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legume.r
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legume.r
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## Code for correlating life history with status (threatened/invasive) of legumes
## Updated 08 March 2008 (CJAB)
## Remove everything
rm(list = ls())
## Import data
setwd("~/Documents/Papers/Plants/Legume threat & invasion/data/")
dat <- read.table("legume4.csv",header=T,sep=",")
## Import NatureServe data for NA species only
#dat <- read.table("C:\\Documents and Settings\\cbradshaw\\My Documents\\Papers\\Extinctions\\Legume threat & invasion\\data\\natureservelegumes.csv",header=T,sep=",")
## Test response
#test.var <- "threat"
test.var <- "IUCN"
#test.var <- "invasive"
#test.var <- "both"
## univariate models only
univ <- "no"
#univ <- "yes"
## Remove IUCN threat classes B and D2 (i.e., those 'restricted in range')
rng.rem <- 1 ## '1' to remove B&D2 species, '0' to keep them
## With or without 'seedsize'
#wseedsize <- 1
wseedsize <- 0
## With height as covariate
#wheightcov <- 1
wheightcov <- 0
## With leaf length as covariate
#wllmaxcov <- 1
wllmaxcov <- 0
## With nominate phylogenetic groups (NPG) instead of subfamily?
wNPG <- "no" ## "no" if random effect should be subfam/tribe
#Convert var to factors
dat$subfam <- factor(dat$subfam)
dat$tribe <- factor(dat$tribe)
#dat$ecores <- factor(ecores)
dat$ndist <- factor(dat$ndist)
dat$curdist <- factor(dat$curdist)
dat$NPG <- factor(dat$NPG)
#dat$range <- factor(ifelse(range == 2 | range == 3, 2, 1))
dat$range <- factor(dat$range, ordered=T)
dat$endem <- factor(dat$endem)
dat$alt <- factor(dat$alt)
dat$hbt <- factor(dat$hbt)
dat$cult <- factor(dat$cult)
#dat$hab <- factor(dat$hab)
dat$hab <- factor(dat$hab, levels = rev(sort(unique(dat$hab))),ordered=T)
dat$mode <- factor(dat$mode)
dat$ht <- factor(dat$ht, ordered=T)
lhtcov <- log10(ifelse(dat$ht == 1, 0.5, (ifelse(dat$ht == 2, 5, 15))))
dat$arm <- factor(dat$arm)
dat$hair <- factor(dat$hair)
dat$leaflmin <- factor(dat$leaflmin)
#dat$leaflmax <- factor(dat$leaflmax)
dat$leaflmax <- factor(dat$leaflmax,ordered=T)
lllmaxcov <- log10(dat$llmaxcov)
dat$leafmarg <- factor(dat$leafmarg)
dat$leaftype <- factor(dat$leaftype)
dat$flordisp <- factor(dat$flordisp)
dat$hook <- factor(dat$hook)
dat$deh <- factor(dat$deh)
dat$seedsize <- factor(dat$seedsize)
dat$seedcoat <- factor(dat$seedcoat)
dat <- data.frame(dat,lhtcov,lllmaxcov)
## Examine NA numbers (%)
attach(dat)
100*(1-(length(na.omit(as.numeric(range)))/length(as.numeric(range))))
100*(1-(length(na.omit(as.numeric(endem)))/length(as.numeric(endem))))
100*(1-(length(na.omit((alt)))/length((alt))))
100*(1-(length(na.omit((hbt)))/length((hbt))))
100*(1-(length(na.omit((cult)))/length((cult))))
100*(1-(length(na.omit((hab)))/length((hab))))
100*(1-(length(na.omit((mode)))/length((mode))))
100*(1-(length(na.omit((ht)))/length((ht))))
100*(1-(length(na.omit((arm)))/length((arm))))
100*(1-(length(na.omit((hair)))/length((hair))))
100*(1-(length(na.omit((leaflmax)))/length((leaflmax))))
100*(1-(length(na.omit((leafmarg)))/length((leafmarg))))
100*(1-(length(na.omit((leaftype)))/length((leaftype))))
100*(1-(length(na.omit((flordisp)))/length((flordisp))))
100*(1-(length(na.omit((hook)))/length((hook))))
100*(1-(length(na.omit((deh)))/length((deh))))
100*(1-(length(na.omit((seedsize)))/length((seedsize))))
100*(1-(length(na.omit((seedcoat)))/length((seedcoat))))
detach(dat)
## Correlation matrix
dat.cor <- na.omit(data.frame(as.integer(dat$range),as.integer(dat$alt),as.integer(dat$hbt),as.integer(dat$hab),as.integer(dat$mode),as.integer(dat$ht),as.integer(dat$arm),as.integer(dat$hair),as.integer(dat$leaflmax),as.integer(dat$flordisp),as.integer(dat$hook),as.integer(dat$deh),as.integer(dat$seedsize)))
colnames(dat.cor) <- c("range","altitude","habitat","habit","life cycle","height","armaments","hair","leaf length","fdisplay","hooks","deh","ssize")
cor(dat.cor,y=NULL,method="spearman")
cor(dat.cor,y=NULL,method="kendall")
## IUCN categories
#IUCN status
#1=EX or EW; 2=CR; 3=EN; 4=VU; 5=LR-cd/nt (NT); 6=DD (removed); 7=Normal; 8=Weedy; 9=Invasive
summary(as.factor(dat$IUCN))
IUCNstat <- as.factor(ifelse(dat$IUCN <= 4, 1, 0))
dat <- data.frame(dat,IUCNstat)
## Choose data subset
## Remove invasive species for threat/not threat analysis
if (test.var == "threat") {
data <- dat[dat$ecores != 1,]
## Change threat code
threat <- as.factor(abs(as.integer(data$ecores)))
data <- data.frame(data,threat)}
## Remove invasive, weedy and normal species for IUCN comparison (EX,EW,CR,EN,VU versus LR)
if (test.var == "IUCN") {
data <- dat[dat$IUCN <=5,]}
## Remove threatened species for invasive/not invasive analysis
if (test.var == "invasive") {
data <- dat[dat$ecores != -1,]
inv <- as.factor(abs(as.integer(data$ecores)))
data <- data.frame(data,inv)}
## Remove 'normal' species for invasive/threatened analysis
if (test.var == "both") {
data <- dat[dat$ecores != 0,]
thinv <- as.factor(ifelse(as.integer(data$ecores) == -1, 1, 0))
data <- data.frame(data,thinv)}
## Remove range-restricted species (IUCN class B2 & D) (for threat)
iucnrge <- ifelse(data$IUCNtyp == "B" | data$IUCNtyp == "D2" | data$IUCNtyp == "BD2", 0, 1)
data <- data.frame(data,iucnrge)
if (rng.rem == 1) {
data <- data[data$iucnrge == 1,]}
## remove NAs for threat status analysis
if (test.var == "threat" & wseedsize == 1) {
data1 <- na.omit(data.frame(data$cult,data$threat,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$alt,data$hbt,data$hab,data$mode,data$ht,data$arm,data$hair,data$leaflmax,data$flordisp,data$hook,data$deh,data$seedsize))
colnames(data1) <- c("cult","threat","subfam","NPG","tribe","gen","range","alt","hbt","hab","mode","ht","arm","hair","leaflmax","flordisp","hook","deh","seedsize")}
