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Kunstler Georges
traitcompet
Commits
204db846
Commit
204db846
authored
Apr 09, 2014
by
Georges Kunstler
Browse files
new report
parent
93f19645
Changes
31
Expand all
Hide whitespace changes
Inline
Side-by-side
R/analysis/glmer.all.output.R
View file @
204db846
...
...
@@ -8,11 +8,11 @@ traits <- c("SLA", "Wood.density","Max.height","Leaf.N","Seed.mass")
type.filling
<-
'species'
files
<-
c
()
for
(
trait
in
traits
){
for
(
model
in
c
(
model.files.lmer.Tf.1
,
model.files.lmer.Tf.2
,
model.files.lmer.Tf.3
,
model.files.lmer.Tf.4
)){
for
(
model
in
c
(
model.files.
g
lmer.Tf.1
,
model.files.
g
lmer.Tf.2
,
model.files.
g
lmer.Tf.3
[
-3
]
,
model.files.
g
lmer.Tf.4
)){
source
(
model
,
local
=
TRUE
)
model.obj
<-
load.model
()
pathout
<-
output.dir.glmer
(
model.obj
$
name
,
trait
,
'all'
,
pathout
<-
output.dir.glmer
(
model.obj
$
name
,
trait
,
type.filling
=
type.filling
)
files
<-
c
(
files
,
file.path
(
pathout
,
"glmer.results.global.rds"
))
...
...
R/analysis/glmer.output-fun.R
View file @
204db846
...
...
@@ -9,7 +9,6 @@ read.glmer.output <- function(file.name){
}
summarise.glmer.output
<-
function
(
x
){
list
(
nobs
=
nobs
(
x
),
R2m
=
Rsquared.glmm.lmer
(
x
)
$
Marginal
,
...
...
@@ -23,6 +22,20 @@ summarise.glmer.output <- function(x){
fixed.var
=
variance.fixed.glmm.lmer
(
x
))
}
summarise.glmer.all.output
<-
function
(
x
){
list
(
nobs
=
nobs
(
x
),
R2m
=
Rsquared.glmm.lmer
(
x
)
$
Marginal
,
R2c
=
Rsquared.glmm.lmer
(
x
)
$
Conditional
,
AIC
=
AIC
(
x
),
deviance
=
deviance
(
x
),
conv
=
x
@
optinfo
$
conv
,
effect.response.var
=
variance.fixed.glmm.lmer.effect.and.response
(
x
),
fixed.coeff.E
=
fixef
(
x
),
fixed.coeff.Std.Error
=
sqrt
(
diag
(
vcov
(
x
))),
fixed.var
=
variance.fixed.glmm.lmer
(
x
),
set.BLUP
=
coef
(
x
)
$
set.id
)
}
summarise.glmer.output.list
<-
function
(
f
){
output.glmer
<-
read.glmer.output
(
f
)
...
...
@@ -35,6 +48,17 @@ summarise.glmer.output.list <- function(f ){
return
(
res
)
}
summarise.glmer.output.list
<-
function
(
f
){
output.glmer
<-
read.glmer.output
(
f
)
if
(
!
is.null
(
output.glmer
)){
res
<-
list
(
files.details
=
files.details.all
(
f
),
glmer.summary
=
summarise.glmer.all.output
(
output.glmer
))
}
else
{
res
<-
NULL
}
return
(
res
)
}
files.details
<-
function
(
x
){
...
...
@@ -43,6 +67,12 @@ files.details <- function(x){
s
[
-
(
1
:
2
)]
}
files.details.all
<-
function
(
x
){
s
<-
data.frame
(
t
(
strsplit
(
x
,
"/"
,
fixed
=
TRUE
)[[
1
]]),
stringsAsFactors
=
FALSE
)
names
(
s
)
<-
c
(
"d1"
,
"d2"
,
"set"
,
"trait"
,
"filling"
,
"model"
,
"file"
)
s
[
-
(
1
:
2
)]
}
#### R squred functions
...
...
R/analysis/glmer.run.all.R
View file @
204db846
...
...
@@ -142,7 +142,7 @@ return((x-mean(x))/sd(x))
}
### get variables for lmer
fun.get.the.variables.for.glmer.tree.id
<-
function
(
data.tree
,
BATOT
,
CWM.tn
,
fun.get.the.variables.for.glmer.
no.
tree.id
<-
function
(
data.tree
,
BATOT
,
CWM.tn
,
abs.CWM.tntf
,
tf
,
min.BA.G
=
50
){
dead
<-
data.tree
[[
"dead"
]]
logD
<-
fun.center.and.standardized.var
(
log
(
data.tree
[[
"D"
]]))
...
