Commit 6f2eba5d authored by kunstler's avatar kunstler
Browse files

lmer plus MAT MAP

parent 5f5c584b
......@@ -35,6 +35,10 @@ model.files.lmer.Tf.2 <- file.path(path.model,
c("model.lmer.LOGLIN.ER.AD.Tf.r.tree.id.set.species.R",
"model.lmer.LOGLIN.ER.AD.Tf.r.tree.id.set.fixed.biomes.species.R"))
model.files.lmer.Tf.3 <- file.path(path.model,
c("model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.set.species.R",
"model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.set.fixed.biomes.species.R"))
model.files.lmer.Tf.Multi <- file.path(path.model,
c("model.lmer.LOGLIN.ER.AD.Tf.Multi.r.set.species.R",
"model.lmer.LOGLIN.ER.AD.Tf.Multi.r.set.fixed.biomes.species.R"))
......
......@@ -33,28 +33,28 @@ samplesize=$1
# qsub Rscript_temp/allf3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.fb2${trait}" -q opt32G -j oe
# # ALL data
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[1], run.lmer,$trait);print('done')\"" > Rscript_temp/allf${trait}.sh
qsub Rscript_temp/allf${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[1], run.lmer,$trait);print('done')\"" > Rscript_temp/allf${trait}.sh
# qsub Rscript_temp/allf${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/allf2${trait}.sh
qsub Rscript_temp/allf2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f2${trait}" -q opt32G -j oe
# # ALL data All census
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.2[1], run.lmer,$trait, data.type = 'all.census');print('done')\"" > Rscript_temp/allcensus${trait}.sh
qsub Rscript_temp/allcensus${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.census${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/allf2${trait}.sh
# qsub Rscript_temp/allf2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f2${trait}" -q opt32G -j oe
# # ALL MAT MAP
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[1], run.lmer,$trait, data.type = 'simple');print('done')\"" > Rscript_temp/allTP${trait}.sh
qsub Rscript_temp/allTP${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.TP${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.2[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'all.census');print('done')\"" > Rscript_temp/allcensus2${trait}.sh
qsub Rscript_temp/allcensus2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.census2${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'simple');print('done')\"" > Rscript_temp/allTP2${trait}.sh
qsub Rscript_temp/allTP2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.TP2${trait}" -q opt32G -j oe
done
# # MULTI
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.Multi[1], run.lmer,'SLA', data.type = 'Multi');print('done')\"" > Rscript_temp/allMulti.sh
qsub Rscript_temp/allMulti.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall.Multi" -q opt32G -j oe
# # # MULTI
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.Multi[1], run.lmer,'SLA', data.type = 'Multi');print('done')\"" > Rscript_temp/allMulti.sh
# qsub Rscript_temp/allMulti.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall.Multi" -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(model.files.lmer.Tf.Multi[2], merge.biomes.TF = TRUE, run.lmer, 'SLA',data.type = 'Multi');print('done')\"" > Rscript_temp/allMulti2.sh
qsub Rscript_temp/allMulti2.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall.Multi2" -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(model.files.lmer.Tf.Multi[2], merge.biomes.TF = TRUE, run.lmer, 'SLA',data.type = 'Multi');print('done')\"" > Rscript_temp/allMulti2.sh
# qsub Rscript_temp/allMulti2.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall.Multi2" -q opt32G -j oe
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