R/trinaryPlots.r
In cmerow/trinaryMaps: Build trinary (not binary) maps thats show upper and lowe bounds on species' ranges
Defines functions
trinaryROCPlot
trinaryMapPlot
Documented in
trinaryMapPlot
trinaryROCPlot
#################################################################
#################################################################
#################################################################
#' Plot trinary map raster
#'
#' This function plots the trinary map raster for a given species. The raster will have three colors: grey for the area with no prediction, blue for the predicted presence area, and red for the predicted absence area. Additionally, if the \code{pres} argument is provided, the function will overlay presence data in grey crosses on the plot. If the \code{shapesToPlot} argument is provided, the function will overlay the specified shapefiles on the plot. If a \code{plotFile} is provided, the plot will be saved to that file. If \code{openFig} is TRUE, the plot will also be opened in the system's default PDF viewer.
#'
#' @param trinaryRaster Trinary map raster created by \code{\link{trinaryMapWorkflow}}.
#' @param plotFile File to save plot. If NULL, plot is not saved.
#' @param pres Presence data to overlay on plot. If NULL, presence data is not included.
#' @param main Title for plot. Default is NULL.
#' @param shapesToPlot List of shapefiles to overlay on plot. Default is NULL.
#' @param openFig Logical indicating whether to open plot in system's default PDF viewer. Default is TRUE.
#'
#' @return None
#'
#' @examples
#' \dontrun{
#' # plot trinary map for species 1
#' trinaryMapPlot(trinaryRaster = trinaryMapSDMPW1$trinaryMap,
#' pres = species1Presences,
#' shapesToPlot = list(world.shp),
#' plotFile = "trinary_map_species1.pdf",
#' openFig = TRUE)
#' }
trinaryMapPlot=function(trinaryRaster,
plotFile=NULL,
pres=NULL,
main=NULL,
shapesToPlot=NULL,
openFig=TRUE){
# for testing
#
if(!is.null(plotFile)) grDevices::pdf(plotFile,h=7,w=7)
if(!is.null(pres)){
if(is.na(projection(pres))) {
projection(pres)=projection(trinaryRaster)
message('The projection for your presences was not specified, so assuming its the same as your rasters')
}
}
if(!is.null(plotFile)) grDevices::pdf(plotFile,h=7,w=7)
raster::image(trinaryRaster==0, xlab='',ylab='',col=c(grey(1,0),'grey80'),xaxt='n', yaxt='n',bty='n',main=main)
raster::image(trinaryRaster==1, xlab='',ylab='',col=c(grey(1,0),'steelblue'),xaxt='n', yaxt='n',bty='n',add=TRUE)
raster::image(trinaryRaster>=2, xlab='',ylab='',col=c(grey(1,0),'red1'),xaxt='n', yaxt='n',bty='n',add=TRUE)
if(!is.null(pres)) graphics::points(pres,col='grey90',pch='+',cex=.4)
if(!is.null(shapesToPlot)) lapply(shapesToPlot,sp::plot,add=T,lwd=.1,border='grey40')
if(!is.null(plotFile)) grDevices::dev.off(); if(openFig) system(paste0('open ',plotFile))
}
#################################################################
#################################################################
#################################################################
#' Plot trinary ROC curve and save the output as pdf file.
#'
#' @param trinaryPlotThings Object of trinary ROC curve, contains xx, y, xout, and y. as its attributes.
#' @param trinaryDF Data frame with trinary ROC curve information, including youden.thresh.roc.x, hi.thresh.roc.x, lo.thresh.roc.x, and trinary.pauc.
#' @param plotFile Path to save the output as pdf file. If NULL, the plot will not be saved.
#' @param openFig Logical, if TRUE, the plot will be shown in a new window.