...
R/analysis/lmer.nolog.all.output.R
View file @
204db846
...
...
@@ -9,7 +9,7 @@ type.filling <- 'species'
files
<-
c
()
for
(
trait
in
traits
){
for
(
model
in
c
(
model.files.lmer.Tf.1
,
model.files.lmer.Tf.2
,
model.files.lmer.Tf.3
,
model.files.lmer.Tf.4
)){
model.files.lmer.Tf.3
,
model.files.lmer.Tf.4
[
-4
]
)){
source
(
model
,
local
=
TRUE
)
model.obj
<-
load.model
()
pathout
<-
output.dir.lmer
(
model.obj
$
name
,
trait
,
'all'
,
...
...
@@ -19,6 +19,7 @@ for (trait in traits){
}
}
out
<-
lapply
(
files
,
summarise.lmer.output.all.list
)
...
...
R/analysis/lmer.output-fun.R
View file @
204db846
This diff is collapsed.
Click to expand it.
R/analysis/lmer.output.all-fun.R
View file @
204db846
...
...
@@ -10,7 +10,7 @@ read.lmer.output <- function(file.name){
summarise.lmer.output
<-
function
(
x
){
summarise.lmer.
all.
output
<-
function
(
x
){
list
(
nobs
=
nobs
(
x
),
R2m
=
Rsquared.glmm.lmer
(
x
)
$
Marginal
,
R2c
=
Rsquared.glmm.lmer
(
x
)
$
Conditional
,
...
...
@@ -21,7 +21,7 @@ summarise.lmer.output <- function(x){
fixed.coeff.E
=
fixef
(
x
),
fixed.coeff.Std.Error
=
sqrt
(
diag
(
vcov
(
x
))),
fixed.var
=
variance.fixed.glmm.lmer
(
x
),
ecocode
.BLUP
=
coef
(
x
)
$
set.id
)
set
.BLUP
=
coef
(
x
)
$
set.id
)
}
...
...
@@ -108,3 +108,24 @@ return(var.vec)
## create a data base from the global data
fun.merge.results.global
<-
function
(
list.res
,
names.param
=
c
(
"(Intercept)"
,
"Tf"
,
"logD"
,
"sumBn"
,
"sumTnBn"
,
"sumTfBn"
,
"sumTnTfBn.abs"
,
"sumTnTfBn.diff"
)){
df.details
<-
data.frame
(
list.res
$
files.details
[
1
:
4
],
list.res
$
lmer.summary
[
1
:
6
])
fun.rep.df
<-
function
(
x
,
df
=
df.details
)
df
n_rep
<-
nrow
(
list.res
$
lmer.summary
$
ecocode.BLUP
)
dat.t
<-
data.frame
(
matrix
(
rep
(
NA
,
n_rep
*
length
(
names.param
)),
nrow
=
n_rep
,
ncol
=
length
(
names.param
)))
names
(
dat.t
)
<-
c
(
names.param
)
dat.t
[,
match
(
names
(
list.res
$
lmer.summary
$
ecocode.BLUP
),
names
(
dat.t
))]
<-
list.res
$
lmer.summary
$
ecocode.BLUP
df.res
<-
data.frame
(
ecocode
=
rownames
(
list.res
$
lmer.summary
$
ecocode.BLUP
),
do.call
(
"rbind"
,
lapply
(
1
:
n_rep
,
fun.rep.df
)),
dat.t
)
return
(
df.res
)
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.AD.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"glmer.LOGLIN.AD.Tf.MAT.MAP"
,
glmer.formula
=
formula
(
"dead~1+Tf+log+MAT+MAP+(1+logD|species.id)+(1|plot.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"
))
glmer.formula
=
formula
(
"dead~1+Tf+
Tf:MAT+Tf:MAP+
log+MAT+MAP+(1+logD|species.id)+(1|plot.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"
))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.E.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"glmer.LOGLIN.E.Tf.MAT.MAP"
,
glmer.formula
=
formula
(
"dead~1+Tf+logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
))
glmer.formula
=
formula
(
"dead~1+Tf+
Tf:MAT+Tf:MAP+
logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.ER.AD.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"glmer.LOGLIN.ER.AD.Tf.MAT.MAP"
,
glmer.formula
=
formula
(
"dead~1+Tf+logD+MAT+MAP+(1-logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"
))
glmer.formula
=
formula
(
"dead~1+Tf+
Tf:MAT+Tf:MAP+
logD+MAT+MAP+(1-logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"
))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.ER.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"glmer.LOGLIN.ER.Tf.MAT.MAP"
,
glmer.formula
=
formula
(
"dead~1+Tf+logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
))
glmer.formula
=
formula
(
"dead~1+Tf+
Tf:MAT+Tf:MAP+
logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.HD.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"glmer.LOGLIN.HD.Tf.MAT.MAP"
,
glmer.formula
=
formula
(
"dead~1+Tf+logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.diff+sumTnTfBn.diff:MAT+sumTnTfBn.diff:MAP+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.diff-1|set.id)"
))
glmer.formula
=
formula
(
"dead~1+Tf+
Tf:MAT+Tf:MAP+
logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.diff+sumTnTfBn.diff:MAT+sumTnTfBn.diff:MAP+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.diff-1|set.id)"
