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Kunstler Georges
traitcompet
Commits
571346b9
Commit
571346b9
authored
Sep 16, 2015
by
Kunstler Georges
Browse files
run ecocode TP
parent
f485ecf0
Changes
7
Hide whitespace changes
Inline
Side-by-side
R/analysis/lmer.run.R
View file @
571346b9
...
...
@@ -39,6 +39,9 @@ model.files.lmer.Tf.2 <- file.path(path.model,
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.4
<-
file.path
(
path.model
,
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.files.lmer.Tf.intra.1
<-
file.path
(
path.model
,
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"
))
...
...
R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.ecocode.fixed.biomes.species.R
0 → 100644
View file @
571346b9
load.model
<-
function
()
{
list
(
name
=
"lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.ecocode.fixed.biomes.species"
,
var.BLUP
=
'ecocode.id'
,
lmer.formula.tree.id
=
formula
(
"logG~1+(1|ecocode.id)+(1|species.id)+(1|plot.id)+biomes.id+Tf+MAT+MAP+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|ecocode.id)+(sumBn-1|ecocode.id)+(sumTfBn-1|ecocode.id)+(sumTnBn-1|ecocode.id)+(sumTnTfBn.abs-1|ecocode.id)"
))
}
R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.ecocode.species.R
0 → 100644
View file @
571346b9
load.model
<-
function
()
{
list
(
name
=
"lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.ecocode.species"
,
var.BLUP
=
'ecocode.id'
,
lmer.formula.tree.id
=
formula
(
"logG~1+(1|ecocode.id)+(1|species.id)+(1|plot.id)+Tf+MAP+MAT+logD+sumBn+sumTfBn+sumTnBn+sumTnTfBn.abs +(logD-1|species.id) +(sumBn-1|species.id)+(Tf-1|ecocode.id)+(sumBn-1|ecocode.id)+(sumTfBn-1|ecocode.id)+(sumTnBn-1|ecocode.id)+(sumTnTfBn.abs-1|ecocode.id)"
))
}
launch.cluster/launch_all_lmer.bash
View file @
571346b9
...
...
@@ -63,12 +63,19 @@ samplesize=$1
# qsub Rscript_temp/allINTRAB2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAB2${trait}" -q opt32G -j oe
# # # ecocode 3
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 = 'simple');print('done')
\"
"
>
Rscript_temp/allECO
${
trait
}
.sh
qsub Rscript_temp/allECO
${
trait
}
.sh
-d
~/trait.competition.workshop
-l
nodes
=
1:ppn
=
1,mem
=
8gb
-N
"lmerall2all.ECO
${
trait
}
"
-q
opt32G
-j
oe
# # #
#
ecocode 3
#
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.2[1], run.lmer,$trait, data.type = 'simple');print('done')\"" > Rscript_temp/allECO${trait}.sh
#
qsub Rscript_temp/allECO${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.ECO${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], run.lmer,merge.biomes.TF = TRUE,
$trait
, data.type = 'simple');print('done')
\"
"
>
Rscript_temp/allECO2
${
trait
}
.sh
qsub Rscript_temp/allECO2
${
trait
}
.sh
-d
~/trait.competition.workshop
-l
nodes
=
1:ppn
=
1,mem
=
8gb
-N
"lmerall2all.ECO2
${
trait
}
"
-q
opt32G
-j
oe
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.2[2], run.lmer,merge.biomes.TF = TRUE,$trait, data.type = 'simple');print('done')\"" > Rscript_temp/allECO2${trait}.sh
# qsub Rscript_temp/allECO2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.ECO2${trait}" -q opt32G -j oe
# # # ecocode TP
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.4[1], run.lmer,
$trait
, data.type = 'simple');print('done')
\"
"
>
Rscript_temp/allECOTP
${
trait
}
.sh
qsub Rscript_temp/allECOTP
${
trait
}
.sh
-d
~/trait.competition.workshop
-l
nodes
=
1:ppn
=
1,mem
=
8gb
-N
"lmerall2all.ECOTP
${
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.4[2], run.lmer,merge.biomes.TF = TRUE,
$trait
, data.type = 'simple');print('done')
\"
"
>
Rscript_temp/allECOTP2
${
trait
}
.sh
qsub Rscript_temp/allECOTP2
${
trait
}
.sh
-d
~/trait.competition.workshop
-l
nodes
=
1:ppn
=
1,mem
=
8gb
-N
"lmerall2all.ECOTP2
${
trait
}
"
-q
opt32G
-j
oe
done
...
...
launch.cluster/launch_all_lmer_sample.bash
0 → 100644
View file @
571346b9
#!/bin/bash
# Georges Kunstler 14/05/2014
# read one variable
export
LD_LIBRARY_PATH
=
/usr/lib64/R/library
mkdir
-p
Rscript_temp
# 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
# # 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
, sample.vec.TF = TRUE);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
, sample.vec.TF = TRUE);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
done
scripts/analysis/results.fig.R
View file @
571346b9
...
...