if (test.var == "threat" & wseedsize == 0) {
data1 <- na.omit(data.frame(data$cult,data$threat,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$alt,data$hbt,data$hab,data$mode,data$ht,data$arm,data$hair,data$leaflmax,data$flordisp,data$hook,data$deh))
colnames(data1) <- c("cult","threat","subfam","NPG","tribe","gen","range","alt","hbt","hab","mode","ht","arm","hair","leaflmax","flordisp","hook","deh")}
if (test.var == "threat" & wseedsize == 1 & wheightcov == 1 & wllmaxcov == 1) {
data1 <- na.omit(data.frame(data$cult,data$threat,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$alt,data$hbt,data$hab,data$mode,data$lhtcov,data$arm,data$hair,data$lllmaxcov,data$flordisp,data$hook,data$deh,data$seedsize))
colnames(data1) <- c("cult","threat","subfam","NPG","tribe","gen","range","alt","hbt","hab","mode","ht","arm","hair","leaflmax","flordisp","hook","deh","seedsize")}
if (test.var == "threat" & wseedsize == 0 & wheightcov == 1 & wllmaxcov == 1) {
data1 <- na.omit(data.frame(data$cult,data$threat,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$alt,data$hbt,data$hab,data$mode,data$lhtcov,data$arm,data$hair,data$lllmaxcov,data$flordisp,data$hook,data$deh))
colnames(data1) <- c("cult","threat","subfam","NPG","tribe","gen","range","alt","hbt","hab","mode","ht","arm","hair","leaflmax","flordisp","hook","deh")}
## remove NAs for IUCN status analysis
if (test.var == "IUCN") {
data1 <- na.omit(data.frame(data$cult,data$IUCNstat,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$alt,data$hbt,data$hab,data$mode,data$ht,data$arm,data$hair,data$leaflmax,data$flordisp,data$hook,data$deh))
colnames(data1) <- c("cult","IUCNstat","subfam","NPG","tribe","gen","range","alt","hbt","hab","mode","ht","arm","hair","leaflmax","flordisp","hook","deh")}
## remove NAs for invasiveness analysis
if (test.var == "invasive" & wseedsize == 1) {
data1 <- na.omit(data.frame(data$inv,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$hab,data$mode,data$arm,data$hair,data$leaflmax,data$flordisp,data$ht,data$deh,data$hook,data$alt,data$hbt,data$seedsize))
colnames(data1) <- c("inv","subfam","NPG","tribe","gen","range","hab","mode","arm","hair","leaflmax","flordisp","ht","deh","hook","alt","hbt","seedsize")}
if (test.var == "invasive" & wseedsize == 0) {
data1 <- na.omit(data.frame(data$inv,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$hab,data$mode,data$arm,data$hair,data$leaflmax,data$flordisp,data$ht,data$deh,data$hook,data$alt,data$hbt))
colnames(data1) <- c("inv","subfam","NPG","tribe","gen","range","hab","mode","arm","hair","leaflmax","flordisp","ht","deh","hook","alt","hbt")}
if (test.var == "invasive" & wseedsize == 1 & wheightcov == 1 & wllmaxcov == 1) {
data1 <- na.omit(data.frame(data$inv,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$hab,data$mode,data$arm,data$hair,data$lllmaxcov,data$flordisp,data$lhtcov,data$deh,data$hook,data$alt,data$hbt,data$seedsize))
colnames(data1) <- c("inv","subfam","NPG","tribe","gen","range","hab","mode","arm","hair","leaflmax","flordisp","ht","deh","hook","alt","hbt","seedsize")}
if (test.var == "invasive" & wseedsize == 0 & wheightcov == 1 & wllmaxcov == 1) {
data1 <- na.omit(data.frame(data$inv,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$hab,data$mode,data$arm,data$hair,data$lllmaxcov,data$flordisp,data$lhtcov,data$deh,data$hook,data$alt,data$hbt))
colnames(data1) <- c("inv","subfam","NPG","tribe","gen","range","hab","mode","arm","hair","leaflmax","flordisp","ht","deh","hook","alt","hbt")}
## remove NAs for both analysis
if (test.var == "both" & wseedsize == 1) {
data1 <- na.omit(data.frame(data$thinv,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$hab,data$mode,data$arm,data$hair,data$leaflmax,data$flordisp,data$ht,data$deh,data$hook,data$alt,data$hbt,data$seedsize))
colnames(data1) <- c("thinv","subfam","NPG","tribe","gen","range","hab","mode","arm","hair","leaflmax","flordisp","ht","deh","hook","alt","hbt","seedsize")}
if (test.var == "both" & wseedsize == 0) {
data1 <- na.omit(data.frame(data$thinv,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$hab,data$mode,data$arm,data$hair,data$leaflmax,data$flordisp,data$ht,data$deh,data$hook,data$alt,data$hbt))
colnames(data1) <- c("thinv","subfam","NPG","tribe","gen","range","hab","mode","arm","hair","leaflmax","flordisp","ht","deh","hook","alt","hbt")}
if (test.var == "both" & wseedsize == 1 & wheightcov == 1 & wllmaxcov == 1) {
data1 <- na.omit(data.frame(data$thinv,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$hab,data$mode,data$arm,data$hair,data$lllmaxcov,data$flordisp,data$lhtcov,data$deh,data$hook,data$alt,data$hbt,data$seedsize))
colnames(data1) <- c("thinv","subfam","NPG","tribe","gen","range","hab","mode","arm","hair","leaflmax","flordisp","ht","deh","hook","alt","hbt","seedsize")}
if (test.var == "both" & wseedsize == 0 & wheightcov == 1 & wllmaxcov == 1) {
data1 <- na.omit(data.frame(data$thinv,data$subfam,data$NPG,data$tribe,data$gen,data$range,data$hab,data$mode,data$arm,data$hair,data$lllmaxcov,data$flordisp,data$lhtcov,data$deh,data$hook,data$alt,data$hbt))
colnames(data1) <- c("thinv","subfam","NPG","tribe","gen","range","hab","mode","arm","hair","leaflmax","flordisp","ht","deh","hook","alt","hbt")}
## remove cultivars (for threat & IUCN)
if (test.var == "threat" | test.var == "IUCN") {
data1 <- data1[data1$cult == 0,]}
## Sample size
dim(data1)[1]
if (test.var == "invasive") {
table(data1$inv)}
if (test.var == "threat") {
table(data1$threat)}
if (test.var == "IUCN") {
table(data1$IUCNstat)}
if (test.var == "both") {
table(data1$thinv)}
## select model type
model.type <- "lmer"
#model.type <- "glm"
## Load libraries
library(MASS)
library(lme4)
library(Matrix)
AICc.lmer <- function(...) {
models <- list(...)
