Nothing
plot.TPidm <-
function(x,chosen.tr="ALL",col="black", ...){
if(!inherits(x,"TPidm")) stop("'x' must be of class 'TPidm'.")
times<-x$times
s<-x$s
t<-x$t
CI<-x$CI
if(chosen.tr[1]=="ALL") chosen.tr<- x$p.trans
if(is.null(x$cov)){
if(is.null(col)) col<-c("black","red")
if(length(col)<2) col<-rep(col,length.out=2)
# CI==TRUE
if(CI==TRUE){
all.probs<-x$all.probs[,,chosen.tr]
# option 1: individual curves with CI
if(length(chosen.tr)==1){
tit<-paste("p",chosen.tr)
timemax<-max(times)*1.04
plot(times,all.probs[,"probs"],type="s",xlab="Time",ylab="Probability",ylim=c(0,1),col=col[1],xlim=c(0,timemax),cex.axis=0.7,cex.lab=0.7,main=tit, ...)
lines(times,all.probs[,"lower"],type="s",lty=3,col=col[2])
lines(times,all.probs[,"upper"],type="s",lty=3,col=col[2])
}else if(length(chosen.tr)>1 & length(chosen.tr)<=3){
N<-seq(1,length(chosen.tr),1)
tpg<-layout(matrix(N,1,length(chosen.tr),byrow=TRUE))
#layout.show(tpg)
for(i in 1:length(chosen.tr)){
tit<-paste("p",chosen.tr[[i]])
timemax<-max(times)*1.04
plot(times,all.probs[,"probs",chosen.tr[[i]]],type="s",xlab="Time",ylab="Probability",ylim=c(0,1),xlim=c(0,timemax),col=col[1],cex.axis=0.7,cex.lab=0.7,main=tit, ...)
lines(times,all.probs[,"lower",chosen.tr[[i]]],type="s",lty=3,col=col[2])
lines(times,all.probs[,"upper",chosen.tr[[i]]],type="s",lty=3,col=col[2])
}
} else {
n.cols<-3
n.rows<-ceiling(length(chosen.tr)/n.cols)
N<-seq(1,length(chosen.tr),1)
if(length(N)<n.cols*n.rows){
m<-n.cols*n.rows-length(N)
N<-c(N,rep(0,m))
}
tpg<-layout(matrix(N,n.rows,n.cols,byrow=TRUE))
#layout.show(tpg)
for(i in 1:length(chosen.tr)){
tit<-paste("p",chosen.tr[[i]])
timemax<-max(times)*1.04
plot(times,all.probs[,"probs",chosen.tr[[i]]],type="s",xlab="Time",ylab="Probability",col=col[1],ylim=c(0,1),xlim=c(0,timemax),cex.axis=0.7,cex.lab=0.7,main=tit, ...)
lines(times,all.probs[,"lower",chosen.tr[[i]]],type="s",lty=3,col=col[2])
lines(times,all.probs[,"upper",chosen.tr[[i]]],type="s",lty=3,col=col[2])
}
}
if(s==0){
title("State Occupation Probabilities", outer=TRUE, line=-1)
} else{
title("Transition Probabilities", outer=TRUE, line=-1)
}
}else{
all.probs<-x$all.probs[,,chosen.tr]
# option 2: individual curves without CI
if(length(chosen.tr)==1){
tit<-paste("p",chosen.tr)
timemax<-max(times)*1.04
plot(times,all.probs,type="s",xlab="Time",ylab="Probability",ylim=c(0,1),xlim=c(0,timemax),col=col[1],cex.axis=0.7,cex.lab=0.7,main=tit, ...)
}else if(length(chosen.tr)>1 & length(chosen.tr)<=3){
N<-seq(1,length(chosen.tr),1)
tpg<-layout(matrix(N,1,length(chosen.tr),byrow=TRUE))
#layout.show(tpg)
for(i in 1:length(chosen.tr)){
tit<-paste("p",chosen.tr[[i]])
timemax<-max(times)*1.04
plot(times,all.probs[,chosen.tr[[i]]],type="s",xlab="Time",ylab="Probability",ylim=c(0,1),xlim=c(0,timemax),col=col[1],cex.axis=0.7,cex.lab=0.7,main=tit, ...)