#' @return None
#' @export
trinaryROCPlot=function(trinaryPlotThings,
trinaryDF,
plotFile=NULL,
openFig=TRUE
#addMapPlot=FALSE
){
# for testing
# trinaryPlotThings=threshs$trinaryPlotThings; trinaryDF=threshs[[1]]; openFig=T; addMapPlot=FALSE
if(!is.null(plotFile)) grDevices::pdf(plotFile,h=1.6*7,w=7.6)
par(mfrow=c(3,2),mar=c(5,4,2,2))
plot(trinaryPlotThings$xx,trinaryPlotThings$y,type='l',lwd=4,ylim=c(0,1.08), main="ROC",xlab='1-specificity', ylab="sensitivity",xlim=c(-.08,1))
#abline(h=0,lty=2)
abline(v=trinaryDF$youden.thresh.roc.x,col='darkgoldenrod2',lty=3,lwd=2)
abline(v=trinaryDF$hi.thresh.roc.x,col='steelblue',lty=3,lwd=2)
abline(v=trinaryDF$lo.thresh.roc.x,col='red1',lty=3,lwd=2)
abline(0,1,lty=2)
#points(trinaryDF$lo.thresh.roc.x,y.lo,pch=21,bg='red1')
points(trinaryDF$youden.thresh.roc.x,trinaryDF$youden.thresh.roc.y,pch=21, bg='darkgoldenrod2')
points(trinaryDF$hi.thresh.roc.x,trinaryDF$hi.thresh.roc.y,pch=21, bg='steelblue')
points(trinaryDF$lo.thresh.roc.x,trinaryDF$lo.thresh.roc.y,pch=21,bg='red1')
text(.8,.2,paste0('pAUC =\n',round(trinaryDF$trinary.pauc,3)),cex=1.5)
text(trinaryDF$youden.thresh.roc.x+.02,trinaryDF$youden.thresh.roc.y-.06, paste0('(',round(trinaryDF$youden.thresh.roc.x,2),',', round(trinaryDF$youden.thresh.roc.y,2),')'), adj=c(0,0), cex=1,col='darkgoldenrod2')
text(trinaryDF$hi.thresh.roc.x+.02,trinaryDF$hi.thresh.roc.y+.04, paste0('(',round(trinaryDF$hi.thresh.roc.x,2),',',round(trinaryDF$hi.thresh.roc.y,2),')'),adj=c(0,0), cex=1,col='steelblue')
text(trinaryDF$lo.thresh.roc.x+.02,trinaryDF$lo.thresh.roc.y-.06, paste0('(',round(trinaryDF$lo.thresh.roc.x,2),',',round(trinaryDF$lo.thresh.roc.y,2),')'),adj=c(0,1), cex=1,col='red1')
# ROC' -----------------------------------------
if(is.null(trinaryPlotThings$y.)) {
plot(.5,.5,col='white', main="ROC'", xlab='1-specificity',ylab="sensitivity'");
graphics::text(.5,.5,'Derivatives were not used for this model.\n 0% and 30% training presence quantiles\n were used instead')
} else {
if(any(is.na(trinaryPlotThings$y.))){ #this catches NAs
keep=which(!is.na(trinaryPlotThings$y.))
x.tmp=trinaryPlotThings$xout[keep]; y.tmp=trinaryPlotThings$y.[keep]
} else { x.tmp=trinaryPlotThings$xout; y.tmp=trinaryPlotThings$y. }
# catch infs; don't need this for second derivs, because those become NA
keep=which(is.finite(y.tmp))
y.tmp=y.tmp[keep]; x.tmp=x.tmp[keep]
if(any(is.infinite(y.tmp))){
plot(.5,.5,col='white', main="ROC'", xlab='1-specificity',ylab="sensitivity'"); graphics::text(.5,.5,'Derivative contains Inf')
} else {
p1=plot(x.tmp,y.tmp,type='l',col='black',log='y', main="ROC'", xlab='1-specificity',ylab="sensitivity''",xlim=c(0,1))
}
abline(h=0,lty=2)
abline(h=1,lty=2)
abline(v=trinaryDF$youden.thresh.roc.x,col='darkgoldenrod2',lty=3,lwd=2)
abline(v=trinaryDF$hi.thresh.roc.x,col='steelblue',lty=3,lwd=2)
abline(v=trinaryDF$lo.thresh.roc.x,col='red1',lty=3,lwd=2)
}
# ROC'' -----------------------------------------
if(is.null(trinaryPlotThings$y..)) {
plot(.5,.5,col='white', main="logmod(ROC'')", xlab='1-specificity',ylab="sensitivity'");
graphics::text(.5,.5,'Derivatives were not used for this model.\n 0% and 30% training presence quantiles\n were used instead')
} else {
if(any(is.na(trinaryPlotThings$y..))){
keep=which(!is.na(trinaryPlotThings$y..))