num.mod <- length(models)
AICcs <- numeric(num.mod)
ns <- numeric(num.mod)
ks <- numeric(num.mod)
AICc.vec <- rep(0,num.mod)
for (i in 1:num.mod) {
n <- models[[i]]@XtX@x[1]
k <- length(models[[i]]@fixef)+sum(models[[i]]@nc)+1
AICcs[i] <- (-2*logLik(models[[i]])[1]) + ((2*k*n)/(n-k-1))
ns[i] <- n
ks[i] <- k
AICc.vec[i] <- AICcs[i]}
return(AICc.vec)}
BIC.lmer <- function(...) {
models <- list(...)
num.mod <- length(models)
BICs <- numeric(num.mod)
ns <- numeric(num.mod)
ks <- numeric(num.mod)
BIC.vec <- rep(0,num.mod)
for (i in 1:num.mod) {
n <- models[[i]]@XtX@x[1]
k <- length(models[[i]]@fixef)+sum(models[[i]]@nc)+1
BICs[i] <- (-2*logLik(models[[i]])) + k*log(n)
ns[i] <- n
ks[i] <- k
BIC.vec[i] <- BICs[i]}
return(BIC.vec)}
# Set functions
AICc.glm <- function(...) {
models <- list(...)
num.mod <- length(models)
AICcs <- numeric(num.mod)
ns <- numeric(num.mod)
ks <- numeric(num.mod)
AICc.vec <- rep(0,num.mod)
for (i in 1:num.mod) {
if (length(models[[i]]$df.residual) == 0) n <- models[[i]]$dims$N else n <- length(models[[i]]$residuals)
if (length(models[[i]]$df.residual) == 0) k <- sum(models[[i]]$dims$ncol) else k <- (length(models[[i]]$coeff))+1
AICcs[i] <- (-2*logLik(models[[i]])) + ((2*k*n)/(n-k-1))
ns[i] <- n
ks[i] <- k
AICc.vec[i] <- AICcs[i]}
return(AICc.vec)}
BIC.glm <- function(...) {
models <- list(...)
num.mod <- length(models)
BICs <- numeric(num.mod)
ns <- numeric(num.mod)
ks <- numeric(num.mod)
BIC.vec <- rep(0,num.mod)
for (i in 1:num.mod) {
if (length(models[[i]]$df.residual) == 0) n <- models[[i]]$dims$N else n <- length(models[[i]]$residuals)
if (length(models[[i]]$df.residual) == 0) k <- sum(models[[i]]$dims$ncol) else k <- (length(models[[i]]$coeff))+1
BICs[i] <- (-2*logLik(models[[i]])) + k*log(n)
ns[i] <- n
ks[i] <- k
BIC.vec[i] <- BICs[i]}
return(BIC.vec)}
k.lmer <- function(x) {
if (length(x$df.residual) == 0) length(x@fixef)+sum(x@nc)+1}
k.glm <- function(x) {
if (length(x$df.residual) == 0) k <- sum(x$dims$ncol) else k <- (length(x$coeff)+1)}
delta.IC <- function(x) x - min(x) ## where x is a vector of an IC
weight.IC <- function(x) (exp(-0.5*x))/sum(exp(-0.5*x)) ## Where x is a vector of dIC
chdev.lmer <- function(x) ((( as.numeric(dev.null) - as.numeric(deviance(x)))/ as.numeric(dev.null)*100))
chdev.glm <- function(x) ((( as.numeric(x[12]) - as.numeric(x[10]))/ as.numeric(x[12]))*100) ## % change in deviance, where x is glm object
n <- dim(data1)[1]
n
#######################
## Define model sets ##
#######################
##########
## lmer ##
##########
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "threat" & wseedsize == 1 & univ == "no") {
## Height-only model
mod.1 <- "threat~ht+(1|subfam/tribe)"
## 'habitat' models
mod.2 <- "threat~range+(1|subfam/tribe)"
mod.3 <- "threat~range+hbt+(1|subfam/tribe)"
mod.4 <- "threat~range+alt+(1|subfam/tribe)"
mod.5 <- "threat~range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.6 <- "threat~mode+(1|subfam/tribe)"
mod.7 <- "threat~hab+(1|subfam/tribe)"
mod.8 <- "threat~mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.9 <- "threat~flordisp+(1|subfam/tribe)"
mod.10 <- "threat~hook+(1|subfam/tribe)"
mod.11 <- "threat~deh+(1|subfam/tribe)"
mod.12 <- "threat~seedsize+(1|subfam/tribe)"
mod.13 <- "threat~hook+deh+(1|subfam/tribe)"
mod.14 <- "threat~flordisp+hook+deh+(1|subfam/tribe)"
mod.15 <- "threat~flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.16 <- "threat~arm+(1|subfam/tribe)"
mod.17 <- "threat~hair+(1|subfam/tribe)"
mod.18 <- "threat~leaflmax+(1|subfam/tribe)"
mod.19 <- "threat~arm+hair+(1|subfam/tribe)"
mod.20 <- "threat~leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.21 <- "threat~range+mode+hab+(1|subfam/tribe)"
mod.22 <- "threat~range+hab+(1|subfam/tribe)"
mod.23 <- "threat~range+hbt+mode+hab+(1|subfam/tribe)"
mod.24 <- "threat~range+alt+mode+hab+(1|subfam/tribe)"
mod.25 <- "threat~range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.26 <- "threat~flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.27 <- "threat~hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.28 <- "threat~deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.29 <- "threat~seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.30 <- "threat~hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.31 <- "threat~flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.32 <- "threat~flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## All above with allometric control (height)
## 'habitat' models
mod.33 <- "threat~ht+range+(1|subfam/tribe)"
mod.34 <- "threat~ht+range+hbt+(1|subfam/tribe)"
mod.35 <- "threat~ht+range+alt+(1|subfam/tribe)"
mod.36 <- "threat~ht+range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.37 <- "threat~ht+mode+(1|subfam/tribe)"
mod.38 <- "threat~ht+hab+(1|subfam/tribe)"
mod.39 <- "threat~ht+mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.40 <- "threat~ht+flordisp+(1|subfam/tribe)"