}
} else {
n.cols<-3
n.rows<-ceiling(length(chosen.tr)/n.cols)
N<-seq(1,length(chosen.tr),1)
if(length(N)<n.cols*n.rows){
m<-n.cols*n.rows-length(N)
N<-c(N,rep(0,m))
}
tpg<-layout(matrix(N,n.rows,n.cols,byrow=TRUE))
#layout.show(tpg)
for(i in 1:length(chosen.tr)){
tit<-paste("p",chosen.tr[[i]])
timemax<-max(times)*1.04
plot(times,all.probs[,chosen.tr[[i]]],type="s",xlab="Time",ylab="Probability",ylim=c(0,1),xlim=c(0,timemax),col=col[1],cex.axis=0.7,cex.lab=0.7,main=tit, ...)
}
}
if(s==0){
title("State Occupation Probabilities", outer=TRUE, line=-1)
} else{
title("Transition Probabilities", outer=TRUE, line=-1)
}
} # if cov=="null"
} else {
maxims<-c(NA)
nnn<-length(x$times)
for(iii in 1:nnn){
maxims[iii]<-max(x$times[iii]$t)
}
timemax<-max(maxims)*1.04
if(is.null(col)) col<-"black"
n.cats<-length(names(x$all.probs))
if(length(col)<n.cats) col<-rep(col,length.out=n.cats)
# CI==TRUE
if(CI==TRUE){
nn<-length(names(x$all.probs))
# option 1: individual curves with CI
if(length(chosen.tr)==1){
tit<-paste("p",chosen.tr)
plot(x$times[1]$t,x$all.probs[1]$CI[,"probs",chosen.tr[[1]]],type="s",xlab="Time",ylab="Probability",ylim=c(0,1),xlim=c(0,timemax),col=col[1],cex.axis=0.7,cex.lab=0.7,main=tit, ...)
lines(x$times[1]$t,x$all.probs[1]$CI[,"lower",chosen.tr[[1]]],type="s",lty=3,col=col[1])
lines(x$times[1]$t,x$all.probs[1]$CI[,"upper",chosen.tr[[1]]],type="s",lty=3,col=col[1])
for(j in 2:nn){
lines(x$times[j]$t,x$all.probs[j]$CI[,"probs",chosen.tr[[1]]],type="s",col=col[j])
lines(x$times[j]$t,x$all.probs[j]$CI[,"lower",chosen.tr[[1]]],type="s",lty=3,col=col[j])
lines(x$times[j]$t,x$all.probs[j]$CI[,"upper",chosen.tr[[1]]],type="s",lty=3,col=col[j])
}
}else if(length(chosen.tr)>1 & length(chosen.tr)<=3){
N<-seq(1,length(chosen.tr),1)
tpg<-layout(matrix(N,1,length(chosen.tr),byrow=TRUE))
#layout.show(tpg)
for(i in 1:length(chosen.tr)){
tit<-paste("p",chosen.tr[[i]])
plot(x$times[1]$t,x$all.probs[1]$CI[,"probs",chosen.tr[[i]]],type="s",xlab="Time",ylab="Probability",col=col[1],ylim=c(0,1),xlim=c(0,timemax),cex.axis=0.7,cex.lab=0.7,main=tit, ...)
lines(x$times[1]$t,x$all.probs[1]$CI[,"lower",chosen.tr[[i]]],type="s",lty=3,col=col[1])
lines(x$times[1]$t,x$all.probs[1]$CI[,"upper",chosen.tr[[i]]],type="s",lty=3,col=col[1])
for(j in 2:nn){
lines(x$times[j]$t,x$all.probs[j]$CI[,"probs",chosen.tr[[i]]],type="s",col=col[j])
lines(x$times[j]$t,x$all.probs[j]$CI[,"lower",chosen.tr[[i]]],type="s",lty=3,col=col[j])
lines(x$times[j]$t,x$all.probs[j]$CI[,"upper",chosen.tr[[i]]],type="s",lty=3,col=col[j])
}
}
} else {
n.cols<-3
n.rows<-ceiling(length(chosen.tr)/n.cols)
N<-seq(1,length(chosen.tr),1)
if(length(N)<n.cols*n.rows){
m<-n.cols*n.rows-length(N)
N<-c(N,rep(0,m))
}
tpg<-layout(matrix(N,n.rows,n.cols,byrow=TRUE))
#layout.show(tpg)
for(i in 1:length(chosen.tr)){
tit<-paste("p",chosen.tr[[i]])
plot(x$times[1]$t,x$all.probs[1]$CI[,"probs",chosen.tr[[i]]],type="s",xlab="Time",ylab="Probability",ylim=c(0,1),xlim=c(0,timemax),col=col[1],cex.axis=0.7,cex.lab=0.7,main=tit, ...)