x.tmp=trinaryPlotThings$xout[keep]; y.tmp=trinaryPlotThings$y..[keep]
} else {x.tmp=trinaryPlotThings$xout; y.tmp=trinaryPlotThings$y..}
if(any(is.infinite(y.tmp)) | all(y.tmp==0)){
plot(.5,.5,col='white', main="logmod(ROC'')", xlab='1-specificity',ylab="logmod(sensitivity'')"); graphics::text(.5,.5,'Derivative contains Inf')
} else {
plot(x.tmp,logmod(y.tmp),type='l',col='black', main="logmod(ROC'')", xlim=c(0,1),xlab='1-specificity',ylab="logmod(sensitivity'')")
}
abline(h=0,lty=2)
abline(v=trinaryDF$youden.thresh.roc.x,col='darkgoldenrod2',lty=3,lwd=2)
abline(v=trinaryDF$hi.thresh.roc.x,col='steelblue',lty=3,lwd=2)
abline(v=trinaryDF$lo.thresh.roc.x,col='red1',lty=3,lwd=2)
}
# inverse ROC -----------------------------------
if(is.null(trinaryPlotThings$y1)) {
plot(.5,.5,col='white', main="Inverse ROC'", xlab='1-sensitivity',ylab='specificity');
graphics::text(.5,.5,'Derivatives were not used for this model.\n 0% and 30% training presence quantiles\n were used instead')
} else {
if(any(is.na(trinaryPlotThings$y1))){
keep=which(!is.na(trinaryPlotThings$y1))
x.tmp=trinaryPlotThings$xx1[keep]; y.tmp=trinaryPlotThings$y1[keep]
} else {x.tmp=trinaryPlotThings$xx1; y.tmp=trinaryPlotThings$y1}
if(any(is.infinite(y.tmp))){
plot(.5,.5,col='white', main="Inverse ROC", xlab='1-sensitivity',ylab='specificity'); graphics::text(.5,.5,'Derivative contains Inf')
} else {
plot(x.tmp,y.tmp,type='l',lwd=4,ylim=c(0,1.08), main='Inverse ROC',xlab='1-sensitivity',ylab='specificity')
}
abline(h=trinaryDF$y.lo.inv,col='red1',lty=3,lwd=2)
abline(v=trinaryDF$x.lo.inv,col='red1',lty=3,lwd=2)
abline(0,1,lty=2)
}
# inverse ROC'' -----------------------------------
if(is.null(trinaryPlotThings$y1..)) {
plot(.5,.5,col='white',main="logmod[(Inverse ROC)'']", xlab='1-sensitivity',ylab="logmod(specificity'')");
graphics::text(.5,.5,'Derivatives were not used for this model.\n 0% and 30% training presence quantiles\n were used instead')
} else {
if(!any(is.finite(trinaryPlotThings$y1..))){
keep=which(!is.na(trinaryPlotThings$y1..))
x.tmp=trinaryPlotThings$x1out[keep]; y.tmp=trinaryPlotThings$y1..[keep]
} else {x.tmp=trinaryPlotThings$x1out; y.tmp=trinaryPlotThings$y1..}
if(any(is.infinite(y.tmp)) | all(y.tmp==0,na.rm=T)){
plot(.5,.5,col='white', main="logmod[(Inverse ROC)'']", xlab='1-sensitivity',ylab="logmod(specificity'')"); graphics::text(.5,.5,'Derivative contains Inf')
} else {
plot(x.tmp,logmod(y.tmp),type='l', main="logmod[(Inverse ROC)'']",xlab='1-sensitivity',ylab="logmod(specificity'')",xlim=c(0,1),ylim=range(logmod(trinaryPlotThings$y1..),na.rm=T))
}
#abline(h=y.lo) # not sure what this was supposed to be... was defined as 1-x.lo.inv in the modeling....
