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brkdn.plot<-function(vars,groups=NA,obs=NA,data,mct="mean",md="std.error",
stagger=NA,dispbar=TRUE,main="Breakdown plot",xlab=NA,ylab=NA,xaxlab=NA,
ylim=NA,type="b",pch=1,lty=1,col=par("fg"),staxx=FALSE,...) {
if(is.na(obs)) {
if(is.na(groups[1]))
stop("Must have at least one factor to subset data")
bygroup<-as.factor(data[[groups]])
grouplevels<-levels(bygroup)
ngroups<-length(grouplevels)
nobs<-length(vars)
obs.pos<-1:nobs
obslevels<-1:nobs
}
else {
if(is.numeric(data[[obs]])) {
obs.pos<-obslevels<-sort(unique(data[[obs]]))
nobs<-length(obslevels)
}
else {
byobs<-as.factor(data[[obs]])
obslevels<-levels(byobs)
nobs<-length(obslevels)
obs.pos<-1:nobs
}
if(is.na(groups)) {
ngroups<-length(vars)
grouplevels<-1:ngroups
}
else {
bygroup<-as.factor(data[[groups]])
grouplevels<-levels(bygroup)
ngroups<-length(grouplevels)
if(length(vars) > 1) {
warning("Group and observation factors are present, only vars[1] is plotted")
vars<-vars[1]
}
}
}
brkdn<-list(matrix(NA,nrow=ngroups,ncol=nobs),
matrix(NA,nrow=ngroups,ncol=nobs))
if(is.na(groups)) {
if(is.na(xlab)) xlab<-"Observation"
xat<-1:nobs
if(is.na(xaxlab[1])) xaxlab<-obslevels
for(group in 1:ngroups) {
for(ob in 1:nobs) {
thisbit<-data[[vars[group]]][data[[obs]] == obslevels[ob]]
if(length(thisbit)) {
if(length(thisbit) > 1) {
brkdn[[1]][group,ob]<-do.call(mct,list(thisbit,na.rm=TRUE))
if(!is.na(md))
brkdn[[2]][group,ob]<-do.call(md,list(thisbit,na.rm=TRUE))
}
else brkdn[[1]][group,ob]<-thisbit
}
}
}
}
else {
if(is.na(obs)) {
if(is.na(xlab)) xlab<-"Variable"
xat<-1:length(vars)
if(is.na(xaxlab[1])) xaxlab<-vars
for(group in 1:ngroups) {
for(ob in 1:nobs) {
thisbit<-data[[vars[ob]]][data[[groups]] == grouplevels[group]]
if(length(thisbit)) {
if(length(thisbit) > 1) {
brkdn[[1]][group,ob]<-do.call(mct,list(thisbit,na.rm=TRUE))
if(!is.na(md))
brkdn[[2]][group,ob]<-do.call(md,list(thisbit,na.rm=TRUE))
}
else brkdn[[1]][group,ob]<-thisbit
}
}
}
}
else {
if(is.na(xlab)) xlab<-"Observation"
xat<-obs.pos
if(is.na(xaxlab[1])) xaxlab<-obslevels
for(group in 1:ngroups) {
for(ob in 1:nobs) {
thisbit<-data[[vars]][data[[groups]] == grouplevels[group] &
data[[obs]] == obslevels[ob]]
if(length(thisbit)) {
if(length(thisbit) > 1) {
brkdn[[1]][group,ob]<-do.call(mct,list(thisbit,na.rm=TRUE))
if(!is.na(md))
brkdn[[2]][group,ob]<-do.call(md,list(thisbit,na.rm=TRUE))
}
else brkdn[[1]][group,ob]<-thisbit
}
}
}
}
}
if(is.na(ylim[1])) {
ylim<-range(brkdn[[1]],na.rm=TRUE)
if(!is.na(md)) {
dlim<-c(min(brkdn[[1]]-brkdn[[2]],na.rm=TRUE),
max(brkdn[[1]]+brkdn[[2]],na.rm=TRUE))
ylim<-c(min(c(ylim[1],dlim[1])),max(c(ylim[2],dlim[2])))
}
}
groupdiv<-ifelse(ngroups < 3,1,ngroups-2)
if(is.na(stagger)) stagger<-0.025-groupdiv*0.0025
if(is.na(ylab)) {
if(length(vars) == 1) ylab<-vars[1]
else ylab<-paste(vars,collapse=" and ")
}
plot(0,xlim=c(obs.pos[1]-0.5,obs.pos[nobs]+0.5),main=main,
xlab=xlab,ylab=ylab,ylim=ylim,type="n",axes=FALSE,...)
box()
if(staxx) staxlab(at=xat,labels=xaxlab)
else axis(1,at=xat,labels=xaxlab)
axis(2)
if(length(pch) < ngroups) pch<-rep(pch,length.out=ngroups)
if(length(col) < ngroups) col<-rep(col,length.out=ngroups)
if(length(lty) < ngroups) lty<-rep(lty,length.out=ngroups)
offinc<-stagger*diff(par("usr")[c(1,2)])
offset<-0
arrow.cap<-0.01-(groupdiv*0.001)
for(group in 1:ngroups) {
points(obs.pos+offset,brkdn[[1]][group,],type=type,col=col[group],
pch=pch[group],lty=lty[group])
if(dispbar)
dispersion(obs.pos+offset,brkdn[[1]][group,],brkdn[[2]][group,],
arrow.cap=arrow.cap,col=col[group])
offset<-ifelse(offset<0,-offset,-offset-offinc)
}
names(brkdn)<-c(mct,md)
return(brkdn)
}
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