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R/plot.jointSurroMed.R
In frailtypack: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
#' Plot Method for a joint surrogate mediation analysis model.
#'
#' Plots the estimated functions associated with the mediation analysis, i.e.
#' \eqn{g(s)}, \eqn{R(t)}
#' as well as the natural direct, indirect and total effects.
#' An option to plot the confidence bands of the function \eqn{g(s)} is available.
#' This option is also implemented for the confidence bands of the functions
#' \eqn{R(t)} and of the natural effects if these confidence bands are available.
#'
#' @aliases plot.jointSurroMed
#' @usage
#' \method{plot}{jointSurroMed}(x,plot.mediation="All",type.plot="Hazard",
#' conf.bands=TRUE,endpoint=2,
#' legend.pos = "topleft",...)
#' @param x An object of class \code{jointSurroMed} from a joint surrogate model
#' with a mediation analysis
#' for longitudinal outcome and a terminal event, i.e., an
#' output from calling \code{jointSurroPenal} function with the option
#' 'mediation' set to TRUE.
#' @param plot.mediation A character string specifying the desired plot.
#' Possible values are "All", "g","Rt" or "Effects". The default is
#' "All" which displays all three plots.
#' @param type.plot A character string specifying the type of curve
#' for the baseline hazards functions. Possible
#' value are "Hazard", or "Survival".
#' @param endpoint An integer specifying for which endpoint should
#' the baseline curves be plotted. Possible values are 0
#' for the surrogate endpoint only and 1 for the final endpoint or 2 for both.
#' Default is 2.
#' @param conf.bands Logical value. Determines whether confidence bands should be
#' plotted. The default is to do so if the confidence bands are available.
#' @param legend.pos The location of the legend can be specified by setting
#' this argument to a single keyword from the list '"bottomright"', '"bottom"',
#' '"bottomleft"', '"left"', '"topleft"', '"top"', '"topright"', '"right"' and
#' '"center"'. The default is '"topleft"'
#' @param ... other unused arguments.
#' @return Print one or several plots for the mediation analysis
#' of a joint surrogate model
#' @seealso \code{\link{jointSurroPenal}}
#' @keywords file
#' @export
"plot.jointSurroMed" <- function (x, plot.mediation="All",type.plot="Hazard", conf.bands=TRUE,endpoint=2,
legend.pos = "topleft",...)
{
#options check
plot.type <- charmatch(plot.mediation, c("All", "g","Rt","Effects"),nomatch = 0)
if (plot.type == 0) {
stop("'plot.mediation' must be one of the following: 'All', 'g','Rt' or 'Effects'")
}
if(!(type.plot %in% c("Hazard","Survival"))){
stop("'type.plot' must be one of the following: 'Hazard' or 'Survival'.")
}
if(!(endpoint %in% c(0,1,2))){
stop("'endpoint' should be one of the following: 0,1 or 2.")
}
if(!(legend.pos %in% c("bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center" ))){
stop("'legend.pos should be one of the following: 'bottomright', 'bottom', 'bottomleft', 'left', 'topleft', 'top', 'topright', 'right', 'center'")
}
if(type.plot=="Hazard"){
if(endpoint==0){
if(conf.bands){
yupp = ifelse(max(x$lamS[,3])<0,0.8*max(x$lamS[,3]),1.2*max(x$lamS[,3]))
ylow = ifelse(min(x$lamS[,2])<0,1.2*max(x$lamS[,2]),0.8*min(x$lamS[,2]))
yy=x$lamS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the surrogate endpoint\nand its 95% confidence bands.",...)
lines(xx,x$lamS[,2],type='l',...)
lines(xx,x$lamS[,3],type='l',...)
}else{
yupp = ifelse(max(x$lamS[,1])<0,0.8*max(x$lamS[,1]),1.2*max(x$lamS[,1]))
ylow = ifelse(min(x$lamS[,1])<0,1.2*min(x$lamS[,1]),0.8*min(x$lamS[,1]))
yy=x$lamS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the surrogate endpoint.",...)
}
}else if(endpoint==1){
if(conf.bands){
yupp = ifelse(max(x$lamT[,3])<0,0.8*max(x$lamT[,3]),1.2*max(x$lamT[,3]))
ylow = ifelse(min(x$lamT[,2])<0,1.2*min(x$lamT[,2]),0.8*min(x$lamT[,2]))
yy=x$lamT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the final endpoint\nand its 95% confidence bands.",...)
lines(xx,x$lamT[,2],type='l',lty=3,...)
lines(xx,x$lamT[,3],type='l',lty=3,...)
}else{
yupp = ifelse(max(x$lamT[,1])<0,0.8*max(x$lamT[,1]),1.2*max(x$lamT[,1]))
ylow = ifelse(min(x$lamT[,1])<0,1.2*min(x$lamT[,1]),0.8*min(x$lamT[,1]))
yy=x$lamT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the final endpoint.",...)
