Commit d4a35297 authored by Georges Kunstler's avatar Georges Kunstler
Browse files

directory issue solved

parent a24f5915
......@@ -8,17 +8,17 @@ pwd
for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); print(getwd());print('done')\"" > Rscript_temp/gdata1$trait.sh
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait);print('done')\"" > Rscript_temp/gdata1$trait.sh
qsub Rscript_temp/gdata1$trait.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "gdata1$trait" -q opt32G -j oe
# # echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > Rscript_temp/gdata2$trait.sh
# # qsub Rscript_temp/gdata2$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata2$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > Rscript_temp/gdata2$trait.sh
# qsub Rscript_temp/gdata2$trait.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "gdata2$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata3$trait.sh
# qsub Rscript_temp/gdata3$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata3$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata3$trait.sh
qsub Rscript_temp/gdata3$trait.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "gdata3$trait" -q opt32G -j oe
# # echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata4$trait.sh
# # qsub Rscript_temp/gdata4$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata4$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata4$trait.sh
# qsub Rscript_temp/gdata4$trait.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "gdata4$trait" -q opt32G -j oe
done
......@@ -7,11 +7,11 @@ mkdir -p Rscript_temp
for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); load.and.save.data.for.lmer($trait);print('done')\"" > Rscript_temp/data1$trait.sh
qsub Rscript_temp/data1$trait.sh -l nodes=1:ppn=1,mem=8gb -N "data1$trait" -q opt32G -j oe
qsub Rscript_temp/data1$trait.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "data1$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); load.and.save.data.for.lmer($trait, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/data3$trait.sh
qsub Rscript_temp/data3$trait.sh -l nodes=1:ppn=1,mem=8gb -N "data3$trait" -q opt32G -j oe
qsub Rscript_temp/data3$trait.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "data3$trait" -q opt32G -j oe
done
......@@ -20,22 +20,22 @@ samplesize=$1
for trait in "'SLA'" "'Wood.density'" "'Max.height'"; do
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(model.files.glmer.Tf.1, run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > Rscript_temp/glmerspecies1${trait}.sh
# qsub Rscript_temp/glmerspecies1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall1${trait}" -q opt32G -j oe
# qsub Rscript_temp/glmerspecies1${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "glmerall1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.2), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > Rscript_temp/glmerspecies2${trait}.sh
qsub Rscript_temp/glmerspecies2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall2${trait}" -q opt32G -j oe
qsub Rscript_temp/glmerspecies2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "glmerall2${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.3), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > Rscript_temp/glmerspecies3${trait}.sh
# qsub Rscript_temp/glmerspecies3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall3${trait}" -q opt32G -j oe
# qsub Rscript_temp/glmerspecies3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "glmerall3${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(model.files.glmer.Tf.1, run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > Rscript_temp/glmerspeciesS1${trait}.sh
# qsub Rscript_temp/glmerspeciesS1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS1${trait}" -q opt32G -j oe
# qsub Rscript_temp/glmerspeciesS1${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "glmerallS1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.2), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > Rscript_temp/glmerspeciesS2${trait}.sh
qsub Rscript_temp/glmerspeciesS2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS2${trait}" -q opt32G -j oe
qsub Rscript_temp/glmerspeciesS2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "glmerallS2${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.3), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > Rscript_temp/glmerspeciesS3${trait}.sh
# qsub Rscript_temp/glmerspeciesS3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS3${trait}" -q opt32G -j oe
# qsub Rscript_temp/glmerspeciesS3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "glmerallS3${trait}" -q opt32G -j oe
......
......@@ -25,7 +25,7 @@ samplesize=$1
for trait in "'SLA'" ; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(c(model.files.jags.Tf.0, model.files.jags.Tf.00), run.jags,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id',iter = $iter, warmup = $warmup, chains = 3, thin = $thin, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesjags${trait}.sh
qsub Rscript_temp/speciesjags${trait}.sh -l nodes=1:ppn=1,mem=16gb -N "jags${trait}" -q opt32G -j oe
qsub Rscript_temp/speciesjags${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=16gb -N "jags${trait}" -q opt32G -j oe
......
......@@ -25,7 +25,7 @@ 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 = $thin, init.TF = TRUE);print('done')\"" > Rscript_temp/speciesjags${trait}.sh
qsub Rscript_temp/speciesjags${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "jags${trait}" -q opt32G -j oe
qsub Rscript_temp/speciesjags${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "jags${trait}" -q opt32G -j oe
......
......@@ -23,12 +23,12 @@ 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 = $samplesize, var.sample = 'ecocode');print('done')\"" > Rscript_temp/species2${trait}.sh
qsub Rscript_temp/species2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2${trait}" -q opt32G -j oe
qsub Rscript_temp/species2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2${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,$trait,type.filling='species', sample.size = NA, var.sample = NA);print('done')\"" > Rscript_temp/species2T${trait}.sh
qsub Rscript_temp/species2T${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2T${trait}" -q opt32G -j oe
qsub Rscript_temp/species2T${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2T${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 = $samplesize, var.sample = 'sp.name');print('done')\"" > Rscript_temp/species2S${trait}.sh
qsub Rscript_temp/species2S${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2S${trait}" -q opt32G -j oe
qsub Rscript_temp/species2S${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2S${trait}" -q opt32G -j oe
done
......@@ -24,13 +24,13 @@ samplesize=$1
for trait in "'SLA'" ; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA1${trait}.sh
qsub Rscript_temp/speciesstanA1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
qsub Rscript_temp/speciesstanA1${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
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 = $warmup, chains = 1, chain_id = 2, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA2${trait}.sh
qsub Rscript_temp/speciesstanA2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA2${trait}" -q opt32G -j oe
qsub Rscript_temp/speciesstanA2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "stanallA2${trait}" -q opt32G -j oe
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 = $warmup, chains = 1, chain_id = 3, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA3${trait}.sh
qsub Rscript_temp/speciesstanA3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA3${trait}" -q opt32G -j oe
qsub Rscript_temp/speciesstanA3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "stanallA3${trait}" -q opt32G -j oe
done
......@@ -24,7 +24,7 @@ samplesize=$1
for trait in "'SLA'" ; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = TRUE);print('done')\"" > Rscript_temp/speciesstanA1${trait}.sh
qsub Rscript_temp/speciesstanA1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
qsub Rscript_temp/speciesstanA1${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
......
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