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### This function is a component of astrochron: An R Package for Astrochronology
### Copyright (C) 2016 Stephen R. Meyers
###
###########################################################################
### noLow: remove lowess smoother from data - (SRM: March 12, 2012; May 31, 2012;
### April 24, 2013; May 20, 2013;
### June 21, 2013; July 22, 2016)
###
###########################################################################
noLow <- function (dat,smooth=.20,output=1,genplot=T,verbose=T)
{
if(verbose) cat("\n----- REMOVING LOWESS SMOOTHER FROM STRATIGRAPHIC SERIES -----\n")
dat<-data.frame(dat)
### fit a LOWESS smoother to data series
smooth.lo <- loess((dat[,2]) ~ dat[,1], degree=1, span= smooth )
y.predict <-predict(smooth.lo, se= TRUE)
if(verbose) print(summary(smooth.lo))
out <- dat
out[2] <- y.predict$fit
resid <- dat
resid[2] <- dat[2] - y.predict$fit
### plot linearly detrended data
if(genplot)
{
par(mfrow=c(2,2))
plot(dat,cex=0.5, xlab="Location", ylab="Value", main="Data with LOWESS Fit"); lines(dat[,1],y.predict$fit,col="red")
plot(resid,cex=0.5, xlab="Location", ylab="Value", main="Residuals from LOWESS Fit"); lines(resid)
### plot the denisty and the histogram together
hist(resid[,2],freq=F, xlab="Value", main="Distribution of Residual Values"); lines(density(resid[,2], bw="nrd0"),col="red"); grid()
### boxplot
boxplot(resid[,2], ylab="Value", main="Boxplot of Residual Values")
### Normal probabilty plot (Normal Q-Q Plot)
# qqnorm(resid[,2]); qqline(out[,2], col="red")
}
if(output==1) return(data.frame(resid))
if(output==2) return(data.frame(out))
### END function noLow
}
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