}
}else{
if(conf.bands){
## S first ...
yupp = ifelse(max(x$lamS[,3])<0,0.8*max(x$lamS[,3]),1.2*max(x$lamS[,3]))
ylow = ifelse(min(x$lamS[,2])<0,1.2*min(x$lamS[,2]),0.8*min(x$lamS[,2]))
yy=x$lamS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the surrogate endpoint\nand its 95% confidence bands.",...)
lines(xx,x$lamS[,2],type='l',lty=3,...)
lines(xx,x$lamS[,3],type='l',lty=3,...)
## Then T
invisible(readline(prompt="Press [Enter] to continue:"))
yupp = ifelse(max(x$lamT[,3])<0,0.8*max(x$lamT[,3]),1.2*max(x$lamT[,3]))
ylow = ifelse(min(x$lamT[,2])<0,1.2*min(x$lamT[,2]),0.8*min(x$lamT[,2]))
yy=x$lamT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the final endpoint\nand its 95% confidence bands.",...)
lines(xx,x$lamT[,2],type='l',lty=3,...)
lines(xx,x$lamT[,3],type='l',lty=3,...)
}else{
## S first ...
yupp = ifelse(max(x$lamS[,1])<0,0.8*max(x$lamS[,1]),1.2*max(x$lamS[,1]))
ylow = ifelse(min(x$lamS[,1])<0,1.2*min(x$lamS[,1]),0.8*min(x$lamS[,1]))
yy=x$lamS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the surrogate endpoint.",...)
## Then T
invisible(readline(prompt="Press [Enter] to continue:"))
yupp = ifelse(max(x$lamT[,1])<0,0.8*max(x$lamT[,1]),1.2*max(x$lamT[,1]))
ylow = ifelse(min(x$lamT[,1])<0,1.2*min(x$lamT[,1]),0.8*min(x$lamT[,1]))
yy=x$lamT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the final endpoint.",...)
}
}
}else{
if(endpoint==0){
if(conf.bands){
yupp = ifelse(max(x$survS[,3])<0,0.8*max(x$survS[,3]),1.2*max(x$survS[,3]))
ylow = ifelse(min(x$survS[,2])<0,1.2*min(x$survS[,2]),0.8*min(x$survS[,2]))
yy=x$survS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the surrogate endpoint\nand its 95% confidence bands.",...)
lines(xx,x$survS[,2],type='l',lty=3,...)
lines(xx,x$survS[,3],type='l',lty=3,...)
}else{
yupp = ifelse(max(x$survS[,1])<0,0.8*max(x$survS[,1]),1.2*max(x$survS[,1]))
ylow = ifelse(min(x$survS[,1])<0,1.2*min(x$survS[,1]),0.8*min(x$survS[,1]))
yy=x$survS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the surrogate endpoint.",...)
}
}else if(endpoint==1){
if(conf.bands){
yupp = ifelse(max(x$survT[,2])<0,0.8*max(x$survT[,2]),1.2*max(x$survT[,2]))
ylow = ifelse(min(x$survT[,3])<0,1.2*min(x$survT[,3]),0.8*min(x$survT[,3]))
yy=x$survT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the final endpoint\nand its 95% confidence bands.",...)
lines(xx,x$survT[,2],type='l',lty=3,...)
lines(xx,x$survT[,3],type='l',lty=3,...)
}else{
yupp = ifelse(max(x$survT[,1])<0,0.8*max(x$survT[,1]),1.2*max(x$survT[,1]))
ylow = ifelse(min(x$survT[,1])<0,1.2*min(x$survT[,1]),0.8*min(x$survT[,1]))
yy=x$survT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the final endpoint.",...)
}
}else{
if(conf.bands){
## S first ...
yupp = ifelse(max(x$survS[,3])<0,0.8*max(x$survS[,3]),1.2*max(x$survS[,3]))
ylow = ifelse(min(x$survS[,2])<0,1.2*min(x$survS[,2]),0.8*min(x$survS[,2]))
yy=x$survS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the surrogate endpoint\nand its 95% confidence bands.",...)
lines(xx,x$survS[,2],type='l',lty=3,...)
lines(xx,x$survS[,3],type='l',lty=3,...)
## Then T
invisible(readline(prompt="Press [Enter] to continue:"))
yupp = ifelse(max(x$survT[,2])<0,0.8*max(x$survT[,2]),1.2*max(x$survT[,2]))
ylow = ifelse(min(x$survT[,3])<0,1.2*min(x$survT[,3]),0.8*min(x$survT[,3]))
yy=x$survT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="HERE Estimated baseline survival function for the final endpoint\nand its 95% confidence bands.",...)
lines(xx,x$survT[,2],type='l',lty=3,...)
lines(xx,x$survT[,3],type='l',lty=3,...)
}else{
## S first ...
yupp = ifelse(max(x$survS[,1])<0,0.8*max(x$survS[,1]),1.2*max(x$survS[,1]))
ylow = ifelse(min(x$survS[,1])<0,1.2*min(x$survS[,1]),0.8*min(x$survS[,1]))
yy=x$survS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the surrogate endpoint.",...)