@@ -16,6 +16,10 @@ names.biomes <- c('Desert', 'Desert', 'Woodland/shrubland', 'Temperate forest',
list.all.results.set
<-
readRDS
(
'output/list.lmer.out.all.NA.simple.set.rds'
)
list.all.results.ecocode
<-
readRDS
(
'output/list.lmer.out.all.NA.simple.ecocode.rds'
)
list.all.results.intra
<-
readRDS
(
'output/list.lmer.out.all.NA.intra.set.rds'
)
...
...
@@ -26,6 +30,13 @@ vec.rel.grad.set <- sapply(list.all.results.set,
function
(
list.t
)
{
max
(
abs
(
list.t
[[
'relgrad'
]]))})
vec.rel.grad.set
<
0.001
fun.get.conv
(
list.all.results.ecocode
)
vec.rel.grad.ecocode
<-
sapply
(
list.all.results.ecocode
,
function
(
list.t
)
{
max
(
abs
(
list.t
[[
'relgrad'
]]))})
vec.rel.grad.ecocode
<
0.001
fun.get.conv
(
list.all.results.intra
)
vec.rel.grad.set
<-
sapply
(
list.all.results.intra
,
function
(
list.t
)
{
max
(
abs
(
list.t
[[
'relgrad'
]]))})
...
...
@@ -102,7 +113,7 @@ dev.off()
pdf
(
'figs/figres12.TP.intra.pdf'
,
height
=
14
,
width
=
16
)
plot.param.mean.and.biomes.fixed
(
list.all.results.intra
,
data.type
=
"intra"
,
models
=
c
(
'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.set.species'
,
'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.set.fixed.biomes.species'
),
'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.set.fixed.biomes.species'
),
traits
=
c
(
'Wood.density'
,
'SLA'
,
'Max.height'
),
param.vec
=
c
(
"sumTnTfBn.abs"
,
"sumTfBn"
,
"sumTnBn"
,
"sumBn.intra"
,
"sumBn.inter"
,
"Tf"
),
...
...
@@ -124,7 +135,8 @@ dev.off()
pdf
(
'figs/figres12.ecocode.pdf'
,
height
=
14
,
width
=
16
)
plot.param.mean.and.biomes.fixed
(
list.all.results.set
,
data.type
=
"simple"
,
plot.param.mean.and.biomes.fixed
(
list.all.results.ecocode
,
data.type
=
"simple"
,
models
=
c
(
'lmer.LOGLIN.ER.AD.Tf.r.ecocode.species'
,
'lmer.LOGLIN.ER.AD.Tf.r.ecocode.fixed.biomes.species'
),
traits
=
c
(
'Wood.density'
,
'SLA'
,
'Max.height'
),
...
...
scripts/format.data/age.swiss.R
0 → 100644
View file @
571346b9
######################### READ DATA read individuals tree data
data.swiss1
<-
read.csv
(
"data/raw/Swiss/LFI12.csv"
,
header
=
TRUE
,
stringsAsFactors
=
FALSE
)
data.swiss2
<-
read.csv
(
"data/raw/Swiss/LFI23.csv"
,
header
=
TRUE
,
stringsAsFactors
=
FALSE
)
data.swiss3
<-
read.csv
(
"data/raw/Swiss/LFI34.csv"
,
header
=
TRUE
,
stringsAsFactors
=
FALSE
)
data.swiss
<-
rbind
(
data.swiss1
,
data.swiss2
,
data.swiss3
)
rm
(
data.swiss1
,
data.swiss2
,
data.swiss3
)
data.swiss
<-
data.swiss
[
order
(
data.swiss
$
BANR
),
]
library
(
dplyr
)
data.age
<-
data.swiss
%>%
group_by
(
CLNR
)
%>%
summarise
(
age.max
=
max
(
ALTERD1
,
na.rm
=
TRUE
))
# plot age dist
library
(
ggplot2
)
theme_simple
<-
function
(){
theme_bw
()
+
theme
(
plot.background
=
element_blank
(),
panel.grid.major
=
element_blank
(),
panel.grid.minor
=
element_blank
(),
legend.title
=
element_blank
(),
strip.background
=
element_blank
(),
legend.key
=
element_blank
(),
legend.position
=
c
(
.1
,
.15
),
strip.text
=
element_text
(
size
=
14
),
axis.title.x
=
element_text
(
size
=
14
),
axis.title.y
=
element_text
(
size
=
14
)
)
+
#draws x and y axis line
theme
(
axis.line
=
element_line
(
color
=
'black'
))
}
pdf
(
'figs/age.swiss.pdf'
)
ggplot
(
data.age
,
aes
(
x
=
age.max
))
+
geom_histogram
(
aes
(
y
=
..density..
),
colour
=
"black"
,
fill
=
"grey"
)
+
geom_density
(,
col
=
'red'
)
+
scale_x_log10
(
limits
=
c
(
1
,
1000
))
+
theme_simple
()
+
ggtitle
(
"Swiss"
)
+
xlab
(
"age (yr.)"
)
dev.off
()
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