abline(h=0,lty=2)
abline(v=trinaryDF$x.lo.inv,col='red1',lty=3,lwd=2)
}
# for third derivative - works but not needed
# # plot(trinaryPlotThings$xout,logmod(y...),type='l',col='black', log='y',xlim=c(0,1),main="ROC'''")
# # abline(h=0,lty=2)
# # abline(v=x.lo,col='darkgoldenrod2',lty=3,lwd=2)
# # abline(v=trinaryDF$hi.thresh.roc.x,col='steelblue',lty=3,lwd=2)
# # abline(v=x.lo,col='red1',lty=3,lwd=2)
# curvature; code works, idea doesn't
# # plot(trinaryPlotThings$xout,c2,type='l',col='black',xlim=c(0,1), main=expression(paste(kappa,"(ROC)")))
# # abline(v=x.lo,col='red1',lty=3,lwd=2)
# # lines(trinaryPlotThings$xout,c2.1,col='grey30')
# # lines(trinaryPlotThings$xout,c2.2,col='grey60')
#abline(v=.y..f(rate,skew),lty=2)
##abline(v=x.root,col='blue',lty=2)
#lines(ss$x,ss$y,col='blue')
# if(addMapPlot){
# print('not done')
# # have to push all these args, which is annoying
# # trinaryMapPlot(trinaryRaster,plotFile,pres=pres, expertRasterPath=expertRasterPath,expertShpPath=expertShpPath,shapesToPlot=shapesToPlot,openFig=T)
# }
if(!is.null(plotFile)) grDevices::dev.off()
if(openFig & !is.null(plotFile)) system(paste0('open ', plotFile))
}
cmerow/trinaryMaps documentation built on April 28, 2023, 6:02 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions trinaryROCPlot trinaryMapPlot
Documented in trinaryMapPlot trinaryROCPlot
#################################################################
#################################################################
#################################################################
#' Plot trinary map raster
#'
#' This function plots the trinary map raster for a given species. The raster will have three colors: grey for the area with no prediction, blue for the predicted presence area, and red for the predicted absence area. Additionally, if the \code{pres} argument is provided, the function will overlay presence data in grey crosses on the plot. If the \code{shapesToPlot} argument is provided, the function will overlay the specified shapefiles on the plot. If a \code{plotFile} is provided, the plot will be saved to that file. If \code{openFig} is TRUE, the plot will also be opened in the system's default PDF viewer.
#'
#' @param trinaryRaster Trinary map raster created by \code{\link{trinaryMapWorkflow}}.
#' @param plotFile File to save plot. If NULL, plot is not saved.
#' @param pres Presence data to overlay on plot. If NULL, presence data is not included.
#' @param main Title for plot. Default is NULL.
#' @param shapesToPlot List of shapefiles to overlay on plot. Default is NULL.
#' @param openFig Logical indicating whether to open plot in system's default PDF viewer. Default is TRUE.