## Then T
invisible(readline(prompt="Press [Enter] to continue:"))
yupp = ifelse(max(x$survT[,1])<0,0.8*max(x$survT[,1]),1.2*max(x$survT[,1]))
ylow = ifelse(min(x$survT[,1])<0,1.2*min(x$survT[,1]),0.8*min(x$survT[,1]))
yy=x$survT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the final endpoint.",...)
}
}
}
if(plot.mediation=="g"){
x<-x$mediation
if(conf.bands==TRUE){
data.rt<-x$data.rt
rt.ci=x$Rt.ci
nie.ci=x$NIE.ci
nde.ci = x$NDE.ci
te.ci =x$TE.ci
data.g=x$data.g
invisible(readline(prompt="Press [Enter] to continue:"))
# plot gamma
ymin.g<-ifelse(min(data.g$lower,na.rm=T)<0,
1.2*min(data.g$lower),
0.8*min(data.g$lower))
ymax.g<-ifelse(max(data.g$upper,na.rm = T)<0,
0.8*max(data.g$upper,na.rm=T),
1.2*max(data.g$upper,na.rm=T))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(S)',
main="Estimated function g(s) with its 95% confidence bands",
ylim=c(ymin.g,ymax.g),...)
lines(x<-data.g$s,y<-data.g$upper,type='l',lty=3,...)
lines(x<-data.g$s,y<-data.g$lower,type='l',lty=3,...)
}else{
#plot without confidence bands
data.rt<-x$data.rt
data.g<-x$data.g
# plot gamma(s)
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(S)',main="Estimated function g(s)",...)
}
}
if(plot.mediation=="Rt"){
x<-x$mediation
if(length(x)==9 & conf.bands){
data.rt<-x$data.rt
rt.ci=x$Rt.ci
nie.ci=x$NIE.ci
nde.ci = x$NDE.ci
te.ci =x$TE.ci
data.g=x$data.g
#plot r(t)
ymin<-ifelse(min(rt.ci$lower,na.rm=T)<0,
1.2*min(rt.ci$lower,na.rm=T),
0.8*min(rt.ci$yuppower,na.rm=T))
ymax<-ifelse(max(rt.ci$upper,na.rm = T)<0,
0.8*max(rt.ci$upper,na.rm=T),
1.2*max(rt.ci$upper,na.rm=T))
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t) with its 95% confidence band",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-rt.ci$upper,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-rt.ci$lower,type='l',lty=2,col="black",...)
}else{
#plot without confidence bands
data.rt<-x$data.rt
data.g<-x$data.g
#plot r(t)
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t)",...)
}
}
if(plot.mediation=="Effects"){
x<-x$mediation
if(length(x)==9 & conf.bands){
data.rt<-x$data.rt
rt.ci=x$Rt.ci
nie.ci=x$NIE.ci
nde.ci = x$NDE.ci
te.ci =x$TE.ci
data.g=x$data.g
#plot effects
invisible(readline(prompt="Press [Enter] to continue:"))
miny <- min(te.ci$lower,nie.ci$lower,nde.ci$lower,na.rm=T)
maxy <-max(te.ci$upper,nie.ci$upper,nde.ci$upper,na.rm=T)
ymin<-ifelse(miny<0,1.2*miny,0.8*miny)
ymax<-ifelse(maxy<0,0.8*maxy,1.2*maxy)
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects with their 95% confidence bands",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="red",...)
lines(x<-data.rt$Time,y<-te.ci$lower,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-nde.ci$lower,type='l',lty=2,col="green",...)
lines(x<-data.rt$Time,y<-nie.ci$lower,type='l',lty=2,col="red",...)
lines(x<-data.rt$Time,y<-te.ci$upper,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-nde.ci$upper,type='l',lty=2,col="green",...)
lines(x<-data.rt$Time,y<-nie.ci$upper,type='l',lty=2,col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}else{
#plot without confidence bands
data.rt<-x$data.rt
data.g<-x$data.g
#plot effect
invisible(readline(prompt="Press [Enter] to continue:"))
ymin<-ifelse(min(data.rt$TE,data.rt$NIE,data.rt$TE)<0,
1.2*min(data.rt$TE,data.rt$NIE,data.rt$TE),
0.8*min(data.rt$TE,data.rt$NIE,data.rt$TE))
ymax<-ifelse(max(data.rt$TE,data.rt$NIE,data.rt$TE)<0,
0.8*max(data.rt$TE,data.rt$NIE,data.rt$TE),
1.2*max(data.rt$TE,data.rt$NIE,data.rt$TE))
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}
}
if(plot.mediation=="All"){
x<-x$mediation
if(length(x)==9 & conf.bands){
data.rt<-x$data.rt
rt.ci=x$Rt.ci
nie.ci=x$NIE.ci
nde.ci = x$NDE.ci
te.ci =x$TE.ci
data.g=x$data.g
invisible(readline(prompt="Press [Enter] to continue:"))
# plot gamma
ymin.g<-ifelse(min(data.g$lower,na.rm=T)<0,
1.2*min(data.g$lower),
0.8*min(data.g$lower))
ymax.g<-ifelse(max(data.g$upper,na.rm = T)<0,
0.8*max(data.g$upper,na.rm=T),
1.2*max(data.g$upper,na.rm=T))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(s)',
main="Estimated function g(s) with 95% confidence bands",
ylim=c(ymin.g,ymax.g),...)
lines(x<-data.g$s,y<-data.g$upper,type='l',lty=3,...)
lines(x<-data.g$s,y<-data.g$lower,type='l',lty=3,...)