mod.41 <- "threat~ht+hook+(1|subfam/tribe)"
mod.42 <- "threat~ht+deh+(1|subfam/tribe)"
mod.43 <- "threat~ht+seedsize+(1|subfam/tribe)"
mod.44 <- "threat~ht+hook+deh+(1|subfam/tribe)"
mod.45 <- "threat~ht+flordisp+hook+deh+(1|subfam/tribe)"
mod.46 <- "threat~ht+flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.47 <- "threat~ht+arm+(1|subfam/tribe)"
mod.48 <- "threat~ht+hair+(1|subfam/tribe)"
mod.49 <- "threat~ht+leaflmax+(1|subfam/tribe)"
mod.50 <- "threat~ht+arm+hair+(1|subfam/tribe)"
mod.51 <- "threat~ht+leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.52 <- "threat~ht+range+mode+hab+(1|subfam/tribe)"
mod.53 <- "threat~ht+range+hab+(1|subfam/tribe)"
mod.54 <- "threat~ht+range+hbt+mode+hab+(1|subfam/tribe)"
mod.55 <- "threat~ht+range+alt+mode+hab+(1|subfam/tribe)"
mod.56 <- "threat~ht+range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.57 <- "threat~ht+flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.58 <- "threat~ht+hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.59 <- "threat~ht+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.60 <- "threat~ht+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.61 <- "threat~ht+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.62 <- "threat~ht+flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.63 <- "threat~ht+flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## saturated model
mod.64 <- "threat~ht+range+hbt+alt+mode+hab+flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## null model
mod.65 <- "threat~1+(1|subfam/tribe)"
## Make model vector
mod.vec <- c(mod.1,mod.2,mod.3,mod.4,mod.5,mod.6,mod.7,mod.8,mod.9,mod.10,mod.11,mod.12,mod.13,mod.14,mod.15,mod.16,mod.17,mod.18,mod.19,mod.20,mod.21,mod.22,mod.23,mod.24,mod.25,mod.26,mod.27,mod.28,mod.29,mod.30,mod.31,mod.32,mod.33,mod.34,mod.35,mod.36,mod.37,mod.38,mod.39,mod.40,mod.41,mod.42,mod.43,mod.44,mod.45,mod.46,mod.47,mod.48,mod.49,mod.50,mod.51,mod.52,mod.53,mod.54,mod.55,mod.56,mod.57,mod.58,mod.59,mod.60,mod.61,mod.62,mod.63,mod.64,mod.65)
}
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "threat" & univ == "yes") {
mod.1 <- "threat~ht+(1|subfam/tribe)"
mod.2 <- "threat~range+(1|subfam/tribe)"
mod.3 <- "threat~hbt+(1|subfam/tribe)"
mod.4 <- "threat~alt+(1|subfam/tribe)"
mod.5 <- "threat~mode+(1|subfam/tribe)"
mod.6 <- "threat~hab+(1|subfam/tribe)"
mod.7 <- "threat~flordisp+(1|subfam/tribe)"
mod.8 <- "threat~hook+(1|subfam/tribe)"
mod.9 <- "threat~deh+(1|subfam/tribe)"
mod.10 <- "threat~arm+(1|subfam/tribe)"
mod.11 <- "threat~hair+(1|subfam/tribe)"
mod.12 <- "threat~leaflmax+(1|subfam/tribe)"
mod.13 <- "threat~1+(1|subfam/tribe)"
## Make model vector
mod.vec <- c(mod.1,mod.2,mod.3,mod.4,mod.5,mod.6,mod.7,mod.8,mod.9,mod.10,mod.11,mod.12,mod.13)
}
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "threat" & wseedsize == 0 & univ == "no") {
## Height-only model
mod.1 <- "threat~ht+(1|subfam/tribe)"
## 'habitat' models
mod.2 <- "threat~range+(1|subfam/tribe)"
mod.3 <- "threat~range+hbt+(1|subfam/tribe)"
mod.4 <- "threat~range+alt+(1|subfam/tribe)"
mod.5 <- "threat~range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.6 <- "threat~mode+(1|subfam/tribe)"
mod.7 <- "threat~hab+(1|subfam/tribe)"
mod.8 <- "threat~mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.9 <- "threat~flordisp+(1|subfam/tribe)"
mod.10 <- "threat~hook+(1|subfam/tribe)"
mod.11 <- "threat~deh+(1|subfam/tribe)"
#mod.12 <- "threat~seedsize+(1|subfam/tribe)"
mod.13 <- "threat~hook+deh+(1|subfam/tribe)"
mod.14 <- "threat~flordisp+hook+deh+(1|subfam/tribe)"
#mod.15 <- "threat~flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.16 <- "threat~arm+(1|subfam/tribe)"
mod.17 <- "threat~hair+(1|subfam/tribe)"
mod.18 <- "threat~leaflmax+(1|subfam/tribe)"
mod.19 <- "threat~arm+hair+(1|subfam/tribe)"
mod.20 <- "threat~leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.21 <- "threat~range+mode+hab+(1|subfam/tribe)"
mod.22 <- "threat~range+hab+(1|subfam/tribe)"
mod.23 <- "threat~range+hbt+mode+hab+(1|subfam/tribe)"
mod.24 <- "threat~range+alt+mode+hab+(1|subfam/tribe)"
mod.25 <- "threat~range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.26 <- "threat~flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.27 <- "threat~hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.28 <- "threat~deh+arm+hair+leaflmax+(1|subfam/tribe)"
#mod.29 <- "threat~seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.30 <- "threat~hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.31 <- "threat~flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
#mod.32 <- "threat~flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## All above with allometric control (height)
## 'habitat' models
mod.33 <- "threat~ht+range+(1|subfam/tribe)"
mod.34 <- "threat~ht+range+hbt+(1|subfam/tribe)"
mod.35 <- "threat~ht+range+alt+(1|subfam/tribe)"
