R/plot.fitmarkov.R

In dave: Functions for "Data Analysis in Vegetation Ecology"

plot.fitmarkov<- function(x,...) {
    zz<- data.frame(x$fitted.data)
    yy<- data.frame(x$raw.data)
    p <- length(yy[1,])
    #     check.ltypes<- is.null(l.types)
    #     if(check.ltypes == TRUE) {
    l.types<- rep(c(1,1,1,1,1,1,1,3,3,3,3,3,3,3),ceiling(p/14))
    #     }
    t<- x$t.measured
    s.types<- seq(1,p,1)
    tmod<- x$t.modeled
    #
    # line widths, types and colors
    #
    # The next 2 lines set defaults
    l.widths<- rep(c(3.6,2.8,2.3,1.9,1.5,1.1,0.6),ceiling(p/7))
    #  colors<- rgb(0,0,0,rep(c(35,70,100,135,175,200,240),ceiling(p/7)),maxColorValue=255) # for b/w
    colors<- rainbow(p)
    # symbol types s.types
    s.types<- rep(1:25,ceiling(p/25))
    #
    # raw plot
    # Upper graph
    plot(c(min(t),max(t)),c(0,1.0),type="n",xlab="Year",ylab="Relative cover",cex.lab=0.8,main="",cex.axis=0.8)
    for (i in 1:p) lines(t,yy[,i],col=colors[i],lty=l.types[i],lwd=l.widths[i])                 # plot raw data
    for (i in 1:p) points(t,yy[,i],col=colors[i],pch=s.types[i],cex=0.6)                        # plot raw data
    legend("topright",names(yy[1:p]),lty=l.types,pch=s.types,ncol=3,bty="n",pt.lwd=1,lwd=l.widths,cex=0.6,col=colors)
    legend("topleft","(a)",bty="n",cex=1.0,inset=c(-0.04,-0.00))
    # Lower graph
    plot(c(min(t),max(t)),c(0,1.0),type="n",xlab="Year",ylab="Relative cover",cex.lab=0.8,main="",cex.axis=0.8)
    for (i in 1:p) lines(tmod,zz[,i],col=colors[i],lty=l.types[i],lwd=l.widths[i])              # plot simulated data
    for (i in 1:p) points(tmod,zz[,i],col=colors[i],pch=s.types[i],cex=0.6)              # plot simulated data
    legend("topright",names(zz[1:p]),lty=l.types,pch=s.types,ncol=3,bty="n",pt.lwd=1,lwd=l.widths,cex=0.6,col=colors)
    legend("topleft","(b)",bty="n",cex=1.0,inset=c(-0.04,-0.00))
}