#plot r(t)
ymin<-ifelse(min(rt.ci$lower,na.rm=T)<0,
1.2*min(rt.ci$lower,na.rm=T),
0.8*min(rt.ci$lower,na.rm=T))
ymax<-ifelse(max(rt.ci$upper,na.rm = T)<0,
0.8*max(rt.ci$upper,na.rm=T),
1.2*max(rt.ci$upper,na.rm=T))
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t) with its 95% confidence band",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-rt.ci$upper,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-rt.ci$lower,type='l',lty=2,col="black",...)
#plot effects
invisible(readline(prompt="Press [Enter] to continue:"))
miny <- min(te.ci$lower,nie.ci$lower,nde.ci$lower,na.rm=T)
maxy <-max(te.ci$upper,nie.ci$upper,nde.ci$upper,na.rm=T)
ymin<-ifelse(miny<0,1.2*miny,0.8*miny)
ymax<-ifelse(maxy<0,0.8*maxy,1.2*maxy)
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects with their 95% confidence bands",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="red",...)
lines(x<-data.rt$Time,y<-te.ci$lower,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-nde.ci$lower,type='l',lty=2,col="green",...)
lines(x<-data.rt$Time,y<-nie.ci$lower,type='l',lty=2,col="red",...)
lines(x<-data.rt$Time,y<-te.ci$upper,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-nde.ci$upper,type='l',lty=2,col="green",...)
lines(x<-data.rt$Time,y<-nie.ci$upper,type='l',lty=2,col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}else if(length(x)==5 & conf.bands){
data.rt<-x$data.rt
data.g=x$data.g
invisible(readline(prompt="Press [Enter] to continue:"))
# plot gamma
ymin.g<-ifelse(min(data.g$lower,na.rm=T)<0,
1.2*min(data.g$lower),
0.8*min(data.g$lower))
ymax.g<-ifelse(max(data.g$upper,na.rm = T)<0,
0.8*max(data.g$upper,na.rm=T),
1.2*max(data.g$upper,na.rm=T))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(s)',
main="Estimated function g(s) with its 95% confidence bands",
ylim=c(ymin.g,ymax.g),...)
lines(x<-data.g$s,y<-data.g$upper,type='l',lty=3,...)
lines(x<-data.g$s,y<-data.g$lower,type='l',lty=3,...)
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t)",...)
#plot effect
invisible(readline(prompt="Press [Enter] to continue:"))
ymin<-ifelse(min(data.rt$TE,data.rt$NIE,data.rt$NDE)<0,
1.2*min(data.rt$TE,data.rt$NIE,data.rt$NDE),
0.8*min(data.rt$TE,data.rt$NIE,data.rt$NDE))
ymax<-ifelse(max(data.rt$TE,data.rt$NIE,data.rt$NDE)<0,
0.8*max(data.rt$TE,data.rt$NIE,data.rt$NDE),
1.2*max(data.rt$TE,data.rt$NIE,data.rt$NDE))
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}else{
#plot without confidence bands
data.rt<-x$data.rt
data.g<-x$data.g
# plot gamma(s)
ymin.g<-ifelse(min(data.g$lower,na.rm=T)<0,
1.2*min(data.g$lower),
0.8*min(data.g$lower))
ymax.g<-ifelse(max(data.g$upper,na.rm = T)<0,
0.8*max(data.g$upper,na.rm=T),
1.2*max(data.g$upper,na.rm=T))
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(s)',
main="Estimated function g(s)",
ylim=c(ymin.g,ymax.g),...)
#plot r(t)
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t)",...)
#plot effect
invisible(readline(prompt="Press [Enter] to continue:"))
ymin<-ifelse(min(data.rt$TE,data.rt$NIE,data.rt$NDE)<0,
1.2*min(data.rt$TE,data.rt$NIE,data.rt$NDE),
0.8*min(data.rt$TE,data.rt$NIE,data.rt$NDE))
ymax<-ifelse(max(data.rt$TE,data.rt$NIE,data.rt$NDE)<0,
0.8*max(data.rt$TE,data.rt$NIE,data.rt$NDE),
1.2*max(data.rt$TE,data.rt$NIE,data.rt$NDE))
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}
}
return(invisible())
}
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#' Plot Method for a joint surrogate mediation analysis model.
#'
#' Plots the estimated functions associated with the mediation analysis, i.e.
#' \eqn{g(s)}, \eqn{R(t)}
#' as well as the natural direct, indirect and total effects.
#' An option to plot the confidence bands of the function \eqn{g(s)} is available.
#' This option is also implemented for the confidence bands of the functions
#' \eqn{R(t)} and of the natural effects if these confidence bands are available.