mod.36 <- "threat~ht+range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.37 <- "threat~ht+mode+(1|subfam/tribe)"
mod.38 <- "threat~ht+hab+(1|subfam/tribe)"
mod.39 <- "threat~ht+mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.40 <- "threat~ht+flordisp+(1|subfam/tribe)"
mod.41 <- "threat~ht+hook+(1|subfam/tribe)"
mod.42 <- "threat~ht+deh+(1|subfam/tribe)"
#mod.43 <- "threat~ht+seedsize+(1|subfam/tribe)"
mod.44 <- "threat~ht+hook+deh+(1|subfam/tribe)"
mod.45 <- "threat~ht+flordisp+hook+deh+(1|subfam/tribe)"
#mod.46 <- "threat~ht+flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.47 <- "threat~ht+arm+(1|subfam/tribe)"
mod.48 <- "threat~ht+hair+(1|subfam/tribe)"
mod.49 <- "threat~ht+leaflmax+(1|subfam/tribe)"
mod.50 <- "threat~ht+arm+hair+(1|subfam/tribe)"
mod.51 <- "threat~ht+leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.52 <- "threat~ht+range+mode+hab+(1|subfam/tribe)"
mod.53 <- "threat~ht+range+hab+(1|subfam/tribe)"
mod.54 <- "threat~ht+range+hbt+mode+hab+(1|subfam/tribe)"
mod.55 <- "threat~ht+range+alt+mode+hab+(1|subfam/tribe)"
mod.56 <- "threat~ht+range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.57 <- "threat~ht+flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.58 <- "threat~ht+hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.59 <- "threat~ht+deh+arm+hair+leaflmax+(1|subfam/tribe)"
#mod.60 <- "threat~ht+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.61 <- "threat~ht+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.62 <- "threat~ht+flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
#mod.63 <- "threat~ht+flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## saturated model
mod.64 <- "threat~ht+range+hbt+alt+mode+hab+flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
## null model
mod.65 <- "threat~1+(1|subfam/tribe)"
## Make model vector
mod.vec <- c(mod.1,mod.2,mod.3,mod.4,mod.5,mod.6,mod.7,mod.8,mod.9,mod.10,mod.11,mod.13,mod.14,mod.16,mod.17,mod.18,mod.19,mod.20,mod.21,mod.22,mod.23,mod.24,mod.25,mod.26,mod.27,mod.28,mod.30,mod.31,mod.33,mod.34,mod.35,mod.36,mod.37,mod.38,mod.39,mod.40,mod.41,mod.42,mod.44,mod.45,mod.47,mod.48,mod.49,mod.50,mod.51,mod.52,mod.53,mod.54,mod.55,mod.56,mod.57,mod.58,mod.59,mod.61,mod.62,mod.64,mod.65)
}
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "threat" & wseedsize == 0 & univ == "no" & wNPG == "yes") {
## Height-only model
mod.1 <- "threat~ht+(1|NPG/tribe)"
## 'habitat' models
mod.2 <- "threat~range+(1|NPG/tribe)"
mod.3 <- "threat~range+hbt+(1|NPG/tribe)"
mod.4 <- "threat~range+alt+(1|NPG/tribe)"
mod.5 <- "threat~range+hbt+alt+(1|NPG/tribe)"
## 'life history' models
mod.6 <- "threat~mode+(1|NPG/tribe)"
mod.7 <- "threat~hab+(1|NPG/tribe)"
mod.8 <- "threat~mode+hab+(1|NPG/tribe)"
## 'reproduction' models
mod.9 <- "threat~flordisp+(1|NPG/tribe)"
mod.10 <- "threat~hook+(1|NPG/tribe)"
mod.11 <- "threat~deh+(1|NPG/tribe)"
#mod.12 <- "threat~seedsize+(1|NPG/tribe)"
mod.13 <- "threat~hook+deh+(1|NPG/tribe)"
mod.14 <- "threat~flordisp+hook+deh+(1|NPG/tribe)"
#mod.15 <- "threat~flordisp+hook+deh+seedsize+(1|NPG/tribe)"
## 'defence' models
mod.16 <- "threat~arm+(1|NPG/tribe)"
mod.17 <- "threat~hair+(1|NPG/tribe)"
mod.18 <- "threat~leaflmax+(1|NPG/tribe)"
mod.19 <- "threat~arm+hair+(1|NPG/tribe)"
mod.20 <- "threat~leaflmax+arm+hair+(1|NPG/tribe)"
## 'habitat' + 'life history' models combined
mod.21 <- "threat~range+mode+hab+(1|NPG/tribe)"
mod.22 <- "threat~range+hab+(1|NPG/tribe)"
mod.23 <- "threat~range+hbt+mode+hab+(1|NPG/tribe)"
mod.24 <- "threat~range+alt+mode+hab+(1|NPG/tribe)"
mod.25 <- "threat~range+hbt+alt+mode+hab+(1|NPG/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.26 <- "threat~flordisp+arm+hair+leaflmax+(1|NPG/tribe)"
mod.27 <- "threat~hook+arm+hair+leaflmax+(1|NPG/tribe)"
mod.28 <- "threat~deh+arm+hair+leaflmax+(1|NPG/tribe)"
#mod.29 <- "threat~seedsize+arm+hair+leaflmax+(1|NPG/tribe)"
mod.30 <- "threat~hook+deh+arm+hair+leaflmax+(1|NPG/tribe)"
mod.31 <- "threat~flordisp+hook+deh+arm+hair+leaflmax+(1|NPG/tribe)"
#mod.32 <- "threat~flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|NPG/tribe)"
## All above with allometric control (height)
## 'habitat' models
mod.33 <- "threat~ht+range+(1|NPG/tribe)"
mod.34 <- "threat~ht+range+hbt+(1|NPG/tribe)"
mod.35 <- "threat~ht+range+alt+(1|NPG/tribe)"
mod.36 <- "threat~ht+range+hbt+alt+(1|NPG/tribe)"
## 'life history' models
mod.37 <- "threat~ht+mode+(1|NPG/tribe)"
mod.38 <- "threat~ht+hab+(1|NPG/tribe)"
mod.39 <- "threat~ht+mode+hab+(1|NPG/tribe)"
## 'reproduction' models
mod.40 <- "threat~ht+flordisp+(1|NPG/tribe)"
mod.41 <- "threat~ht+hook+(1|NPG/tribe)"
mod.42 <- "threat~ht+deh+(1|NPG/tribe)"
#mod.43 <- "threat~ht+seedsize+(1|NPG/tribe)"
mod.44 <- "threat~ht+hook+deh+(1|NPG/tribe)"
mod.45 <- "threat~ht+flordisp+hook+deh+(1|NPG/tribe)"
#mod.46 <- "threat~ht+flordisp+hook+deh+seedsize+(1|NPG/tribe)"
## 'defence' models
mod.47 <- "threat~ht+arm+(1|NPG/tribe)"
mod.48 <- "threat~ht+hair+(1|NPG/tribe)"
