Updates the confidence intervals of the f.plot.spec function @ f.plot.spec.R; adds an option with CI = 95% or CI = 90% // deafult is 95%

Author: abaresch

R/f.plot.spec.R

@@ -18,7 +18,8 @@ f.plot.spec <- function(
   xlim=NULL,          ## vector to change the default xlim of the plots (ex xlim = c(500, 2400))
   position='topright',## Position of the legend (see base function legend for help)
   type='Reflectance', ## Name of the y axis and of the legend
-  plot_label=NULL     ## optional label for plot
+  plot_label=NULL ,   ## optional label for plot
+  CI = 95             ## confidence interval, default 95% ; can also be 90%  
 ){
   if(mean(as.matrix(Z),na.rm=TRUE)>1){Z=Z/100} ## Check if the spectra are in pc [0,100] or in [0,1]
   if(is.null(xlim)){xlim=c(min(wv),max(wv))}
@@ -27,12 +28,23 @@ f.plot.spec <- function(
 
   plot(x=NULL,y=NULL,ylim=c(0,100),xlim=xlim,xlab="Wavelength (nm)",
        ylab=paste0(type," (%)"),main=plot_label)
+       
+  if(CI==95){
+  	ci_text="95% CI"     
+  polygon(c(wv ,rev(wv)),c(spectra_quantiles[6,]*100, rev(spectra_quantiles[2,]*100)),
+          col="#99CC99",border=NA)
+          }
+          
+   if(CI==90){
+  	ci_text="90% CI"     
   polygon(c(wv ,rev(wv)),c(spectra_quantiles[5,]*100, rev(spectra_quantiles[3,]*100)),
           col="#99CC99",border=NA)
+          }         
+          
   lines(wv,mean_spec*100,lwd=2, lty=1, col="black")
   lines(wv,spectra_quantiles[1,]*100, lty=3, col="grey40")
   lines(wv,spectra_quantiles[7,]*100, lty=3, col="grey40")
-  legend(position,legend=c(paste("Mean",type),"Min/Max", "95% CI"),lty=c(1,3,1),
+  legend(position,legend=c(paste("Mean",type),"Min/Max", ci_text),lty=c(1,3,1),
          lwd=c(2,1,10),col=c("black","grey40","#99CC99"),bty="n")
   box(lwd=2.2)
 }