#'
#' @aliases plot.jointSurroMed
#' @usage
#' \method{plot}{jointSurroMed}(x,plot.mediation="All",type.plot="Hazard",
#' conf.bands=TRUE,endpoint=2,
#' legend.pos = "topleft",...)
#' @param x An object of class \code{jointSurroMed} from a joint surrogate model
#' with a mediation analysis
#' for longitudinal outcome and a terminal event, i.e., an
#' output from calling \code{jointSurroPenal} function with the option
#' 'mediation' set to TRUE.
#' @param plot.mediation A character string specifying the desired plot.
#' Possible values are "All", "g","Rt" or "Effects". The default is
#' "All" which displays all three plots.
#' @param type.plot A character string specifying the type of curve
#' for the baseline hazards functions. Possible
#' value are "Hazard", or "Survival".
#' @param endpoint An integer specifying for which endpoint should
#' the baseline curves be plotted. Possible values are 0
#' for the surrogate endpoint only and 1 for the final endpoint or 2 for both.
#' Default is 2.
#' @param conf.bands Logical value. Determines whether confidence bands should be
#' plotted. The default is to do so if the confidence bands are available.
#' @param legend.pos The location of the legend can be specified by setting
#' this argument to a single keyword from the list '"bottomright"', '"bottom"',
#' '"bottomleft"', '"left"', '"topleft"', '"top"', '"topright"', '"right"' and
#' '"center"'. The default is '"topleft"'
#' @param ... other unused arguments.
#' @return Print one or several plots for the mediation analysis
#' of a joint surrogate model
#' @seealso \code{\link{jointSurroPenal}}
#' @keywords file
#' @export
"plot.jointSurroMed" <- function (x, plot.mediation="All",type.plot="Hazard", conf.bands=TRUE,endpoint=2,
legend.pos = "topleft",...)
{
#options check
plot.type <- charmatch(plot.mediation, c("All", "g","Rt","Effects"),nomatch = 0)
if (plot.type == 0) {
stop("'plot.mediation' must be one of the following: 'All', 'g','Rt' or 'Effects'")
}
if(!(type.plot %in% c("Hazard","Survival"))){
stop("'type.plot' must be one of the following: 'Hazard' or 'Survival'.")
}
if(!(endpoint %in% c(0,1,2))){
stop("'endpoint' should be one of the following: 0,1 or 2.")
}
if(!(legend.pos %in% c("bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center" ))){
stop("'legend.pos should be one of the following: 'bottomright', 'bottom', 'bottomleft', 'left', 'topleft', 'top', 'topright', 'right', 'center'")
}
if(type.plot=="Hazard"){
if(endpoint==0){
if(conf.bands){
yupp = ifelse(max(x$lamS[,3])<0,0.8*max(x$lamS[,3]),1.2*max(x$lamS[,3]))
ylow = ifelse(min(x$lamS[,2])<0,1.2*max(x$lamS[,2]),0.8*min(x$lamS[,2]))
yy=x$lamS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the surrogate endpoint\nand its 95% confidence bands.",...)
lines(xx,x$lamS[,2],type='l',...)
lines(xx,x$lamS[,3],type='l',...)
}else{
yupp = ifelse(max(x$lamS[,1])<0,0.8*max(x$lamS[,1]),1.2*max(x$lamS[,1]))
ylow = ifelse(min(x$lamS[,1])<0,1.2*min(x$lamS[,1]),0.8*min(x$lamS[,1]))
yy=x$lamS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the surrogate endpoint.",...)
}
}else if(endpoint==1){
if(conf.bands){
yupp = ifelse(max(x$lamT[,3])<0,0.8*max(x$lamT[,3]),1.2*max(x$lamT[,3]))
ylow = ifelse(min(x$lamT[,2])<0,1.2*min(x$lamT[,2]),0.8*min(x$lamT[,2]))
yy=x$lamT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the final endpoint\nand its 95% confidence bands.",...)
lines(xx,x$lamT[,2],type='l',lty=3,...)
lines(xx,x$lamT[,3],type='l',lty=3,...)
}else{
yupp = ifelse(max(x$lamT[,1])<0,0.8*max(x$lamT[,1]),1.2*max(x$lamT[,1]))
ylow = ifelse(min(x$lamT[,1])<0,1.2*min(x$lamT[,1]),0.8*min(x$lamT[,1]))
yy=x$lamT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the final endpoint.",...)
}
}else{
if(conf.bands){
## S first ...
yupp = ifelse(max(x$lamS[,3])<0,0.8*max(x$lamS[,3]),1.2*max(x$lamS[,3]))
ylow = ifelse(min(x$lamS[,2])<0,1.2*min(x$lamS[,2]),0.8*min(x$lamS[,2]))
yy=x$lamS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the surrogate endpoint\nand its 95% confidence bands.",...)
lines(xx,x$lamS[,2],type='l',lty=3,...)
lines(xx,x$lamS[,3],type='l',lty=3,...)