#'
#' @return None
#'
#' @examples
#' \dontrun{
#' # plot trinary map for species 1
#' trinaryMapPlot(trinaryRaster = trinaryMapSDMPW1$trinaryMap,
#' pres = species1Presences,
#' shapesToPlot = list(world.shp),
#' plotFile = "trinary_map_species1.pdf",
#' openFig = TRUE)
#' }
trinaryMapPlot=function(trinaryRaster,
plotFile=NULL,
pres=NULL,
main=NULL,
shapesToPlot=NULL,
openFig=TRUE){
# for testing
#
if(!is.null(plotFile)) grDevices::pdf(plotFile,h=7,w=7)
if(!is.null(pres)){
if(is.na(projection(pres))) {
projection(pres)=projection(trinaryRaster)
message('The projection for your presences was not specified, so assuming its the same as your rasters')
}
}
if(!is.null(plotFile)) grDevices::pdf(plotFile,h=7,w=7)
raster::image(trinaryRaster==0, xlab='',ylab='',col=c(grey(1,0),'grey80'),xaxt='n', yaxt='n',bty='n',main=main)
raster::image(trinaryRaster==1, xlab='',ylab='',col=c(grey(1,0),'steelblue'),xaxt='n', yaxt='n',bty='n',add=TRUE)
raster::image(trinaryRaster>=2, xlab='',ylab='',col=c(grey(1,0),'red1'),xaxt='n', yaxt='n',bty='n',add=TRUE)
if(!is.null(pres)) graphics::points(pres,col='grey90',pch='+',cex=.4)
if(!is.null(shapesToPlot)) lapply(shapesToPlot,sp::plot,add=T,lwd=.1,border='grey40')
if(!is.null(plotFile)) grDevices::dev.off(); if(openFig) system(paste0('open ',plotFile))
}
#################################################################
#################################################################
#################################################################
#' Plot trinary ROC curve and save the output as pdf file.
#'
#' @param trinaryPlotThings Object of trinary ROC curve, contains xx, y, xout, and y. as its attributes.
#' @param trinaryDF Data frame with trinary ROC curve information, including youden.thresh.roc.x, hi.thresh.roc.x, lo.thresh.roc.x, and trinary.pauc.
#' @param plotFile Path to save the output as pdf file. If NULL, the plot will not be saved.
#' @param openFig Logical, if TRUE, the plot will be shown in a new window.
#' @return None
#' @export
trinaryROCPlot=function(trinaryPlotThings,
trinaryDF,
plotFile=NULL,
openFig=TRUE
#addMapPlot=FALSE
){
# for testing
# trinaryPlotThings=threshs$trinaryPlotThings; trinaryDF=threshs[[1]]; openFig=T; addMapPlot=FALSE
if(!is.null(plotFile)) grDevices::pdf(plotFile,h=1.6*7,w=7.6)
par(mfrow=c(3,2),mar=c(5,4,2,2))
plot(trinaryPlotThings$xx,trinaryPlotThings$y,type='l',lwd=4,ylim=c(0,1.08), main="ROC",xlab='1-specificity', ylab="sensitivity",xlim=c(-.08,1))
#abline(h=0,lty=2)
abline(v=trinaryDF$youden.thresh.roc.x,col='darkgoldenrod2',lty=3,lwd=2)
abline(v=trinaryDF$hi.thresh.roc.x,col='steelblue',lty=3,lwd=2)
abline(v=trinaryDF$lo.thresh.roc.x,col='red1',lty=3,lwd=2)
abline(0,1,lty=2)
#points(trinaryDF$lo.thresh.roc.x,y.lo,pch=21,bg='red1')
points(trinaryDF$youden.thresh.roc.x,trinaryDF$youden.thresh.roc.y,pch=21, bg='darkgoldenrod2')
points(trinaryDF$hi.thresh.roc.x,trinaryDF$hi.thresh.roc.y,pch=21, bg='steelblue')
points(trinaryDF$lo.thresh.roc.x,trinaryDF$lo.thresh.roc.y,pch=21,bg='red1')
text(.8,.2,paste0('pAUC =\n',round(trinaryDF$trinary.pauc,3)),cex=1.5)
text(trinaryDF$youden.thresh.roc.x+.02,trinaryDF$youden.thresh.roc.y-.06, paste0('(',round(trinaryDF$youden.thresh.roc.x,2),',', round(trinaryDF$youden.thresh.roc.y,2),')'), adj=c(0,0), cex=1,col='darkgoldenrod2')
text(trinaryDF$hi.thresh.roc.x+.02,trinaryDF$hi.thresh.roc.y+.04, paste0('(',round(trinaryDF$hi.thresh.roc.x,2),',',round(trinaryDF$hi.thresh.roc.y,2),')'),adj=c(0,0), cex=1,col='steelblue')
text(trinaryDF$lo.thresh.roc.x+.02,trinaryDF$lo.thresh.roc.y-.06, paste0('(',round(trinaryDF$lo.thresh.roc.x,2),',',round(trinaryDF$lo.thresh.roc.y,2),')'),adj=c(0,1), cex=1,col='red1')
# ROC' -----------------------------------------
if(is.null(trinaryPlotThings$y.)) {
plot(.5,.5,col='white', main="ROC'", xlab='1-specificity',ylab="sensitivity'");
graphics::text(.5,.5,'Derivatives were not used for this model.\n 0% and 30% training presence quantiles\n were used instead')
} else {
if(any(is.na(trinaryPlotThings$y.))){ #this catches NAs
keep=which(!is.na(trinaryPlotThings$y.))
