaf.N'"
-for trait in "'SLA'" "'Wood.density'" "'Max.height'"; do
-
-  	# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1,model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/species1${trait}.sh
-	# qsub trait.workshop/species1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall1${trait}" -q opt32G -j oe
-
-  	# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.3,model.files.lmer.Tf.4), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/species2${trait}.sh
-	# qsub trait.workshop/species2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2${trait}" -q opt32G -j oe
-
-  	# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.5, run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/species3${trait}.sh
-	# qsub trait.workshop/species3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall3${trait}" -q opt32G -j oe
-
-  	# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/species1S${trait}.sh
-	# qsub trait.workshop/species1S${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall1S${trait}" -q opt32G -j oe
-
-  	# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.3, model.files.lmer.Tf.4), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/species2S${trait}.sh
-	# qsub trait.workshop/species2S${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2S${trait}" -q opt32G -j oe
-
-  	# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.5, run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/speciesS3${trait}.sh
-	# qsub trait.workshop/speciesS3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerallS3${trait}" -q opt32G -j oe
-
-# CAT model 
-  	echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.CAT.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id', cat.TF = TRUE);print('done')\"" > trait.workshop/speciesCAT1${trait}.sh
-	qsub trait.workshop/speciesCAT1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerallCAT1${trait}" -q opt32G -j oe
-
-  	echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.CAT.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id', cat.TF = TRUE);print('done')\"" > trait.workshop/speciesCATS1${trait}.sh
-	qsub trait.workshop/speciesCATS1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerallCATS1${trait}" -q opt32G -j oe
-
-done

launch.cluster/launch_all_lmer_biomes.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=$1
-# "'Seed.mass'" "'Leaf.N'"
-for trait in "'SLA'" "'Wood.density'" "'Max.height'"; do
-  for biome in "'Temperate rain forest'" "'Temperate grassland desert'" "'Tropical rain forest'"  "'Tropical forest savanna'" "'Boreal forest'"  "'Woodland shrubland'"  "'Temperate forest'"; do
-
-  	echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1, run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id', select.biome = $biome);print('done')\"" > trait.workshop/species1${trait}_"${biome}".sh
-	qsub trait.workshop/species1${trait}_"${biome}".sh -l nodes=1:ppn=1,mem=8gb -N "lmerall1${trait}" -q opt32G -j oe
-
-  done
-done
-