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Kunstler Georges
traitcompet
Commits
8593643c
Commit
8593643c
authored
Sep 14, 2015
by
kunstler
Browse files
launch jags not in parallel
parent
a77de9cc
Changes
3
Hide whitespace changes
Inline
Side-by-side
R/analysis/jags.output-fun.R
View file @
8593643c
...
...
@@ -6,76 +6,28 @@ read.jags.output <- function(file.name){
tryCatch
(
readRDS
(
file.name
),
error
=
function
(
cond
)
return
(
NULL
))
# Choose a return value in case of error
}
summarise.jags.output
<-
function
(
x
,
probs
=
c
(
0.05
,
0.1
,
0.5
,
0.9
,
0.95
)){
summarise.jags.output
<-
function
(
x
,
param.to.save
=
c
(
'intercept'
,
'mean_logD'
,
'mean_Tf'
,
'mean_sumBn'
,
'mean_sumTfBn'
,
'mean_sumTnBn'
,
'mean_sumTnTfBn_abs'
)){
list
(
niter
=
x
$
n.iter
,
Rhat
=
max
(
x
$
BUGSoutput
$
summary
[,
"Rhat"
]),
DIC
=
x
$
BUGSoutput
$
DIC
,
deviance
=
quantile
(
x
$
BUGSoutput
$
sims.matrix
[,
"deviance"
],
probs
=
probs
),
slope.trait
=
if
(
sum
(
colnames
(
x
$
BUGSoutput
$
sims.matrix
)
==
"slope.trait"
)
>
0
)
{
quantile
(
x
$
BUGSoutput
$
sims.matrix
[,
"slope.trait"
],
probs
=
probs
)}
else
{
rep
(
NA
,
length
(
probs
))},
slope.trait.r
=
if
(
sum
(
colnames
(
x
$
BUGSoutput
$
sims.matrix
)
==
"slope.trait.r"
)
>
0
)
{
quantile
(
x
$
BUGSoutput
$
sims.matrix
[,
"slope.trait.r"
],
probs
=
probs
)}
else
{
rep
(
NA
,
length
(
probs
))},
slope.trait.e
=
if
(
sum
(
colnames
(
x
$
BUGSoutput
$
sims.matrix
)
==
"slope.trait.e"
)
>
0
)
{
quantile
(
x
$
BUGSoutput
$
sims.matrix
[,
"slope.trait.e"
],
probs
=
probs
)}
else
{
rep
(
NA
,
length
(
probs
))},
slope.trait.re
=
if
(
sum
(
colnames
(
x
$
BUGSoutput
$
sims.matrix
)
==
"slope.trait.re"
)
>
0
)
{
quantile
(
x
$
BUGSoutput
$
sims.matrix
[,
"slope.trait.re"
],
probs
=
probs
)}
else
{
rep
(
NA
,
length
(
probs
))},
intercept.trait
=
if
(
sum
(
colnames
(
x
$
BUGSoutput
$
sims.matrix
)
==
"intercept.trait"
)
>
0
)
{
quantile
(
x
$
BUGSoutput
$
sims.matrix
[,
"intercept.trait"
],
probs
=
probs
)}
else
{
rep
(
NA
,
length
(
probs
))})
summary
=
x
$
BUGSoutput
$
summary
[
param.to.save
,],
DIC
=
x
$
BUGSoutput
$
DIC
,
deviance
=
quantile
(
x
$
BUGSoutput
$
sims.matrix
[,
"deviance"
],
probs
=
c
(
0.025
,
0.5
,
0.975
)))
}
summarise.jags.output.table
<-
function
(
f
,
probs
=
c
(
0.05
,
0.1
,
0.5
,
0.9
,
0.95
)
){
data.frame
(
probs
=
probs
,
files.details
(
f
),
as.data.frame
(
summarise.jags.output
(
read.jags.output
(
f
),
probs
=
probs
)),
row.names
=
NULL
)
}
summarise.jags.output.table.old
<-
function
(
f
,
probs
=
c
(
0.05
,
0.1
,
0.5
,
0.9
,
0.95
)
){
data.frame
(
probs
=
probs
,
files.details.old
(
f
),
as.data.frame
(
summarise.jags.output
(
read.jags.output
(
f
),
probs
=
probs
)),
row.names
=
NULL
)
list
(
file.names
=
files.details
(
f
),
list.summary
=
summarise.jags.output
(
read.jags.output
(
f
)))
}
files.details
<-
function
(
x
){
s
<-
data.frame
(
t
(
strsplit
(
x
,
"/"
,
fixed
=
TRUE
)[[
1
]]),
stringsAsFactors
=
FALSE
)
names
(
s
)
<-
c
(
"d1"
,
"d2"
,
"model"
,
"trait"
,
"set"
,
"ecocode"
,
"file"
)
s
}
files.details.old
<-
function
(
x
){
s
<-
t
(
strsplit
(
x
,
"/"
,
fixed
=
TRUE
)[[
1
]])
if
(
grepl
(
"SLA"
,
s
[,
5
])
==
1
){
z
<-
"SLA"
}
if
(
grepl
(
"Leaf.N"
,
s
[,
5
])
==
1
){
z
<-
"Leaf.N"
}
if
(
grepl
(
"Seed.mass"
,
s
[,
5
])
==
1
){
z
<-
"Seed.mass"
}
if
(
grepl
(
"Wood.density"
,
s
[,
5
])
==
1
){
z
<-
"Wood.density"
}
if
(
grepl
(
"Max.height"
,
s
[,
5
])
==
1
){
z
<-
"Max.height"
}
if
(
grepl
(
"NULL"
,
s
[,
5
])
==
1
){
u
<-
"NULL"
}
if
(
grepl
(
"AD"
,
s
[,
5
])
==
1
){
u
<-
"AD"
}
if
(
grepl
(
"HD"
,
s
[,
5
])
==
1
){
u
<-
"HD"
}
if
(
grepl
(
"RE"
,
s
[,
5
])
==
1
){
u
<-
"RE"
}
if
(
grepl
(
"RE2"
,
s
[,
5
])
==
1
){
u
<-
"RE2"
}
s
<-
data.frame
(
s
,
trait
=
z
,
model
=
u
)
names
(
s
)
<-
c
(
"d1"
,
"d2"
,
"set"
,
"ecocode"
,
"file"
,
"traits"
,
"model"
)
s
}
plot.param.quant
<-
function
(
x
,
y.mat
,
param.name
,
ecocode
){
...
