chron.ci {dplR} R Documentation

## Build Mean Value Chronology with Confidence Intervals

### Description

This function builds a mean value chronology with bootstrapped confidence intervals, typically from a data.frame of detrended ring widths as produced by detrend.

### Usage

chron.ci(x, biweight=TRUE, conf=0.95, R=100)


### Arguments

 x a data.frame of (usually detrended) ring widths with rownames(x) containing years and colnames(x) containing each series ID such as produced by read.rwl biweight logical flag. If TRUE then a robust mean is calculated using tbrm. conf numeric. A scalar for the confidence level. R integer. The number of bootstrap replicates.

### Details

This either averages the rows of the data.frame using a mean or a robust mean (the so-called standard chronology) and calculates boostrapped confidence intervals using the normal approximation. The function will fail if there are any rows in x that contain only one sample and in practice there should be several samples in a row. One of the guiding principles of bootstrapping is that the population is to the sample as the sample is to the bootstrap samples.

### Value

An object of of class data.frame with the standard chronology, the upper and lower confidence interval, and the sample depth. The years are stored as row numbers.

### Author(s)

Andy Bunn.

read.rwl, detrend, boot, boot.ci

### Examples

library(graphics)
library(utils)
data(wa082)
# truncate to a sample depth of five
wa082Trunc <- wa082[rowSums(!is.na(wa082))>4,]
# detrend
wa082RWI <- detrend(wa082Trunc, method="AgeDepSpline")
# bootstrap the chronology and
wa082Crn <- chron.ci(wa082RWI, biweight = TRUE, R = 100, conf = 0.99)
wa082Crn$yrs <- time(wa082Crn) xx <- c(wa082Crn$yrs,rev(wa082Crn$yrs)) yy <- c(wa082Crn$lowerCI,rev(wa082Crn$upperCI)) plot(wa082Crn$yrs,wa082Crn$std,type="n",ylim=range(yy), ylab="RWI",xlab="Year",main="Chronology with CI") polygon(x=xx,y=yy,col = "grey",border = NA) lines(wa082Crn$yrs,wa082Crn\$std)