Commit ef28eec4 authored by Kunstler Georges's avatar Kunstler Georges
Browse files

launch null model TP

parent aa205e1c
......@@ -30,6 +30,9 @@ 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.0b <- file.path(path.model,
c("model.lmer.LOGLIN.MAT.MAP.r.set.species.R",
"model.lmer.LOGLIN.MAT.MAP.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"))
......
......@@ -63,7 +63,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 1
- Traits: Wood density, SLA, and Maximum height
- Source trait data: local
- Evidences of disturbances and succession dynamics: "The plot has been struck by hurricanes in 1989 and in 1998[@Uriarte-2009]. In addition, two-third of the plot is a secondary forest on land previously used for agriculture and logging[Uriarte-2009]."
- Evidences of disturbances and succession dynamics: "The plot has been struck by hurricanes in 1989 and in 1998[@Uriarte-2009]. In addition, two-third of the plot is a secondary forest on land previously used for agriculture and logging[@Uriarte-2009]."
- Contact of person in charge of data formatting: Plot data: J. Thompson (jiom@ceh.ac.uk) and J. Zimmerman (esskz@ites.upr.edu), Traits data: N. Swenson (swensonn@msu.edu )
- Comments:
- References:
......@@ -254,14 +254,14 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Kooyman, R.M. and Westoby, M. (2009) Costs of height gain in rainforest saplings: main stem scaling, functional traits and strategy variation across 75 species. Annals of Botany 104: 987-993.
- Kooyman, R.M., Rossetto, M., Allen, C. and Cornwell, W. (2012) Australian tropical and sub-tropical rainforest: phylogeny, functional biogeography and environmental gradients. Biotropica 44: 668-679.
## Age distribution of some forest data analysed.
## Age distribution for Europe and North America.
![Age distribution of forest area in 20-year age class for France, Switzerland and Sweden, estimated by Vilen et al.[@Vilen-2012]. The last class plotted at 150 years is for age > 140 years (except for Sweden where the last class 110 is age > 100 years).](../../figs/age_europe.pdf)
![Age distribution of forest area in 20-year age class for North America (USA and Canada), estimated by Pan et al.[@Pan-2011]. The last class plotted at 150 years is for age > 140 years.](../../figs/age_na.pdf)
# Supplementary discussion
## Trait effects and potential mechanisms
......
......@@ -53,7 +53,7 @@ list.t <- dlply(dat, 1, paste_name_data)
writeLines(unlist(list.t[dat[["Country"]]]))
```
## Age distribution of some forest data analysed.
## Age distribution for Europe and North America.
![Age distribution of forest area in 20-year age class for France, Switzerland and Sweden, estimated by Vilen et al.[@Vilen-2012]. The last class plotted at 150 years is for age > 140 years (except for Sweden where the last class 110 is age > 100 years).](../../figs/age_europe.pdf)
......
......@@ -103,16 +103,16 @@ pandoc.table(cor.mat,
list.all.results <-
readRDS.root('output/list.lmer.out.all.NA.simple.set.rds')
lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.set.species
mat.param <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
extract.param, list.res = list.all.results,
model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species',
model = 'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.set.species',
param.vec = c("(Intercept)", "logD", "Tf","sumBn",
"sumTnBn","sumTfBn", "sumTnTfBn.abs")))
mat.param.sd <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
extract.param.sd, list.res = list.all.results,
model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species',
model = 'lmer.LOGLIN.ER.AD.Tf.MAP.MAT.r.set.species',
param.vec = c("(Intercept)", "logD", "Tf","sumBn",
"sumTnBn","sumTfBn", "sumTnTfBn.abs")))
mat.R2c <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
......@@ -120,10 +120,10 @@ mat.R2c <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species'))
mat.R2m <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
extract.R2m, list.res = list.all.results,
model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species'))
model = 'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.set.species'))
mat.AIC <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
extract.AIC, list.res = list.all.results,
model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species'))
model = 'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r.set.species'))
mat.AIC.0 <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
extract.AIC, list.res = list.all.results,
model = 'lmer.LOGLIN.r.set.species'))
......
......@@ -21,7 +21,7 @@
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% % use microtype if available
% \IfFileExists{microtype.sty}{%
% \usepackage{microtype}
% \usepackage{microtype}
% \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
% }{}
......
......@@ -30,6 +30,14 @@ samplesize=$1
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[2], merge.biomes.TF = TRUE, run.lmer,$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${trait}" -q opt32G -j oe
# # ALL data 0b
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0b[1], run.lmer,$trait);print('done')\"" > Rscript_temp/all0b${trait}.sh
qsub Rscript_temp/all0b${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${trait}.sh
qsub Rscript_temp/all02b${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.02b${trait}" -q opt32G -j oe
# # # ALL data 1
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[1], run.lmer,$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
......@@ -63,19 +71,19 @@ 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${trait}" -q opt32G -j oe
# # # # ecocode TP
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.4[1], run.lmer,$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${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.4[2], run.lmer,merge.biomes.TF = TRUE,$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
......
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