x.tmp=trinaryPlotThings$xout[keep]; y.tmp=trinaryPlotThings$y.[keep]
} else { x.tmp=trinaryPlotThings$xout; y.tmp=trinaryPlotThings$y. }
# catch infs; don't need this for second derivs, because those become NA
keep=which(is.finite(y.tmp))
y.tmp=y.tmp[keep]; x.tmp=x.tmp[keep]
if(any(is.infinite(y.tmp))){
plot(.5,.5,col='white', main="ROC'", xlab='1-specificity',ylab="sensitivity'"); graphics::text(.5,.5,'Derivative contains Inf')
} else {
p1=plot(x.tmp,y.tmp,type='l',col='black',log='y', main="ROC'", xlab='1-specificity',ylab="sensitivity''",xlim=c(0,1))
}
abline(h=0,lty=2)
abline(h=1,lty=2)
abline(v=trinaryDF$youden.thresh.roc.x,col='darkgoldenrod2',lty=3,lwd=2)
abline(v=trinaryDF$hi.thresh.roc.x,col='steelblue',lty=3,lwd=2)
abline(v=trinaryDF$lo.thresh.roc.x,col='red1',lty=3,lwd=2)
}
# ROC'' -----------------------------------------
if(is.null(trinaryPlotThings$y..)) {
plot(.5,.5,col='white', main="logmod(ROC'')", xlab='1-specificity',ylab="sensitivity'");
graphics::text(.5,.5,'Derivatives were not used for this model.\n 0% and 30% training presence quantiles\n were used instead')
} else {
if(any(is.na(trinaryPlotThings$y..))){
keep=which(!is.na(trinaryPlotThings$y..))
x.tmp=trinaryPlotThings$xout[keep]; y.tmp=trinaryPlotThings$y..[keep]
} else {x.tmp=trinaryPlotThings$xout; y.tmp=trinaryPlotThings$y..}
if(any(is.infinite(y.tmp)) | all(y.tmp==0)){
plot(.5,.5,col='white', main="logmod(ROC'')", xlab='1-specificity',ylab="logmod(sensitivity'')"); graphics::text(.5,.5,'Derivative contains Inf')
} else {
plot(x.tmp,logmod(y.tmp),type='l',col='black', main="logmod(ROC'')", xlim=c(0,1),xlab='1-specificity',ylab="logmod(sensitivity'')")
}
abline(h=0,lty=2)
abline(v=trinaryDF$youden.thresh.roc.x,col='darkgoldenrod2',lty=3,lwd=2)
abline(v=trinaryDF$hi.thresh.roc.x,col='steelblue',lty=3,lwd=2)
abline(v=trinaryDF$lo.thresh.roc.x,col='red1',lty=3,lwd=2)
}
# inverse ROC -----------------------------------
if(is.null(trinaryPlotThings$y1)) {
plot(.5,.5,col='white', main="Inverse ROC'", xlab='1-sensitivity',ylab='specificity');
graphics::text(.5,.5,'Derivatives were not used for this model.\n 0% and 30% training presence quantiles\n were used instead')
} else {
if(any(is.na(trinaryPlotThings$y1))){
keep=which(!is.na(trinaryPlotThings$y1))
x.tmp=trinaryPlotThings$xx1[keep]; y.tmp=trinaryPlotThings$y1[keep]
} else {x.tmp=trinaryPlotThings$xx1; y.tmp=trinaryPlotThings$y1}
if(any(is.infinite(y.tmp))){
plot(.5,.5,col='white', main="Inverse ROC", xlab='1-sensitivity',ylab='specificity'); graphics::text(.5,.5,'Derivative contains Inf')