mod.49 <- "threat~ht+leaflmax+(1|NPG/tribe)"
mod.50 <- "threat~ht+arm+hair+(1|NPG/tribe)"
mod.51 <- "threat~ht+leaflmax+arm+hair+(1|NPG/tribe)"
## 'habitat' + 'life history' models combined
mod.52 <- "threat~ht+range+mode+hab+(1|NPG/tribe)"
mod.53 <- "threat~ht+range+hab+(1|NPG/tribe)"
mod.54 <- "threat~ht+range+hbt+mode+hab+(1|NPG/tribe)"
mod.55 <- "threat~ht+range+alt+mode+hab+(1|NPG/tribe)"
mod.56 <- "threat~ht+range+hbt+alt+mode+hab+(1|NPG/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.57 <- "threat~ht+flordisp+arm+hair+leaflmax+(1|NPG/tribe)"
mod.58 <- "threat~ht+hook+arm+hair+leaflmax+(1|NPG/tribe)"
mod.59 <- "threat~ht+deh+arm+hair+leaflmax+(1|NPG/tribe)"
#mod.60 <- "threat~ht+seedsize+arm+hair+leaflmax+(1|NPG/tribe)"
mod.61 <- "threat~ht+hook+deh+arm+hair+leaflmax+(1|NPG/tribe)"
mod.62 <- "threat~ht+flordisp+hook+deh+arm+hair+leaflmax+(1|NPG/tribe)"
#mod.63 <- "threat~ht+flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|NPG/tribe)"
## saturated model
mod.64 <- "threat~ht+range+hbt+alt+mode+hab+flordisp+hook+deh+arm+hair+leaflmax+(1|NPG/tribe)"
## null model
mod.65 <- "threat~1+(1|NPG/tribe)"
## Make model vector
mod.vec <- c(mod.1,mod.2,mod.3,mod.4,mod.5,mod.6,mod.7,mod.8,mod.9,mod.10,mod.11,mod.13,mod.14,mod.16,mod.17,mod.18,mod.19,mod.20,mod.21,mod.22,mod.23,mod.24,mod.25,mod.26,mod.27,mod.28,mod.30,mod.31,mod.33,mod.34,mod.35,mod.36,mod.37,mod.38,mod.39,mod.40,mod.41,mod.42,mod.44,mod.45,mod.47,mod.48,mod.49,mod.50,mod.51,mod.52,mod.53,mod.54,mod.55,mod.56,mod.57,mod.58,mod.59,mod.61,mod.62,mod.64,mod.65)
}
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "IUCN" & wseedsize == 0 & univ == "no") {
## Height-only model
mod.1 <- "IUCNstat~ht+(1|subfam/tribe)"
## 'habitat' models
mod.2 <- "IUCNstat~range+(1|subfam/tribe)"
mod.3 <- "IUCNstat~hbt+(1|subfam/tribe)"
mod.4 <- "IUCNstat~alt+(1|subfam/tribe)"
## 'life history' models
mod.5 <- "IUCNstat~mode+(1|subfam/tribe)"
mod.6 <- "IUCNstat~hab+(1|subfam/tribe)"
## 'reproduction' models
mod.7 <- "IUCNstat~flordisp+(1|subfam/tribe)"
mod.8 <- "IUCNstat~hook+(1|subfam/tribe)"
mod.9 <- "IUCNstat~deh+(1|subfam/tribe)"
## 'defence' models
mod.10 <- "IUCNstat~arm+(1|subfam/tribe)"
mod.11<- "IUCNstat~hair+(1|subfam/tribe)"
mod.12 <- "IUCNstat~leaflmax+(1|subfam/tribe)"
## null model
mod.13 <- "IUCNstat~1+(1|subfam/tribe)"
## Make model vector
mod.vec <- c(mod.1,mod.2,mod.3,mod.4,mod.5,mod.6,mod.7,mod.8,mod.9,mod.10,mod.11,mod.13)
}
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "invasive" & wseedsize == 1 & univ == "no") {
## Height-only model
mod.1 <- "inv~ht+(1|subfam/tribe)"
## 'habitat' models
mod.2 <- "inv~range+(1|subfam/tribe)"
mod.3 <- "inv~range+hbt+(1|subfam/tribe)"
mod.4 <- "inv~range+alt+(1|subfam/tribe)"
mod.5 <- "inv~range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.6 <- "inv~mode+(1|subfam/tribe)"
mod.7 <- "inv~hab+(1|subfam/tribe)"
mod.8 <- "inv~mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.9 <- "inv~flordisp+(1|subfam/tribe)"
mod.10 <- "inv~hook+(1|subfam/tribe)"
mod.11 <- "inv~deh+(1|subfam/tribe)"
mod.12 <- "inv~seedsize+(1|subfam/tribe)"
mod.13 <- "inv~hook+deh+(1|subfam/tribe)"
mod.14 <- "inv~flordisp+hook+deh+(1|subfam/tribe)"
mod.15 <- "inv~flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.16 <- "inv~arm+(1|subfam/tribe)"
mod.17 <- "inv~hair+(1|subfam/tribe)"
mod.18 <- "inv~leaflmax+(1|subfam/tribe)"
mod.19 <- "inv~arm+hair+(1|subfam/tribe)"
mod.20 <- "inv~leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.21 <- "inv~range+mode+hab+(1|subfam/tribe)"
mod.22 <- "inv~range+hab+(1|subfam/tribe)"
mod.23 <- "inv~range+hbt+mode+hab+(1|subfam/tribe)"
mod.24 <- "inv~range+alt+mode+hab+(1|subfam/tribe)"
mod.25 <- "inv~range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.26 <- "inv~flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.27 <- "inv~hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.28 <- "inv~deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.29 <- "inv~seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.30 <- "inv~hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.31 <- "inv~flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.32 <- "inv~flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## All above with allometric control (height)
## 'habitat' models
mod.33 <- "inv~ht+range+(1|subfam/tribe)"
mod.34 <- "inv~ht+range+hbt+(1|subfam/tribe)"
mod.35 <- "inv~ht+range+alt+(1|subfam/tribe)"
mod.36 <- "inv~ht+range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.37 <- "inv~ht+mode+(1|subfam/tribe)"
mod.38 <- "inv~ht+hab+(1|subfam/tribe)"
mod.39 <- "inv~ht+mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.40 <- "inv~ht+flordisp+(1|subfam/tribe)"
mod.41 <- "inv~ht+hook+(1|subfam/tribe)"
mod.42 <- "inv~ht+deh+(1|subfam/tribe)"
mod.43 <- "inv~ht+seedsize+(1|subfam/tribe)"
mod.44 <- "inv~ht+hook+deh+(1|subfam/tribe)"
