R: Plot a Tree-Ring Chronology

crn.plot {dplR} | R Documentation

## Plot a Tree-Ring Chronology

### Description

This function makes a default plot of a tree-ring chronology from a `data.frame` of the type produced by `chron`.

### Usage

    crn.plot(crn, add.spline = FALSE, nyrs = NULL, f = 0.5,
             crn.line.col='grey50',spline.line.col='red',
             samp.depth.col='grey90',
             samp.depth.border.col='grey80',
             crn.lwd=1,spline.lwd=1.5,
             abline.pos=1,abline.col='black',
             abline.lty=1,abline.lwd=1,
             xlab="Time",ylab="RWI",...)

    ## S3 method for class 'crn'
    plot(x, ...)

### Arguments

`x, crn` | a `data.frame` e.g., as produced by `chron`. The `data.frame` should have the years in `rownames(crn)`, the chronologies in the columns. Optionally, the last column can contain the sample depth named `"samp.depth"`. If the data are produced via `chron` the object will be of class "crn" and the generic plot method can be used
`add.spline` | a `logical` flag. Will add a line with a smoothing spline using `ffcsaps`
`nyrs` | a number giving the rigidity of the smoothing spline. Defaults to 0.33 times the length of the first chronology if `nyrs` is `NULL`
`f` | a number between 0 and 1 giving the frequency response or wavelength cutoff. Defaults to 0.5
`crn.line.col` | color for the x line
`spline.line.col` | color for the spline (if added)
`samp.depth.col` | color for the sample depth polygon (if present)
`samp.depth.border.col` | border color for the sample depth polygon (if present)
`crn.lwd` | line width for the x line
`spline.lwd` | line width for the spline (if added)
`abline.pos` | position for a reference abline on the y-axis. No line added if NULL
`abline.col` | color for the reference abline (if added)
`abline.lty` | line type the reference abline (if added)
`abline.lwd` | line width for the reference abline (if added)
`xlab` | default label for x axis
`ylab` | default label for y axis
`...` | Additional arguments to pass to `plot`. The scale of the secondary y axis (sample depth) can be controlled with argument `ylim2`.

### Details

This makes a plot of one or more tree-ring chronologies.

### Value

None. Invoked for side effect (plot).

### Author(s)

Andy Bunn. Patched and improved by Mikko Korpela.

### See Also

`chron`

### Examples

    library(graphics)
    library(utils)
    data(cana157)
    crn.plot(cana157)
    plot(cana157, main='Twisted Tree Heartrot Hill')
    # with added spline
    crn.plot(cana157,add.spline=TRUE, nyrs=32)
    ## Without sample depth
    cana157.mod <- cana157
    cana157.mod$samp.depth <- NULL
    crn.plot(cana157.mod, add.spline = TRUE)
    ## A raw ring-width chronology with prewhitening
    data(ca533)
    ca533.raw.crn <- chron(ca533, prefix = "CAM", prewhiten=TRUE)
    plot(ca533.raw.crn,ylab='mm',
         abline.pos=mean(ca533.raw.crn[,1],na.rm = TRUE))

    ## Not run:
      # not pretty - but illustrates the coloring options
      my.cols <- c("#3182BD","#9ECAE1","#DEEBF7","#31A354","#A1D99B","#E5F5E0")
      crn.plot(cana157,add.spline=TRUE,nyrs=32,
                 crn.line.col=my.cols[5],
                 spline.line.col=my.cols[4],
                 samp.depth.col=my.cols[3],
                 samp.depth.border.col=my.cols[2],
                 abline.col=my.cols[1],
                 crn.lwd=1.5,spline.lwd=3,
                 abline.lwd=1,
                 xlab="Year", ylab="RWI")

    ## End(Not run)

[Package dplR version 1.7.1 Index]