## Then T
invisible(readline(prompt="Press [Enter] to continue:"))
yupp = ifelse(max(x$lamT[,3])<0,0.8*max(x$lamT[,3]),1.2*max(x$lamT[,3]))
ylow = ifelse(min(x$lamT[,2])<0,1.2*min(x$lamT[,2]),0.8*min(x$lamT[,2]))
yy=x$lamT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the final endpoint\nand its 95% confidence bands.",...)
lines(xx,x$lamT[,2],type='l',lty=3,...)
lines(xx,x$lamT[,3],type='l',lty=3,...)
}else{
## S first ...
yupp = ifelse(max(x$lamS[,1])<0,0.8*max(x$lamS[,1]),1.2*max(x$lamS[,1]))
ylow = ifelse(min(x$lamS[,1])<0,1.2*min(x$lamS[,1]),0.8*min(x$lamS[,1]))
yy=x$lamS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the surrogate endpoint.",...)
## Then T
invisible(readline(prompt="Press [Enter] to continue:"))
yupp = ifelse(max(x$lamT[,1])<0,0.8*max(x$lamT[,1]),1.2*max(x$lamT[,1]))
ylow = ifelse(min(x$lamT[,1])<0,1.2*min(x$lamT[,1]),0.8*min(x$lamT[,1]))
yy=x$lamT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Hazard',
main="Estimated baseline hazard function for the final endpoint.",...)
}
}
}else{
if(endpoint==0){
if(conf.bands){
yupp = ifelse(max(x$survS[,3])<0,0.8*max(x$survS[,3]),1.2*max(x$survS[,3]))
ylow = ifelse(min(x$survS[,2])<0,1.2*min(x$survS[,2]),0.8*min(x$survS[,2]))
yy=x$survS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the surrogate endpoint\nand its 95% confidence bands.",...)
lines(xx,x$survS[,2],type='l',lty=3,...)
lines(xx,x$survS[,3],type='l',lty=3,...)
}else{
yupp = ifelse(max(x$survS[,1])<0,0.8*max(x$survS[,1]),1.2*max(x$survS[,1]))
ylow = ifelse(min(x$survS[,1])<0,1.2*min(x$survS[,1]),0.8*min(x$survS[,1]))
yy=x$survS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the surrogate endpoint.",...)
}
}else if(endpoint==1){
if(conf.bands){
yupp = ifelse(max(x$survT[,2])<0,0.8*max(x$survT[,2]),1.2*max(x$survT[,2]))
ylow = ifelse(min(x$survT[,3])<0,1.2*min(x$survT[,3]),0.8*min(x$survT[,3]))
yy=x$survT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the final endpoint\nand its 95% confidence bands.",...)
lines(xx,x$survT[,2],type='l',lty=3,...)
lines(xx,x$survT[,3],type='l',lty=3,...)
}else{
yupp = ifelse(max(x$survT[,1])<0,0.8*max(x$survT[,1]),1.2*max(x$survT[,1]))
ylow = ifelse(min(x$survT[,1])<0,1.2*min(x$survT[,1]),0.8*min(x$survT[,1]))
yy=x$survT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the final endpoint.",...)
}
}else{
if(conf.bands){
## S first ...
yupp = ifelse(max(x$survS[,3])<0,0.8*max(x$survS[,3]),1.2*max(x$survS[,3]))
ylow = ifelse(min(x$survS[,2])<0,1.2*min(x$survS[,2]),0.8*min(x$survS[,2]))
yy=x$survS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the surrogate endpoint\nand its 95% confidence bands.",...)
lines(xx,x$survS[,2],type='l',lty=3,...)
lines(xx,x$survS[,3],type='l',lty=3,...)
## Then T
invisible(readline(prompt="Press [Enter] to continue:"))
yupp = ifelse(max(x$survT[,2])<0,0.8*max(x$survT[,2]),1.2*max(x$survT[,2]))
ylow = ifelse(min(x$survT[,3])<0,1.2*min(x$survT[,3]),0.8*min(x$survT[,3]))
yy=x$survT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="HERE Estimated baseline survival function for the final endpoint\nand its 95% confidence bands.",...)
lines(xx,x$survT[,2],type='l',lty=3,...)
lines(xx,x$survT[,3],type='l',lty=3,...)
}else{
## S first ...
yupp = ifelse(max(x$survS[,1])<0,0.8*max(x$survS[,1]),1.2*max(x$survS[,1]))
ylow = ifelse(min(x$survS[,1])<0,1.2*min(x$survS[,1]),0.8*min(x$survS[,1]))
yy=x$survS[,1]
xx=x$xS
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the surrogate endpoint.",...)
## Then T
invisible(readline(prompt="Press [Enter] to continue:"))
yupp = ifelse(max(x$survT[,1])<0,0.8*max(x$survT[,1]),1.2*max(x$survT[,1]))
ylow = ifelse(min(x$survT[,1])<0,1.2*min(x$survT[,1]),0.8*min(x$survT[,1]))
yy=x$survT[,1]
xx=x$xT
plot(xx,yy,ylim=c(ylow,yupp),type='l',
col="black", xlab="Time",ylab='Survival',
main="Estimated baseline survival function for the final endpoint.",...)