))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.R.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"glmer.LOGLIN.R.Tf.MAT.MAP"
,
glmer.formula
=
formula
(
"dead~1+Tf+logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTfBn-1|set.id)"
))
glmer.formula
=
formula
(
"dead~1+Tf+
Tf:MAT+Tf:MAP+
logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTfBn-1|set.id)"
))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.nocomp.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"glmer.LOGLIN.simplecomp.Tf.MAT.MAP"
,
glmer.formula
=
formula
(
"dead~1+Tf+logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)"
))
glmer.formula
=
formula
(
"dead~1+Tf+
Tf:MAT+Tf:MAP+
logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)"
))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.simplecomp.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"glmer.LOGLIN.simplecomp.Tf.MAT.MAP"
,
glmer.formula
=
formula
(
"dead~1+Tf+logD+MAT+MAP+(1+logD|species.id)+(1|set.id)+(1|plot.id)+sumBn+sumBn:MAT+sumBn:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)"
))
glmer.formula
=
formula
(
"dead~1+Tf+
Tf:MAT+Tf:MAP+
logD+MAT+MAP+(1+logD|species.id)+(1|set.id)+(1|plot.id)+sumBn+sumBn:MAT+sumBn:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)"
))
}
...
...
R/analysis/model.lmer.all/model.lmer.LOGLIN.AD.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"lmer.LOGLIN.ER.Tf.MAT.MAP"
,
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+MAT+MAP+logD+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(logD-1|species.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"
))
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+
Tf:MAT+Tf:MAP+
MAT+MAP+logD+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(logD-1|species.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"
))
}
...
...
R/analysis/model.lmer.all/model.lmer.LOGLIN.AD.Tf.randomset.R
deleted
100644 → 0
View file @
93f19645
load.model
<-
function
()
{
list
(
name
=
"lmer.LOGLIN.AD.Tf.randomset"
,
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+logD+sumBn+sumTnTfBn.abs+(logD-1|species.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"
))
}
R/analysis/model.lmer.all/model.lmer.LOGLIN.E.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"lmer.LOGLIN.E.Tf.MAT.MAP"
,
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(logD-1|species.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
)
)
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+
Tf:MAT+Tf:MAP+
logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(logD-1|species.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
)
)
}
...
...
R/analysis/model.lmer.all/model.lmer.LOGLIN.E.Tf.randomset.R
deleted
100644 → 0
View file @
93f19645
load.model
<-
function
()
{
list
(
name
=
"lmer.LOGLIN.E.Tf.randomset"
,
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+logD+sumBn+sumTnBn+(logD-1|species.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
)
)
}
R/analysis/model.lmer.all/model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"lmer.LOGLIN.ER.AD.Tf.MAT.MAP"
,
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+MAT+MAP+logD+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(logD-1|species.id)+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-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)+Tf+
Tf:MAT+Tf:MAP+
MAT+MAP+logD+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(logD-1|species.id)+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"
))
}
...
...
R/analysis/model.lmer.all/model.lmer.LOGLIN.ER.Tf.MAT.MAP.R
View file @
204db846
load.model
<-
function
()
{
list
(
name
=
"lmer.LOGLIN.ER.Tf.MAT.MAP"
,
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+MAT+MAP+logD+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(logD-1|species.id)+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
))
lmer.formula.tree.id
=
formula
(
"logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+
Tf:MAT+Tf:MAP+
MAT+MAP+logD+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(logD-1|species.id)+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"
))
}
...
...
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