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Commit ab8d4e95 authored by Kunstler Georges's avatar Kunstler Georges
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launch intra null

parent 8bf80732
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R/analysis/lmer.run.R
View file @ ab8d4e95
...@@ -45,6 +45,9 @@ model.files.lmer.Tf.3 <- file.path(path.model, ...@@ -45,6 +45,9 @@ model.files.lmer.Tf.3 <- file.path(path.model,
model.files.lmer.Tf.4 <- file.path(path.model, model.files.lmer.Tf.4 <- file.path(path.model,
c("model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.ecocode.species.R", c("model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.ecocode.species.R",
"model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.ecocode.fixed.biomes.species.R")) "model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.ecocode.fixed.biomes.species.R"))
model.files.lmer.Tf.intra.0 <- file.path(path.model,
c("model.lmer.LOGLIN.intra.r.set.species.R",
"model.lmer.LOGLIN.intra.r.set.fixed.biomes.species.R"))
model.files.lmer.Tf.intra.1 <- file.path(path.model, model.files.lmer.Tf.intra.1 <- file.path(path.model,
c("model.lmer.LOGLIN.ER.AD.Tf.intra.r.set.species.R", c("model.lmer.LOGLIN.ER.AD.Tf.intra.r.set.species.R",
"model.lmer.LOGLIN.ER.AD.Tf.intra.r.set.fixed.biomes.species.R")) "model.lmer.LOGLIN.ER.AD.Tf.intra.r.set.fixed.biomes.species.R"))
......
R/analysis/model.lmer/model.lmer.LOGLIN.MAT.MAP.intra.r.set.fixed.biomes.species.R 0 → 100644
View file @ ab8d4e95
load.model <- function () {
list(name="lmer.LOGLIN.MAT.MAP.intra.r.set.fixed.biomes.species",
var.BLUP = 'set.id',
lmer.formula.tree.id=formula("logG~1+biomes.id+MAT+MAP+logD+sumBn.inter+sumBn.inter:biomes.id+sumBn.intra+sumBn.intra:biomes.id +(1+logD+sumBn.inter+sumBn.intra||species.id)+(1|plot.id)+(1+sumBn.inter+sumBn.intra||set.id)"))
}
R/analysis/model.lmer/model.lmer.LOGLIN.MAT.MAP.intra.r.set.species.R 0 → 100644
View file @ ab8d4e95
load.model <- function () {
list(name="lmer.LOGLIN.MAT.MAP.intra.r.set.species",
var.BLUP = 'set.id',
lmer.formula.tree.id=formula("logG~1+logD+sumBn.inter+MAT+MAP+sumBn.intra+(1+logD+sumBn.inter+sumBn.intra||species.id)+(1|plot.id)+(1+sumBn.inter+sumBn.intra||set.id)"))
}
docs/paper/extended_data.R
View file @ ab8d4e95
...@@ -107,6 +107,9 @@ pandoc.table(cor.mat, ...@@ -107,6 +107,9 @@ pandoc.table(cor.mat,
list.all.results <- list.all.results <-
readRDS.root('output/list.lmer.out.all.NA.simple.set.rds') readRDS.root('output/list.lmer.out.all.NA.simple.set.rds')
list.all.results.intra <-
readRDS('output/list.lmer.out.all.NA.intra.set.rds')
mat.param <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'), mat.param <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
extract.param, list.res = list.all.results, extract.param, list.res = list.all.results,
......
launch.cluster/launch_all_lmer.bash
View file @ ab8d4e95
...@@ -22,53 +22,61 @@ samplesize=$1 ...@@ -22,53 +22,61 @@ samplesize=$1
# "'Seed.mass'" "'Leaf.N'" # "'Seed.mass'" "'Leaf.N'"
for trait in "'SLA'" "'Wood.density'" "'Max.height'" ; do for trait in "'SLA'" "'Wood.density'" "'Max.height'" ; do
# # ALL data 0 # # # ALL data 0
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[1], run.lmer,$trait);print('done')\"" > Rscript_temp/all0${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[1], run.lmer,$trait);print('done')\"" > Rscript_temp/all0${trait}.sh
qsub Rscript_temp/all0${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.0${trait}" -q opt32G -j oe # qsub Rscript_temp/all0${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.0${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/all02${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/all02${trait}.sh
qsub Rscript_temp/all02${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.02${trait}" -q opt32G -j oe # qsub Rscript_temp/all02${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.02${trait}" -q opt32G -j oe
# # ALL data 0b # # # ALL data 0b
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0b[1], run.lmer,$trait);print('done')\"" > Rscript_temp/all0b${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0b[1], run.lmer,$trait);print('done')\"" > Rscript_temp/all0b${trait}.sh
qsub Rscript_temp/all0b${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.0b${trait}" -q opt32G -j oe # qsub Rscript_temp/all0b${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.0b${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0b[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/all02b${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0b[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/all02b${trait}.sh
qsub Rscript_temp/all02b${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.02b${trait}" -q opt32G -j oe # qsub Rscript_temp/all02b${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.02b${trait}" -q opt32G -j oe
# # ALL data 1 # # # ALL data 1
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[1], run.lmer,$trait);print('done')\"" > Rscript_temp/allf${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[1], run.lmer,$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${trait}" -q opt32G -j oe # qsub Rscript_temp/allf${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${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[2], merge.biomes.TF = TRUE, run.lmer,$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${trait}" -q opt32G -j oe # qsub Rscript_temp/allf2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f2${trait}" -q opt32G -j oe
# # ALL data 1 # # # ALL data 1
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[1], run.lmer,$trait);print('done')\"" > Rscript_temp/allTP${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[1], run.lmer,$trait);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${trait}" -q opt32G -j oe # qsub Rscript_temp/allTP${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.TP${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/allTP2${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[2], merge.biomes.TF = TRUE, run.lmer,$trait);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${trait}" -q opt32G -j oe # qsub Rscript_temp/allTP2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.TP2${trait}" -q opt32G -j oe
# # INTRA 1 # # INTRA 0
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.1[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA${trait}.sh echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.0[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA0${trait}.sh
qsub Rscript_temp/allINTRA${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA${trait}" -q opt32G -j oe qsub Rscript_temp/allINTRA0${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA0${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.1[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA2${trait}.sh echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.0[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA02${trait}.sh
qsub Rscript_temp/allINTRA2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA2${trait}" -q opt32G -j oe qsub Rscript_temp/allINTRA02${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA02${trait}" -q opt32G -j oe
# # INTRA 2 # # # INTRA 1
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.2[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAB${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.1[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA${trait}.sh
qsub Rscript_temp/allINTRAB${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAB${trait}" -q opt32G -j oe # qsub Rscript_temp/allINTRA${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.2[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAB2${trait}.sh # echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.1[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA2${trait}.sh
qsub Rscript_temp/allINTRAB2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAB2${trait}" -q opt32G -j oe # qsub Rscript_temp/allINTRA2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA2${trait}" -q opt32G -j oe
# # # INTRA 2
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.2[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAB${trait}.sh
# qsub Rscript_temp/allINTRAB${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAB${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.2[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAB2${trait}.sh
# qsub Rscript_temp/allINTRAB2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAB2${trait}" -q opt32G -j oe
# # # # # ecocode 3 # # # # # ecocode 3
......
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