}
}
}
if(plot.mediation=="g"){
x<-x$mediation
if(conf.bands==TRUE){
data.rt<-x$data.rt
rt.ci=x$Rt.ci
nie.ci=x$NIE.ci
nde.ci = x$NDE.ci
te.ci =x$TE.ci
data.g=x$data.g
invisible(readline(prompt="Press [Enter] to continue:"))
# plot gamma
ymin.g<-ifelse(min(data.g$lower,na.rm=T)<0,
1.2*min(data.g$lower),
0.8*min(data.g$lower))
ymax.g<-ifelse(max(data.g$upper,na.rm = T)<0,
0.8*max(data.g$upper,na.rm=T),
1.2*max(data.g$upper,na.rm=T))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(S)',
main="Estimated function g(s) with its 95% confidence bands",
ylim=c(ymin.g,ymax.g),...)
lines(x<-data.g$s,y<-data.g$upper,type='l',lty=3,...)
lines(x<-data.g$s,y<-data.g$lower,type='l',lty=3,...)
}else{
#plot without confidence bands
data.rt<-x$data.rt
data.g<-x$data.g
# plot gamma(s)
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(S)',main="Estimated function g(s)",...)
}
}
if(plot.mediation=="Rt"){
x<-x$mediation
if(length(x)==9 & conf.bands){
data.rt<-x$data.rt
rt.ci=x$Rt.ci
nie.ci=x$NIE.ci
nde.ci = x$NDE.ci
te.ci =x$TE.ci
data.g=x$data.g
#plot r(t)
ymin<-ifelse(min(rt.ci$lower,na.rm=T)<0,
1.2*min(rt.ci$lower,na.rm=T),
0.8*min(rt.ci$yuppower,na.rm=T))
ymax<-ifelse(max(rt.ci$upper,na.rm = T)<0,
0.8*max(rt.ci$upper,na.rm=T),
1.2*max(rt.ci$upper,na.rm=T))
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t) with its 95% confidence band",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-rt.ci$upper,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-rt.ci$lower,type='l',lty=2,col="black",...)
}else{
#plot without confidence bands
data.rt<-x$data.rt
data.g<-x$data.g
#plot r(t)
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t)",...)
}
}
if(plot.mediation=="Effects"){
x<-x$mediation
if(length(x)==9 & conf.bands){
data.rt<-x$data.rt
rt.ci=x$Rt.ci
nie.ci=x$NIE.ci
nde.ci = x$NDE.ci
te.ci =x$TE.ci
data.g=x$data.g
#plot effects
invisible(readline(prompt="Press [Enter] to continue:"))
miny <- min(te.ci$lower,nie.ci$lower,nde.ci$lower,na.rm=T)
maxy <-max(te.ci$upper,nie.ci$upper,nde.ci$upper,na.rm=T)
ymin<-ifelse(miny<0,1.2*miny,0.8*miny)
ymax<-ifelse(maxy<0,0.8*maxy,1.2*maxy)
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects with their 95% confidence bands",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="red",...)
lines(x<-data.rt$Time,y<-te.ci$lower,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-nde.ci$lower,type='l',lty=2,col="green",...)
lines(x<-data.rt$Time,y<-nie.ci$lower,type='l',lty=2,col="red",...)
lines(x<-data.rt$Time,y<-te.ci$upper,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-nde.ci$upper,type='l',lty=2,col="green",...)
lines(x<-data.rt$Time,y<-nie.ci$upper,type='l',lty=2,col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}else{
#plot without confidence bands
data.rt<-x$data.rt
data.g<-x$data.g
#plot effect
invisible(readline(prompt="Press [Enter] to continue:"))
ymin<-ifelse(min(data.rt$TE,data.rt$NIE,data.rt$TE)<0,
1.2*min(data.rt$TE,data.rt$NIE,data.rt$TE),
0.8*min(data.rt$TE,data.rt$NIE,data.rt$TE))
ymax<-ifelse(max(data.rt$TE,data.rt$NIE,data.rt$TE)<0,
0.8*max(data.rt$TE,data.rt$NIE,data.rt$TE),
1.2*max(data.rt$TE,data.rt$NIE,data.rt$TE))
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}
}
if(plot.mediation=="All"){
x<-x$mediation
if(length(x)==9 & conf.bands){
data.rt<-x$data.rt
rt.ci=x$Rt.ci
nie.ci=x$NIE.ci
nde.ci = x$NDE.ci
te.ci =x$TE.ci
data.g=x$data.g
invisible(readline(prompt="Press [Enter] to continue:"))
# plot gamma
ymin.g<-ifelse(min(data.g$lower,na.rm=T)<0,
1.2*min(data.g$lower),
0.8*min(data.g$lower))
ymax.g<-ifelse(max(data.g$upper,na.rm = T)<0,
0.8*max(data.g$upper,na.rm=T),
1.2*max(data.g$upper,na.rm=T))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(s)',
main="Estimated function g(s) with 95% confidence bands",
ylim=c(ymin.g,ymax.g),...)
lines(x<-data.g$s,y<-data.g$upper,type='l',lty=3,...)
lines(x<-data.g$s,y<-data.g$lower,type='l',lty=3,...)