lines(x$times[1]$t,x$all.probs[1]$CI[,"lower",chosen.tr[[i]]],type="s",lty=3,col=col[1])
lines(x$times[1]$t,x$all.probs[1]$CI[,"upper",chosen.tr[[i]]],type="s",lty=3,col=col[1])
for(j in 2:nn){
lines(x$times[j]$t,x$all.probs[j]$CI[,"probs",chosen.tr[[i]]],type="s",col=col[j])
lines(x$times[j]$t,x$all.probs[j]$CI[,"lower",chosen.tr[[i]]],type="s",lty=3,col=col[j])
lines(x$times[j]$t,x$all.probs[j]$CI[,"upper",chosen.tr[[i]]],type="s",lty=3,col=col[j])
}
}
}
if(s==0){
title("State Occupation Probabilities", outer=TRUE, line=-1)
} else{
title("Transition Probabilities", outer=TRUE, line=-1)
}
}else{
nn<-length(names(x$all.probs))
# option 2: individual curves without CI
if(length(chosen.tr)==1){
tit<-paste("p",chosen.tr)
plot(x$times[1]$t,x$all.probs[1]$probs[,,chosen.tr],type="s",xlab="Time",ylab="Probability",col=col[1],ylim=c(0,1),xlim=c(0,timemax),cex.axis=0.7,cex.lab=0.7,main=tit, ...)
for(j in 2:nn){
lines(x$times[j]$t,x$all.probs[j]$probs[,,chosen.tr],type="s",col=col[j])
}
}else if(length(chosen.tr)>1 & length(chosen.tr)<=3){
N<-seq(1,length(chosen.tr),1)
tpg<-layout(matrix(N,1,length(chosen.tr),byrow=TRUE))
#layout.show(tpg)
for(i in 1:length(chosen.tr)){
tit<-paste("p",chosen.tr[[i]])
plot(x$times[1]$t,x$all.probs[1]$probs[,,chosen.tr[[i]]],type="s",xlab="Time",ylab="Probability",ylim=c(0,1),xlim=c(0,timemax),col=col[1],cex.axis=0.7,cex.lab=0.7,main=tit, ...)
for(j in 2:nn){
lines(x$times[j]$t,x$all.probs[j]$probs[,,chosen.tr[[i]]],type="s",col=col[j])
}
}
} else {
nn<-length(names(x$all.probs))
n.cols<-3
n.rows<-ceiling(length(chosen.tr)/n.cols)
N<-seq(1,length(chosen.tr),1)
if(length(N)<n.cols*n.rows){
m<-n.cols*n.rows-length(N)
N<-c(N,rep(0,m))
}
tpg<-layout(matrix(N,n.rows,n.cols,byrow=TRUE))
#layout.show(tpg)
for(i in 1:length(chosen.tr)){
tit<-paste("p",chosen.tr[[i]])
plot(x$times[1]$t,x$all.probs[1]$probs[,,chosen.tr[[i]]],type="s",xlab="Time",ylab="Probability",ylim=c(0,1),xlim=c(0,timemax),col=col[1],cex.axis=0.7,cex.lab=0.7,main=tit, ...)
for(j in 2:nn){
lines(x$times[j]$t,x$all.probs[j]$probs[,,chosen.tr[[i]]],type="s",col=col[j])
}
}
}
if(s==0){
title("State Occupation Probabilities", outer=TRUE, line=-1)
} else{
title("Transition Probabilities", outer=TRUE, line=-1)
}
} # if CI==TRUE
}
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.