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### This function is a component of astrochron: An R Package for Astrochronology
### Copyright (C) 2016 Stephen R. Meyers
###
###########################################################################
### rmNA: remove NA's- (SRM: May 11, 2016; July 22, 2016)
###
###########################################################################
rmNA <- function (dat, genplot=T, verbose=T)
{
if(verbose) cat("\n----- REMOVING STRATIGRAPHIC LEVELS THAT CONTAIN 'NA' ENTRIES -----\n")
dat <- data.frame(dat)
ipts <- length(dat[,1])
if(verbose) cat(" * Number of rows (stratigraphic levels)=", ipts,"\n")
cols=length(dat)
if(verbose) cat(" * Number of columns=", cols,"\n")
numNA=sum(is.na(dat))
if(verbose) cat(" * Number of NA values identified=", numNA,"\n")
# processes each stratigraphic level (row), delete if it has an NA in any column
dat=na.omit(dat)
newpts=length(dat[,1])
if(verbose) cat(" * Number of rows (stratigraphic levels) following culling=",newpts,"\n")
if(cols == 2 && genplot)
{
### plots
par(mfrow=c(2,2))
plot(dat,cex=0.5,xlab="Location",ylab="Value",main="Data Series"); lines(dat)
### plot the denisty and the histogram together
hist(dat[,2],freq=F,xlab="Value",main="Distribution of isoloated values"); lines(density(dat[,2], bw="nrd0"),col="red")
### boxplot
boxplot(dat[,2],ylab="Value",main="Boxplot for isolated values")
### Normal probabilty plot (Normal Q-Q Plot)
qqnorm(dat[,2]); qqline(dat[,2], col="red")
}
return(dat)
### END function rmNA
}
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