mod.45 <- "inv~ht+flordisp+hook+deh+(1|subfam/tribe)"
mod.46 <- "inv~ht+flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.47 <- "inv~ht+arm+(1|subfam/tribe)"
mod.48 <- "inv~ht+hair+(1|subfam/tribe)"
mod.49 <- "inv~ht+leaflmax+(1|subfam/tribe)"
mod.50 <- "inv~ht+arm+hair+(1|subfam/tribe)"
mod.51 <- "inv~ht+leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.52 <- "inv~ht+range+mode+hab+(1|subfam/tribe)"
mod.53 <- "inv~ht+range+hab+(1|subfam/tribe)"
mod.54 <- "inv~ht+range+hbt+mode+hab+(1|subfam/tribe)"
mod.55 <- "inv~ht+range+alt+mode+hab+(1|subfam/tribe)"
mod.56 <- "inv~ht+range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.57 <- "inv~ht+flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.58 <- "inv~ht+hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.59 <- "inv~ht+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.60 <- "inv~ht+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.61 <- "inv~ht+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.62 <- "inv~ht+flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.63 <- "inv~ht+flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## saturated model
mod.64 <- "inv~ht+range+hbt+alt+mode+hab+flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## null model
mod.65 <- "inv~1+(1|subfam/tribe)"
## Make model vector
mod.vec <- c(mod.1,mod.2,mod.3,mod.4,mod.5,mod.6,mod.7,mod.8,mod.9,mod.10,mod.11,mod.12,mod.13,mod.14,mod.15,mod.16,mod.17,mod.18,mod.19,mod.20,mod.21,mod.22,mod.23,mod.24,mod.25,mod.26,mod.27,mod.28,mod.29,mod.30,mod.31,mod.32,mod.33,mod.34,mod.35,mod.36,mod.37,mod.38,mod.39,mod.40,mod.41,mod.42,mod.43,mod.44,mod.45,mod.46,mod.47,mod.48,mod.49,mod.50,mod.51,mod.52,mod.53,mod.54,mod.55,mod.56,mod.57,mod.58,mod.59,mod.60,mod.61,mod.62,mod.63,mod.64,mod.65)
}
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "invasive" & univ == "yes") {
mod.1 <- "inv~ht+(1|subfam/tribe)"
mod.2 <- "inv~range+(1|subfam/tribe)"
mod.3 <- "inv~hbt+(1|subfam/tribe)"
mod.4 <- "inv~alt+(1|subfam/tribe)"
mod.5 <- "inv~mode+(1|subfam/tribe)"
mod.6 <- "inv~hab+(1|subfam/tribe)"
mod.7 <- "inv~flordisp+(1|subfam/tribe)"
mod.8 <- "inv~hook+(1|subfam/tribe)"
mod.9 <- "inv~deh+(1|subfam/tribe)"
mod.10 <- "inv~arm+(1|subfam/tribe)"
mod.11 <- "inv~hair+(1|subfam/tribe)"
mod.12 <- "inv~leaflmax+(1|subfam/tribe)"
mod.13 <- "inv~1+(1|subfam/tribe)"
## Make model vector
mod.vec <- c(mod.1,mod.2,mod.3,mod.4,mod.5,mod.6,mod.7,mod.8,mod.9,mod.10,mod.11,mod.12,mod.13)
}
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "invasive" & wseedsize == 0 & univ == "no") {
## Height-only model
mod.1 <- "inv~ht+(1|subfam/tribe)"
## 'habitat' models
mod.2 <- "inv~range+(1|subfam/tribe)"
mod.3 <- "inv~range+hbt+(1|subfam/tribe)"
mod.4 <- "inv~range+alt+(1|subfam/tribe)"
mod.5 <- "inv~range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.6 <- "inv~mode+(1|subfam/tribe)"
mod.7 <- "inv~hab+(1|subfam/tribe)"
mod.8 <- "inv~mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.9 <- "inv~flordisp+(1|subfam/tribe)"
mod.10 <- "inv~hook+(1|subfam/tribe)"
mod.11 <- "inv~deh+(1|subfam/tribe)"
#mod.12 <- "inv~seedsize+(1|subfam/tribe)"
mod.13 <- "inv~hook+deh+(1|subfam/tribe)"
mod.14 <- "inv~flordisp+hook+deh+(1|subfam/tribe)"
#mod.15 <- "inv~flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.16 <- "inv~arm+(1|subfam/tribe)"
mod.17 <- "inv~hair+(1|subfam/tribe)"
mod.18 <- "inv~leaflmax+(1|subfam/tribe)"
mod.19 <- "inv~arm+hair+(1|subfam/tribe)"
mod.20 <- "inv~leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.21 <- "inv~range+mode+hab+(1|subfam/tribe)"
mod.22 <- "inv~range+hab+(1|subfam/tribe)"
mod.23 <- "inv~range+hbt+mode+hab+(1|subfam/tribe)"
mod.24 <- "inv~range+alt+mode+hab+(1|subfam/tribe)"
mod.25 <- "inv~range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.26 <- "inv~flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.27 <- "inv~hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.28 <- "inv~deh+arm+hair+leaflmax+(1|subfam/tribe)"
#mod.29 <- "inv~seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.30 <- "inv~hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.31 <- "inv~flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
#mod.32 <- "inv~flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## All above with allometric control (height)
## 'habitat' models
mod.33 <- "inv~ht+range+(1|subfam/tribe)"
mod.34 <- "inv~ht+range+hbt+(1|subfam/tribe)"
mod.35 <- "inv~ht+range+alt+(1|subfam/tribe)"
mod.36 <- "inv~ht+range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.37 <- "inv~ht+mode+(1|subfam/tribe)"
mod.38 <- "inv~ht+hab+(1|subfam/tribe)"
mod.39 <- "inv~ht+mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.40 <- "inv~ht+flordisp+(1|subfam/tribe)"
mod.41 <- "inv~ht+hook+(1|subfam/tribe)"
mod.42 <- "inv~ht+deh+(1|subfam/tribe)"
#mod.43 <- "inv~ht+seedsize+(1|subfam/tribe)"
mod.44 <- "inv~ht+hook+deh+(1|subfam/tribe)"
mod.45 <- "inv~ht+flordisp+hook+deh+(1|subfam/tribe)"
