Commit caff6b59 authored by kunstler's avatar kunstler
Browse files

output new

parent 719867f2
......@@ -200,8 +200,10 @@ segments( unlist(x + 1.96*sd), y-small.bar, unlist(x +1.96*sd), y+small.bar, .
fun.col.param <- function(){
t.col <- c('black', '#e41a1c', '#377eb8',
'#1f78b4', '#a6cee3',
'#984ea3', '#4daf4a', '#ff7f00')
names(t.col) <- c('logD', "Tf","sumBn", "sumTnBn",
names(t.col) <- c('logD', "Tf","sumBn", "sumBn.intra", "sumBn.inter",
"sumTnBn",
"sumTfBn", "sumTnTfBn.abs")
return(t.col)
}
......@@ -417,7 +419,7 @@ easyPredCI.param <- function(list.res, type, newdata, alpha=0.05) {
## construct 95% Normal CIs on the link scale and
## transform back to the response (probability) scale:
crit <- -qnorm(alpha/2)
if (type %in% c('alphar', 'alphae', 'alphal')) inter <- beta[4]
if (type %in% c('alphar', 'alphae', 'alphal')) inter <- beta[4]
if (type == 'maxG') inter <- beta[1]
cbind(newdata,
pred = pred - inter,
......@@ -1243,7 +1245,7 @@ if(p == 'maxG'){
if(t == 'Specific leaf area'){
if(p == 'maxG'){
fun.plot.param.tf(df = df.t,
param.sel = p,
param.sel = p,
xlab = expression(paste('Specific leaf area (m', m^2, ' m', g^-1, ')')),
col.param = col.vec[names.param[p]],
expr.param = expr.p.vec[p], add.ylab.TF = FALSE, cex.lab = 1.1, cex.axis =0.85, cex = 1)
......@@ -1259,7 +1261,7 @@ if(p == 'maxG'){
if(t == 'Maximum height'){
if(p == 'maxG'){
fun.plot.param.tf(df = df.t,
param.sel = p,
param.sel = p,
xlab = expression(paste('Maximum height (m)')),
col.param = col.vec[names.param[p]],
expr.param = expr.p.vec[p], add.ylab.TF = FALSE, cex.lab = 1.1, cex.axis =0.85, cex = 1)
......@@ -1347,7 +1349,7 @@ fun.plot.param.tf(df = filter(data.param,
par(mai=c(big.m , big.m,0.2,0.1), xpd = TRUE)
fun.plot.param.tf(df = filter(data.param,
traits == "Wood density"),
param.sel = 'alphar',
param.sel = 'alphar',
xlab = expression(
paste('Wood density (mg m', m^-3, ')')),
col.param = "#4daf4a",
......@@ -1358,7 +1360,7 @@ fun.plot.param.tf(df = filter(data.param,
par(mai=c(0.2, big.m,small.m,0.1), xpd = TRUE)
fun.plot.param.tf(df = filter(data.param,
traits == "Specific leaf area"),
param.sel = 'maxG',xlab = NA, xaxt= 'n',
param.sel = 'maxG',xlab = NA, xaxt= 'n',
col.param = "#e41a1c",
expr.param = expression(paste('Max growth ',
(m[1] %*% t[f]))))
......@@ -1366,7 +1368,7 @@ fun.plot.param.tf(df = filter(data.param,
par(mai=c(big.m , big.m,0.2,0.1), xpd = TRUE)
fun.plot.param.tf(df = filter(data.param,
traits == "Specific leaf area"),
param.sel = 'alphae',
param.sel = 'alphae',
xlab = expression(
paste('Specific leaf area (m', m^2, ' m', g^-1, ')')) ,
col.param = "#984ea3",
......
......@@ -6,35 +6,12 @@ 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.0.rds',
## models = c(model.files.lmer.Tf.0),
## 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.simple.set.rds',
models = c(model.files.lmer.Tf.0, model.files.lmer.Tf.1),
models = c(model.files.lmer.Tf.0, model.files.lmer.Tf.1, model.files.lmer.Tf.2,
model.files.lmer.Tf.3, model.files.lmer.Tf.4),
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.simple.set.TP.rds',
## models = c(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.all.census.set.rds',
## models = c(model.files.lmer.Tf.2),
## traits = c("SLA", "Wood.density", "Max.height"),
## data.type = 'all.census'
## )
## format.all.output.lmer(file.name = "NA.wwf.results.nolog.all.rds",
## list.file.name = 'list.lmer.out.all.NA.simple.set.Multi.rds',
## models = c(model.files.lmer.Tf.Multi),
## traits = c("Multi"),
## data.type = 'Multi'
## )
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