#plot r(t)
ymin<-ifelse(min(rt.ci$lower,na.rm=T)<0,
1.2*min(rt.ci$lower,na.rm=T),
0.8*min(rt.ci$lower,na.rm=T))
ymax<-ifelse(max(rt.ci$upper,na.rm = T)<0,
0.8*max(rt.ci$upper,na.rm=T),
1.2*max(rt.ci$upper,na.rm=T))
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t) with its 95% confidence band",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-rt.ci$upper,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-rt.ci$lower,type='l',lty=2,col="black",...)
#plot effects
invisible(readline(prompt="Press [Enter] to continue:"))
miny <- min(te.ci$lower,nie.ci$lower,nde.ci$lower,na.rm=T)
maxy <-max(te.ci$upper,nie.ci$upper,nde.ci$upper,na.rm=T)
ymin<-ifelse(miny<0,1.2*miny,0.8*miny)
ymax<-ifelse(maxy<0,0.8*maxy,1.2*maxy)
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects with their 95% confidence bands",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="red",...)
lines(x<-data.rt$Time,y<-te.ci$lower,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-nde.ci$lower,type='l',lty=2,col="green",...)
lines(x<-data.rt$Time,y<-nie.ci$lower,type='l',lty=2,col="red",...)
lines(x<-data.rt$Time,y<-te.ci$upper,type='l',lty=2,col="black",...)
lines(x<-data.rt$Time,y<-nde.ci$upper,type='l',lty=2,col="green",...)
lines(x<-data.rt$Time,y<-nie.ci$upper,type='l',lty=2,col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}else if(length(x)==5 & conf.bands){
data.rt<-x$data.rt
data.g=x$data.g
invisible(readline(prompt="Press [Enter] to continue:"))
# plot gamma
ymin.g<-ifelse(min(data.g$lower,na.rm=T)<0,
1.2*min(data.g$lower),
0.8*min(data.g$lower))
ymax.g<-ifelse(max(data.g$upper,na.rm = T)<0,
0.8*max(data.g$upper,na.rm=T),
1.2*max(data.g$upper,na.rm=T))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(s)',
main="Estimated function g(s) with its 95% confidence bands",
ylim=c(ymin.g,ymax.g),...)
lines(x<-data.g$s,y<-data.g$upper,type='l',lty=3,...)
lines(x<-data.g$s,y<-data.g$lower,type='l',lty=3,...)
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t)",...)
#plot effect
invisible(readline(prompt="Press [Enter] to continue:"))
ymin<-ifelse(min(data.rt$TE,data.rt$NIE,data.rt$NDE)<0,
1.2*min(data.rt$TE,data.rt$NIE,data.rt$NDE),
0.8*min(data.rt$TE,data.rt$NIE,data.rt$NDE))
ymax<-ifelse(max(data.rt$TE,data.rt$NIE,data.rt$NDE)<0,
0.8*max(data.rt$TE,data.rt$NIE,data.rt$NDE),
1.2*max(data.rt$TE,data.rt$NIE,data.rt$NDE))
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}else{
#plot without confidence bands
data.rt<-x$data.rt
data.g<-x$data.g
# plot gamma(s)
ymin.g<-ifelse(min(data.g$lower,na.rm=T)<0,
1.2*min(data.g$lower),
0.8*min(data.g$lower))
ymax.g<-ifelse(max(data.g$upper,na.rm = T)<0,
0.8*max(data.g$upper,na.rm=T),
1.2*max(data.g$upper,na.rm=T))
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.g$s,y<-data.g$g,type='l',col="black",
xlab="Time",ylab='g(s)',
main="Estimated function g(s)",
ylim=c(ymin.g,ymax.g),...)
#plot r(t)
invisible(readline(prompt="Press [Enter] to continue:"))
plot(x<-data.rt$Time,y<-data.rt$Rt,type='l',col="black",
xlab="Time",ylab='R(t)',main="Estimated R(t)",...)
#plot effect
invisible(readline(prompt="Press [Enter] to continue:"))
ymin<-ifelse(min(data.rt$TE,data.rt$NIE,data.rt$NDE)<0,
1.2*min(data.rt$TE,data.rt$NIE,data.rt$NDE),
0.8*min(data.rt$TE,data.rt$NIE,data.rt$NDE))
ymax<-ifelse(max(data.rt$TE,data.rt$NIE,data.rt$NDE)<0,
0.8*max(data.rt$TE,data.rt$NIE,data.rt$NDE),
1.2*max(data.rt$TE,data.rt$NIE,data.rt$NDE))
plot(x<-data.rt$Time,y<-data.rt$TE,type='l',col="black",
xlab="Time",ylab='Effects',main="Estimated natural effects",
ylim=c(ymin,ymax),...)
lines(x<-data.rt$Time,y<-data.rt$NIE,type='l',col="green",...)
lines(x<-data.rt$Time,y<-data.rt$NDE,type='l',col="red",...)
legend(legend.pos,legend=c("Total effect","Direct effect","Indirect effect"),
col=c("black","green","red"),lty=1)
}
}
return(invisible())
}
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