From cb7917e8ba695f83366bd7d727a19f27cc3cfbe2 Mon Sep 17 00:00:00 2001
From: kunstler <georges.kunstler@gmail.com>
Date: Sat, 30 May 2015 15:36:23 +0200
Subject: [PATCH] add null model
---
R/analysis/lmer.run.R | 3 ++
...GLIN.ER.AD.Tf.r.set.fixed.biomes.species.R | 4 +-
...l.lmer.LOGLIN.r.set.fixed.biomes.species.R | 6 +++
.../model.lmer.LOGLIN.r.set.species.R | 8 ++++
launch.cluster/launch_all_lmer.bash | 37 +++++++++++--------
5 files changed, 41 insertions(+), 17 deletions(-)
create mode 100644 R/analysis/model.lmer/model.lmer.LOGLIN.r.set.fixed.biomes.species.R
create mode 100644 R/analysis/model.lmer/model.lmer.LOGLIN.r.set.species.R
diff --git a/R/analysis/lmer.run.R b/R/analysis/lmer.run.R
index e2b935c..00833dc 100644
--- a/R/analysis/lmer.run.R
+++ b/R/analysis/lmer.run.R
@@ -27,6 +27,9 @@ run.model.for.set.one.trait <- function(model.file, fun.model, trait,
#=====================================================================
path.model <- "R/analysis/model.lmer"
+model.files.lmer.Tf.0 <- file.path(path.model,
+ c("model.lmer.LOGLIN.r.set.species.R",
+ "model.lmer.LOGLIN.r.set.fixed.biomes.species.R"))
model.files.lmer.Tf.1 <- file.path(path.model,
c("model.lmer.LOGLIN.ER.AD.Tf.r.set.species.R",
"model.lmer.LOGLIN.ER.AD.Tf.r.set.fixed.biomes.species.R"))
diff --git a/R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.r.set.fixed.biomes.species.R b/R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.r.set.fixed.biomes.species.R
index 7d535d2..9145d04 100644
--- a/R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.r.set.fixed.biomes.species.R
+++ b/R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.r.set.fixed.biomes.species.R
@@ -1,6 +1,6 @@
load.model <- function () {
- list(name="lmer.LOGLIN.ER.AD.Tf.r.set.fixed.biomes.species",
+ list(name="lmer.LOGLIN.r.set.fixed.biomes.species",
var.BLUP = 'set.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 +(logD-1|species.id) +(sumBn-1|species.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTfBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.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 +(logD-1|species.id) +(sumBn-1|species.id)+(sumBn-1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTfBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
}
diff --git a/R/analysis/model.lmer/model.lmer.LOGLIN.r.set.fixed.biomes.species.R b/R/analysis/model.lmer/model.lmer.LOGLIN.r.set.fixed.biomes.species.R
new file mode 100644
index 0000000..087e7ae
--- /dev/null
+++ b/R/analysis/model.lmer/model.lmer.LOGLIN.r.set.fixed.biomes.species.R
@@ -0,0 +1,6 @@
+load.model <- function () {
+ list(name="lmer.LOGLIN.r.set.fixed.biomes.species",
+ var.BLUP = 'set.id',
+ lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+biomes.id+logD+sumBn+sumBn:biomes.id +(logD-1|species.id) +(sumBn-1|species.id)+(sumBn-1|set.id)"))
+}
+
diff --git a/R/analysis/model.lmer/model.lmer.LOGLIN.r.set.species.R b/R/analysis/model.lmer/model.lmer.LOGLIN.r.set.species.R
new file mode 100644
index 0000000..008f0fa
--- /dev/null
+++ b/R/analysis/model.lmer/model.lmer.LOGLIN.r.set.species.R
@@ -0,0 +1,8 @@
+load.model <- function () {
+ list(name="lmer.LOGLIN.r.set.species",
+ var.BLUP = 'set.id',
+ lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+logD+sumBn +(logD-1|species.id) +(sumBn-1|species.id)+(sumBn-1|set.id)"))
+}
+
+
+
diff --git a/launch.cluster/launch_all_lmer.bash b/launch.cluster/launch_all_lmer.bash
index cf16d4c..dea36ca 100644
--- a/launch.cluster/launch_all_lmer.bash
+++ b/launch.cluster/launch_all_lmer.bash
@@ -22,30 +22,37 @@ samplesize=$1
# "'Seed.mass'" "'Leaf.N'"
for trait in "'SLA'" "'Wood.density'" "'Max.height'" ; do
-
# # ALL data
- echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[1], run.lmer,$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${trait}" -q opt32G -j oe
+ echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[1], run.lmer,$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${trait}" -q opt32G -j oe
+
+
+ echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[2], merge.biomes.TF = TRUE, run.lmer,$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${trait}" -q opt32G -j oe
+
+# # # ALL data
+# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[1], run.lmer,$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${trait}" -q opt32G -j oe
- echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[2], merge.biomes.TF = TRUE, run.lmer,$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${trait}" -q opt32G -j oe
+# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[2], merge.biomes.TF = TRUE, run.lmer,$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${trait}" -q opt32G -j oe
+# # # ALL MAT MAP
+# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[1], run.lmer,$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${trait}" -q opt32G -j oe
- echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[2], merge.biomes.TF = TRUE, run.lmer,$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${trait}" -q opt32G -j oe
+# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[2], merge.biomes.TF = TRUE, run.lmer,$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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