...
launch.cluster/launch_all_jags.bash
View file @
8593643c
...
...
@@ -25,10 +25,10 @@ samplesize=$1
for
trait
in
"'SLA'"
"'Wood.density'"
"'Max.height'"
;
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(model.files.jags.Tf.1[1], run.jags.b, trait =
$trait
,data.type='simple', sample.size = NA, var.sample = 'wwf',iter =
$iter
, warmup =
$warmup
, chains = 3, thin =
$thin
, init.TF = FALSE
, method = 'parallel'
);print('done')
\"
"
>
Rscript_temp/speciesjags
${
trait
}
.sh
echo
"/usr/local/R/R-3.1.1/bin/Rscript -e
\"
source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(model.files.jags.Tf.1[1], run.jags.b, trait =
$trait
,data.type='simple', sample.size = NA, var.sample = 'wwf',iter =
$iter
, warmup =
$warmup
, chains = 3, thin =
$thin
, init.TF = FALSE);print('done')
\"
"
>
Rscript_temp/speciesjags
${
trait
}
.sh
qsub Rscript_temp/speciesjags
${
trait
}
.sh
-d
~/trait.competition.workshop
-l
nodes
=
1:ppn
=
4,mem
=
16gb
-N
"jags
${
trait
}
"
-q
opt32G
-j
oe
echo
"/usr/local/R/R-3.1.1/bin/Rscript -e
\"
source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(model.files.jags.Tf.1[2], run.jags.b, trait =
$trait
,data.type='simple', sample.size = NA, var.sample = 'wwf',iter =
$iter
, warmup =
$warmup
, chains = 3, thin =
$thin
, init.TF = FALSE, merge.biomes.TF = TRUE
, method = 'parallel'
);print('done')
\"
"
>
Rscript_temp/speciesjags2
${
trait
}
.sh
echo
"/usr/local/R/R-3.1.1/bin/Rscript -e
\"
source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(model.files.jags.Tf.1[2], run.jags.b, trait =
$trait
,data.type='simple', sample.size = NA, var.sample = 'wwf',iter =
$iter
, warmup =
$warmup
, chains = 3, thin =
$thin
, init.TF = FALSE, merge.biomes.TF = TRUE);print('done')
\"
"
>
Rscript_temp/speciesjags2
${
trait
}
.sh
qsub Rscript_temp/speciesjags2
${
trait
}
.sh
-d
~/trait.competition.workshop
-l
nodes
=
1:ppn
=
4,mem
=
16gb
-N
"jags2
${
trait
}
"
-q
opt32G
-j
oe
done
scripts/analysis/lmer.all.no.log.output.R
View file @
8593643c
...
...
@@ -7,17 +7,17 @@ source("R/analysis/lmer.run.R")
## ## save list of all output for NA
## format.all.output.lmer(file.name = "NA.wwf.results.nolog.all.rds",
## list.file.name = 'list.lmer.out.all.NA.simple.set.rds',
## models = c(model.files.lmer.Tf.0, model.files.lmer.Tf.1,
## model.files.lmer.Tf.2, model.files.lmer.Tf.3),
## traits = c("SLA", "Wood.density", "Max.height"))
format.all.output.lmer
(
file.name
=
"NA.wwf.results.nolog.all.rds"
,
list.file.name
=
'list.lmer.out.all.NA.intra.set.rds'
,
models
=
c
(
model.files.lmer.Tf.intra.1
,
model.files.lmer.Tf.intra.2
),
traits
=
c
(
"SLA"
,
"Wood.density"
,
"Max.height"
),
data.type
=
'intra'
)
list.file.name
=
'list.lmer.out.all.NA.simple.set.rds'
,
models
=
c
(
model.files.lmer.Tf.0
,
model.files.lmer.Tf.1
,
model.files.lmer.Tf.2
,
model.files.lmer.Tf.3
),
traits
=
c
(
"SLA"
,
"Wood.density"
,
"Max.height"
))
## format.all.output.lmer(file.name = "NA.wwf.results.nolog.all.rds",
## list.file.name = 'list.lmer.out.all.NA.intra.set.rds',
## models = c(model.files.lmer.Tf.intra.1,
## model.files.lmer.Tf.intra.2),
## traits = c("SLA", "Wood.density", "Max.height"),
## data.type = 'intra')
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