} else {
plot(x.tmp,y.tmp,type='l',lwd=4,ylim=c(0,1.08), main='Inverse ROC',xlab='1-sensitivity',ylab='specificity')
}
abline(h=trinaryDF$y.lo.inv,col='red1',lty=3,lwd=2)
abline(v=trinaryDF$x.lo.inv,col='red1',lty=3,lwd=2)
abline(0,1,lty=2)
}
# inverse ROC'' -----------------------------------
if(is.null(trinaryPlotThings$y1..)) {
plot(.5,.5,col='white',main="logmod[(Inverse ROC)'']", xlab='1-sensitivity',ylab="logmod(specificity'')");
graphics::text(.5,.5,'Derivatives were not used for this model.\n 0% and 30% training presence quantiles\n were used instead')
} else {
if(!any(is.finite(trinaryPlotThings$y1..))){
keep=which(!is.na(trinaryPlotThings$y1..))
x.tmp=trinaryPlotThings$x1out[keep]; y.tmp=trinaryPlotThings$y1..[keep]
} else {x.tmp=trinaryPlotThings$x1out; y.tmp=trinaryPlotThings$y1..}
if(any(is.infinite(y.tmp)) | all(y.tmp==0,na.rm=T)){
plot(.5,.5,col='white', main="logmod[(Inverse ROC)'']", xlab='1-sensitivity',ylab="logmod(specificity'')"); graphics::text(.5,.5,'Derivative contains Inf')
} else {
plot(x.tmp,logmod(y.tmp),type='l', main="logmod[(Inverse ROC)'']",xlab='1-sensitivity',ylab="logmod(specificity'')",xlim=c(0,1),ylim=range(logmod(trinaryPlotThings$y1..),na.rm=T))
}
#abline(h=y.lo) # not sure what this was supposed to be... was defined as 1-x.lo.inv in the modeling....
abline(h=0,lty=2)
abline(v=trinaryDF$x.lo.inv,col='red1',lty=3,lwd=2)
}
# for third derivative - works but not needed
# # plot(trinaryPlotThings$xout,logmod(y...),type='l',col='black', log='y',xlim=c(0,1),main="ROC'''")
# # abline(h=0,lty=2)
# # abline(v=x.lo,col='darkgoldenrod2',lty=3,lwd=2)
# # abline(v=trinaryDF$hi.thresh.roc.x,col='steelblue',lty=3,lwd=2)
# # abline(v=x.lo,col='red1',lty=3,lwd=2)
# curvature; code works, idea doesn't
# # plot(trinaryPlotThings$xout,c2,type='l',col='black',xlim=c(0,1), main=expression(paste(kappa,"(ROC)")))
# # abline(v=x.lo,col='red1',lty=3,lwd=2)
# # lines(trinaryPlotThings$xout,c2.1,col='grey30')
# # lines(trinaryPlotThings$xout,c2.2,col='grey60')
#abline(v=.y..f(rate,skew),lty=2)
##abline(v=x.root,col='blue',lty=2)
#lines(ss$x,ss$y,col='blue')
# if(addMapPlot){
# print('not done')
# # have to push all these args, which is annoying
# # trinaryMapPlot(trinaryRaster,plotFile,pres=pres, expertRasterPath=expertRasterPath,expertShpPath=expertShpPath,shapesToPlot=shapesToPlot,openFig=T)
# }
if(!is.null(plotFile)) grDevices::dev.off()
if(openFig & !is.null(plotFile)) system(paste0('open ', plotFile))
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.