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### This function is a component of astrochron: An R Package for Astrochronology
### Copyright (C) 2015 Stephen R. Meyers
###
###########################################################################
### clipIt: clip or mute stratigraphic series below a theshold value to transfer
### power to modulator (SRM: December 25, 2013; January 5, 2014; July 22, 2016)
###
###########################################################################
clipIt <- function (dat,thresh=NULL,clipval=NULL,clipdiv=NULL,genplot=T,verbose=T)
{
if (verbose) cat("\n----- CLIP STRATIGRAPHIC SERIES -----\n")
dat<-data.frame(dat)
# make copy for clipping
dat2 <- dat
ipts <- length(dat[,1])
if (verbose) cat(" * Number of data points=", ipts,"\n")
dave <- colMeans(dat[2])
dmax <- max(dat[2])
dmin <- min(dat[2])
if(is.null(thresh))
{
thresh <- dave
if(verbose) cat(" * Will use mean value as clipping threshold\n")
}
if(is.null(clipval)) clipval <- thresh
if(clipval > dmax && verbose) cat(" * WARNING: threshold is above maximum value\n")
if(clipval < dmin && verbose) cat(" * WARNING: threshold is below minimum value\n")
if(is.null(clipdiv))
{
dat2[dat2[2]<thresh,2] <- clipval
}
if(!is.null(clipdiv))
{
dat2[dat2[2]<thresh,2] <- dat2[dat2[2]<thresh,2]/clipdiv
}
if(genplot)
{
### plots
par(mfrow=c(2,2))
plot(dat,cex=0.5,xlab="Location",ylab="Value",main="Original (black) and Clipped (red) Data", type="l"); points(dat2, col="red",cex=0.5)
### plot the denisty and the histogram together
hist(dat2[,2],freq=F); lines(density(dat2[,2], bw="nrd0"),col="red"); grid()
### boxplot
boxplot(dat2[,2])
### Normal probabilty plot (Normal Q-Q Plot)
qqnorm(dat2[,2]); qqline(dat2[,2], col="red")
}
return(dat2)
### END function clipIt
}
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