From 3b4923ffa9581053a89a3a57f10b3f80e13142fb Mon Sep 17 00:00:00 2001 From: Corey Bradshaw Date: Sat, 29 Oct 2022 19:25:33 +1030 Subject: [PATCH] Update WilliamsPGR.R --- scripts/WilliamsPGR.R | 6 ------ 1 file changed, 6 deletions(-) diff --git a/scripts/WilliamsPGR.R b/scripts/WilliamsPGR.R index f17e8ae..4bf8f81 100644 --- a/scripts/WilliamsPGR.R +++ b/scripts/WilliamsPGR.R @@ -15,7 +15,6 @@ library(rcarbon) library(stringr) # import raw radiometric dates -setwd("~/Documents/Papers/Palaeo/Sahul/Aus hum N trajectories/data/Williams' data") RCdates <- read.csv("radiometricdates.csv") head(RCdates) @@ -181,14 +180,12 @@ factor(RCnotmarine$matClass) dim(RCnotmarine) table(RCnotmarine$matClass) CALnotmarine <- calibrate(x=RCnotmarine$RCage, errors=RCnotmarine$RCerr, ids=RCnotmarine$labcode, calCurves="shcal20") -#multiplot(CALnotmarine, decreasing=T, rescale=T, HPD=T) CALnotmarine.summ <- summary(CALnotmarine) RCmarine <- subset(RCsortlim, matClass=="marine" | matClass=='otolith') dim(RCmarine) table(RCmarine$matClass) CALmarine <- calibrate(x=RCmarine$RCage, errors=RCmarine$RCerr, ids=RCmarine$labcode, calCurves="marine20", verbose=T) -#length(which.CalDates(CALmarine, BP<=50000&BP>=4000, p=0.5)) CALmarine.summ <- summary(CALmarine) dim(CALmarine.summ) head(CALnotmarine.summ) @@ -277,8 +274,6 @@ for (i in 1:iter) { # Williams' approach # apply df=25 smoothing spline to time series num.dates.ss <- smooth.spline(x=intMDvec, y=num.dates, df=25) - #plot(intMDvec, num.dates, type="l", xlab="calendear years BP", ylab="number of radiocarbon dates") - #lines(intMDvec, num.dates.ss$y, lwd=2, col="red") # taphonomic correction #num.dates.taphc <- num.dates.ss$y / rnorm(length(taph.corr.interp$t), taph.corr.interp$corr, taph.corr.interp$sd) @@ -286,7 +281,6 @@ for (i in 1:iter) { # mean annual growth rate GRann.mat[i,2:(length(intMDvec))] <- (diff(nDatesCorr.mat[i,])*0.5)/nDatesCorr.mat[i,][1:(length(nDatesCorr.mat[i,])-1)] - #plot(intMDvec[-length(intMDvec)], GRann, type="l",ylim=c(-0.2,1)) # instantaneous exponential rate of increase r.mat[i,2:(length(intMDvec))] <- log(nDatesCorr.mat[i,][2:length(nDatesCorr.mat[i,])] / nDatesCorr.mat[i,][1:(length(nDatesCorr.mat[i,])-1)])