#mod.46 <- "inv~ht+flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.47 <- "inv~ht+arm+(1|subfam/tribe)"
mod.48 <- "inv~ht+hair+(1|subfam/tribe)"
mod.49 <- "inv~ht+leaflmax+(1|subfam/tribe)"
mod.50 <- "inv~ht+arm+hair+(1|subfam/tribe)"
mod.51 <- "inv~ht+leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.52 <- "inv~ht+range+mode+hab+(1|subfam/tribe)"
mod.53 <- "inv~ht+range+hab+(1|subfam/tribe)"
mod.54 <- "inv~ht+range+hbt+mode+hab+(1|subfam/tribe)"
mod.55 <- "inv~ht+range+alt+mode+hab+(1|subfam/tribe)"
mod.56 <- "inv~ht+range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.57 <- "inv~ht+flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.58 <- "inv~ht+hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.59 <- "inv~ht+deh+arm+hair+leaflmax+(1|subfam/tribe)"
#mod.60 <- "inv~ht+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.61 <- "inv~ht+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.62 <- "inv~ht+flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
#mod.63 <- "inv~ht+flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## saturated model
mod.64 <- "inv~ht+range+hbt+alt+mode+hab+flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
## null model
mod.65 <- "inv~1+(1|subfam/tribe)"
## Make model vector
mod.vec <- c(mod.1,mod.2,mod.3,mod.4,mod.5,mod.6,mod.7,mod.8,mod.9,mod.10,mod.11,mod.13,mod.14,mod.16,mod.17,mod.18,mod.19,mod.20,mod.21,mod.22,mod.23,mod.24,mod.25,mod.26,mod.27,mod.28,mod.30,mod.31,mod.33,mod.34,mod.35,mod.36,mod.37,mod.38,mod.39,mod.40,mod.41,mod.42,mod.44,mod.45,mod.47,mod.48,mod.49,mod.50,mod.51,mod.52,mod.53,mod.54,mod.55,mod.56,mod.57,mod.58,mod.59,mod.61,mod.62,mod.64,mod.65)
}
## New a priori mod.vec sets
if (model.type == "lmer" & test.var == "both" & wseedsize == 1 & univ == "no") {
## Height-only model
mod.1 <- "thinv~ht+(1|subfam/tribe)"
## 'habitat' models
mod.2 <- "thinv~range+(1|subfam/tribe)"
mod.3 <- "thinv~range+hbt+(1|subfam/tribe)"
mod.4 <- "thinv~range+alt+(1|subfam/tribe)"
mod.5 <- "thinv~range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.6 <- "thinv~mode+(1|subfam/tribe)"
mod.7 <- "thinv~hab+(1|subfam/tribe)"
mod.8 <- "thinv~mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.9 <- "thinv~flordisp+(1|subfam/tribe)"
mod.10 <- "thinv~hook+(1|subfam/tribe)"
mod.11 <- "thinv~deh+(1|subfam/tribe)"
mod.12 <- "thinv~seedsize+(1|subfam/tribe)"
mod.13 <- "thinv~hook+deh+(1|subfam/tribe)"
mod.14 <- "thinv~flordisp+hook+deh+(1|subfam/tribe)"
mod.15 <- "thinv~flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.16 <- "thinv~arm+(1|subfam/tribe)"
mod.17 <- "thinv~hair+(1|subfam/tribe)"
mod.18 <- "thinv~leaflmax+(1|subfam/tribe)"
mod.19 <- "thinv~arm+hair+(1|subfam/tribe)"
mod.20 <- "thinv~leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.21 <- "thinv~range+mode+hab+(1|subfam/tribe)"
mod.22 <- "thinv~range+hab+(1|subfam/tribe)"
mod.23 <- "thinv~range+hbt+mode+hab+(1|subfam/tribe)"
mod.24 <- "thinv~range+alt+mode+hab+(1|subfam/tribe)"
mod.25 <- "thinv~range+hbt+alt+mode+hab+(1|subfam/tribe)"
## 'reproduction' + 'defence' & 'leaf type' models combined
mod.26 <- "thinv~flordisp+arm+hair+leaflmax+(1|subfam/tribe)"
mod.27 <- "thinv~hook+arm+hair+leaflmax+(1|subfam/tribe)"
mod.28 <- "thinv~deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.29 <- "thinv~seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
mod.30 <- "thinv~hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.31 <- "thinv~flordisp+hook+deh+arm+hair+leaflmax+(1|subfam/tribe)"
mod.32 <- "thinv~flordisp+hook+deh+seedsize+arm+hair+leaflmax+(1|subfam/tribe)"
## All above with allometric control (height)
## 'habitat' models
mod.33 <- "thinv~ht+range+(1|subfam/tribe)"
mod.34 <- "thinv~ht+range+hbt+(1|subfam/tribe)"
mod.35 <- "thinv~ht+range+alt+(1|subfam/tribe)"
mod.36 <- "thinv~ht+range+hbt+alt+(1|subfam/tribe)"
## 'life history' models
mod.37 <- "thinv~ht+mode+(1|subfam/tribe)"
mod.38 <- "thinv~ht+hab+(1|subfam/tribe)"
mod.39 <- "thinv~ht+mode+hab+(1|subfam/tribe)"
## 'reproduction' models
mod.40 <- "thinv~ht+flordisp+(1|subfam/tribe)"
mod.41 <- "thinv~ht+hook+(1|subfam/tribe)"
mod.42 <- "thinv~ht+deh+(1|subfam/tribe)"
mod.43 <- "thinv~ht+seedsize+(1|subfam/tribe)"
mod.44 <- "thinv~ht+hook+deh+(1|subfam/tribe)"
mod.45 <- "thinv~ht+flordisp+hook+deh+(1|subfam/tribe)"
mod.46 <- "thinv~ht+flordisp+hook+deh+seedsize+(1|subfam/tribe)"
## 'defence' models
mod.47 <- "thinv~ht+arm+(1|subfam/tribe)"
mod.48 <- "thinv~ht+hair+(1|subfam/tribe)"
mod.49 <- "thinv~ht+leaflmax+(1|subfam/tribe)"
mod.50 <- "thinv~ht+arm+hair+(1|subfam/tribe)"
mod.51 <- "thinv~ht+leaflmax+arm+hair+(1|subfam/tribe)"
## 'habitat' + 'life history' models combined
mod.52 <- "thinv~ht+range+mode+hab+(1|subfam/tribe)"
mod.53 <- "thinv~ht+range+hab+(1|subfam/tribe)"
mod.54 <- "thinv~ht+range+hbt+mode+hab+(1|subfam/tribe)"
mod.55 <- "thinv~ht+range+alt+mode+hab+(1|subfam/tribe)"