From 29b23ea29b95016beedb6c05e4387ba6b6adf04c Mon Sep 17 00:00:00 2001
From: kunstler <georges.kunstler@gmail.com>
Date: Fri, 29 May 2015 22:25:34 +0200
Subject: [PATCH] log MAT MAP
---
R/analysis/lmer.run.R | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/R/analysis/lmer.run.R b/R/analysis/lmer.run.R
index c664316..4efb1df 100644
--- a/R/analysis/lmer.run.R
+++ b/R/analysis/lmer.run.R
@@ -170,7 +170,7 @@ load.data.for.lmer <- function(trait, data.type,
df <- dplyr::filter(df, set == select.set.)
}
if(!is.na(sample.size.) ){
- if(sample.size. < length(unique(df$plot))){
+ if(sample.size. < length(unique(df$plot))){
if(!sample.vec.TF.){
if(sample.size. > length(unique(df$plot))){
sample.size. <- length(unique(df$plot))}
@@ -335,11 +335,11 @@ return(as.vector(scale(x, ...)))
get.variables <- function(data.tree, BATOT, CWM.tn,
abs.CWM.tntf, tf, ecocode.var = 'wwf',
- min.BA.G = 40){
+ min.BA.G = 40, min.MAT = 10){
logG <- scale.d(log(data.tree[["BA.G"]] + min.BA.G+1))
logD <- scale.d(log(data.tree[["D"]]))
-MAT <- scale.d(data.tree[["MAT"]])
-MAP <- scale.d(data.tree[["MAP"]])
+MAT <- scale.d(log(data.tree[["MAT"]]+min.MAT))
+MAP <- scale.d(log(data.tree[["MAP"]]))
species.id <- as.character(factor(data.tree[["sp.name"]]))
plot.id <- as.character(factor(data.tree[["plot"]]))
tree.id <- as.character(factor(data.tree[["tree.id"]]))
@@ -375,11 +375,11 @@ return(data.frame(logG = logG,
get.variables.Multi <- function(data.tree, BATOT, Multi.type = 'a',
ecocode.var = 'wwf',
- min.BA.G = 40){
+ min.BA.G = 40, min.MAT = 10){
logG <- scale.d(log(data.tree[["BA.G"]] + min.BA.G+1))
logD <- scale.d(log(data.tree[["D"]]))
-MAT <- scale.d(data.tree[["MAT"]])
-MAP <- scale.d(data.tree[["MAP"]])
+MAT <- scale.d(log(data.tree[["MAT"]]+min.MAT))
+MAP <- scale.d(log(data.tree[["MAP"]]))
species.id <- as.character(factor(data.tree[["sp.name"]]))
plot.id <- as.character(factor(data.tree[["plot"]]))
tree.id <- as.character(factor(data.tree[["tree.id"]]))
@@ -443,11 +443,11 @@ return(data.frame(logG = logG,
get.variables.cat <- function(data.tree, BATOT, CWM.tn,
abs.CWM.tntf, tf, ecocode.var = 'wwf',
- min.BA.G = 40){
+ min.BA.G = 40, min.MAT = 10){
logG <- scale.d(log(data.tree[["BA.G"]]+min.BA.G+1))
logD <- scale.d(log(data.tree[["D"]]))
-MAT <- scale.d(data.tree[["MAT"]])
-MAP <- scale.d(data.tree[["MAP"]])
+MAT <- scale.d(log(data.tree[["MAT"]]+min.MAT))
+MAP <- scale.d(log(data.tree[["MAP"]]))
species.id <- factor(data.tree[["sp.name"]])
plot.id <- factor(data.tree[["plot"]])
tree.id <- factor(data.tree[["tree.id"]])
--
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