# NOT RUN {
####### Calathea ovandensis
data(calathea)
calathea_pool<-calathea[['pooled']]
## Create plots like FIGURE 7 in Horvitz et al 1997
##PLOTS
plots<- split(calathea[-17], rep(1:4,each=4))
## use Mean matrix since pooled not available by plot
plots<- lapply(plots, mean)
Cm<-LTRE(plots, calathea_pool)
pe<-sapply(Cm, sum)
barplot(pe, xlab="Plot", ylab="Plot effect" , ylim=c(-.25, .25),
col="blue", las=1)
abline(h=0)
box()
title(expression(italic("Calathea ovandensis")))
##YEARS -- split recycles vector
yrs<-split(calathea[-17], 1:4)
yrs <- lapply(yrs, mean)
names(yrs)<-1982:1985
Cm<-LTRE(yrs, calathea_pool)
ye<-sapply(Cm, sum)
barplot(ye, xlab="Year", ylab="Year effect" , ylim=c(-.25, .25), col="blue", las=1)
abline(h=0)
box()
title(expression(italic("Calathea ovandensis")))
## INTERACTION
Cm<-LTRE(calathea[-17], calathea_pool)
ie<-sapply(Cm, sum)
## minus plot, year effects
ie<- ie - rep(pe, each=4) - rep(ye, 4)
names(ie)<-NULL
names(ie)[seq(1,16,4)]<-1:4
barplot(ie, xlab="Plot (years 82-83 to 85-86)", ylab="Interaction effect" ,
ylim=c(-.25, .25), col="blue", las=1)
abline(h=0)
box()
title(expression(italic("Calathea ovandensis")))
####### Mimulus
## Pooled M. cardinalis reference matrix kindly provided by Amy Angert 1/2/2008.
m_card_pool<-matrix( c(
1.99e-01, 8.02e+02, 5.82e+03, 3.05e+04,
2.66e-05, 7.76e-02, 2.31e-02, 1.13e-03,
7.94e-06, 8.07e-02, 3.22e-01, 2.16e-01,
2.91e-07, 1.58e-02, 1.15e-01, 6.01e-01), byrow=TRUE, nrow=4)
## Population effects using pooled population matrices
data(monkeyflower)
card<-subset(monkeyflower, species=="cardinalis" & year=="pooled")
## split rows into list of 4 matrices
Atrt<-lapply(split(as.matrix(card[,4:19]), 1:4), matrix, nrow=4, byrow=TRUE)
names(Atrt)<-card$site
Cm<-LTRE(Atrt, m_card_pool)
x<-sapply(Cm, sum)
x
names(x)<-c("BU", "RP", "WA", "CA")
## Plot like Figure 2A in Angert (2006)
op<-par(mar=c(5,5,4,1))
barplot(x, xlab="Population", ylab="", xlim=c(0,6.5), ylim=c(-.4, .4),
las=1, space=.5, col="blue")
abline(h=0)
mtext(expression(paste(sum(a[ij]), " contributions")), 2, 3.5)
title(expression(paste(italic("M. cardinalis"), " Population effects")))
box()
## and Plot like Figure 3A
x<-matrix(unlist(Cm), nrow=4, byrow=TRUE)
colnames(x)<-paste("a", rep(1:4, each=4), 1:4, sep="")
bp<-barplot(x[1:2,], beside=TRUE, ylim=c(-.2,.2), las=1,
xlab="Transition", ylab="", xaxt='n')
mtext(expression(paste("Contribution of ", a[ij], "to variation in ", lambda)), 2, 3.5)
## rotate labels
text(bp[1,]-0.5, -.22, labels=colnames(x), srt=45, xpd=TRUE)
title(expression(paste(italic("M. cardinalis"), " Range center")))
box()
par(op)
# }
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