Commit 0a6ffb09 authored by Georges Kunstler's avatar Georges Kunstler
Browse files

new lmer output processing

parent b85582e8
......@@ -4,24 +4,19 @@ source("R/analysis/lmer.output-fun.R")
source("R/analysis/lmer.run.R")
## LOOP OVER FILES AND NOT SCAN ALL FILES
traits <- c("SLA", "Wood.density","Max.height")
type.filling <- 'species'
## LOOP OVER FILES AND NOT SCAN ALL FILES SAMPLE PER ECOCODE
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,
model.files.lmer.Tf.5,
model.files.lmer.Tf.CAT.1,
model.files.lmer.Tf.CAT.2)){
model.files.lmer.Tf.2)){
source(model, local = TRUE)
model.obj <- load.model()
pathout <- output.dir('lmer', model.obj$name, trait, 'all.no.log',
type.filling=type.filling)
files <- c(files,file.path(pathout,"ecocode.id.results.nolog.all.rds"))
files <- c(files,file.path(pathout,"ecocode.results.nolog.all.rds"))
}
}
......@@ -32,25 +27,21 @@ names(out) <- lapply(lapply(files,files.details.all),
collapse="_"))
### remove missing
out <- out[!unlist(lapply(out,FUN=function(x) is.null(x$lmer.summary)))]
saveRDS(out,file='output/list.lmer.out.all.ecocode.id.no.log.rds')
saveRDS(out,file='output/list.lmer.out.all.ecocode.no.log.rds')
## LOOP OVER FILES AND NOT SCAN ALL FILES
traits <- c("SLA", "Wood.density","Max.height")
## LOOP OVER FILES AND NOT SCAN ALL FILES SAMPLE PER SP.NAME
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.5,
model.files.lmer.Tf.CAT.1,
model.files.lmer.Tf.CAT.2)){
model.files.lmer.Tf.2)){
source(model, local = TRUE)
model.obj <- load.model()
pathout <- output.dir('lmer', model.obj$name, trait, 'all.no.log',
type.filling=type.filling)
files <- c(files,file.path(pathout,"species.id.results.nolog.all.rds"))
files <- c(files,file.path(pathout,"sp.name.results.nolog.all.rds"))
}
}
......@@ -61,6 +52,31 @@ names(out) <- lapply(lapply(files,files.details.all),
collapse="_"))
### remove missing
out <- out[!unlist(lapply(out,FUN=function(x) is.null(x$lmer.summary)))]
saveRDS(out,file='output/list.lmer.out.all.species.id.no.log.rds')
saveRDS(out,file='output/list.lmer.out.all.sp.name.no.log.rds')
## LOOP OVER FILES AND NOT SCAN ALL FILES NO SAMPLE
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)){
source(model, local = TRUE)
model.obj <- load.model()
pathout <- output.dir('lmer', model.obj$name, trait, 'all.no.log',
type.filling=type.filling)
files <- c(files,file.path(pathout,"NA.results.nolog.all.rds"))
}
}
out <- lapply(files, summarise.lmer.output.all.list)
names(out) <- lapply(lapply(files,files.details.all),
function(x) paste(as.vector(x[names(x) != 'file']),
collapse="_"))
### remove missing
out <- out[!unlist(lapply(out,FUN=function(x) is.null(x$lmer.summary)))]
saveRDS(out,file='output/list.lmer.out.all.NA.no.log.rds')
%Functional traits have globally consistent effects on plant competition
% Functional traits have globally consistent effects on plant competition
% Georges Kunstler; David A Coomes; Daniel Falster; Francis Hui;
Rob Kooyman; Daniel Laughlin Lourens Poorter; Mark Vanderwel;
Ghislain Vieilledent; Joe Wright; Masahiro Aiba; John Caspersen;
Sylvie Gourlet-Fleury; Marc Hanewinkel; Bruno Herault; Hiroko Kurokawa;
Yusuke Onoda; Maria Uriarte; Sarah Richardson; Paloma Ruiz;
I-Fang Sun; Goran Ståhl; Nathan Swenson; Jill Thompson; Miguel Zavala;
Hongcheng Zeng; Jess Zimmerman; Niklaus E Zimmermann; Mark Westoby.
% BES-SFE Annual Meeting
David A. Coomes, Daniel Falster, Francis Hui, Rob Kooyman, Daniel Laughlin Lourens Poorter, Mark Vanderwel, Ghislain Vieilledent, Mark Westoby, Joe Wright, John Caspersen, Hongcheng Zeng, Sylvie Gourlet-Fleury Bruno Herault, Goran Ståhl, Jill Thompson, Sarah Richardson, Paloma Ruiz, I-Fang Sun, Nathan Swenson, Maria Uriarte, Miguel Zavala, Niklaus E. Zimmermann, Marc Hanewinkel, Jess Zimmerman, Yusuke Onoda, Hiroko Kurokawa, Masahiro Aiba.
Competition is a very important type of ecological interaction, especially in terrestrial vegetation where plants greatly modify the local environment for each other. Competition has influence on growth of individuals and survival, on how species mixtures will change over time into the future, and on community composition. However firm generalizations have yet to be established about outcomes of competition among tree species. Here we show how key species traits have consistent influences on growth and competition. The data sources are very large, including national forest inventories monitoring growth in sometimes millions of trees, and we here synthesize across a global set of such inventories plus also several large forest-monitoring plots. Some traits have strong effect on the growth rate of the species. Then traits in part determine the tolerance to competition and the impact of the competitor. A notable generalization is that trait values that favour tolerance to competition also render species slow growing in absence of competition. There is also a small but detectable benefit in reducing competition from trait-dissimilarity between focal plant and its competitors. The trait-based picture that emerges is much simpler and more general than a quantification of competition coefficients between each pair of species, which is intractable at the global scale. Our results demonstrate that traits may be used to predict competitive interactions between forest tree species at a large scale. We anticipate that our results can have profound influence on trait model of community assembly.
Competition is a very important type of ecological interaction, especially in terrestrial vegetation where plants greatly modify the local environment for each other. Competitive interactions influence the growth and survival of individuals, and thereby change community composition over time into the future. However firm generalizations have yet to be established about outcomes of competition among species. Here we show that key species’ traits have consistent influences on growth and competition. Our analysis synthesize individuals tree growth data for more than 3-millions trees across a global set of national forest inventories plus also several large forest-monitoring plots. Some traits have a strong effect on the growth rate of the species. Then traits in part determine the tolerance to competition and the impact of competitor’s on a focal tree. A notable generalization is that trait values that favour tolerance to competition also render species slow growing in absence of competition. There is also a small but detectable benefit in reducing competition from trait-dissimilarity between a focal plant and its competitors. The trait-based picture that emerges is much simpler and more general than a quantification of competition coefficients between each pair of species, which is intractable at the global scale. Our results demonstrate that traits may be used to predict competitive interactions in forests at a large scale. We also anticipate our results to have a profound influence on trait-based-models of community.
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