plot.rarecol {PAICE}

Plot rarefaction curve of colonization events

Description

Plots for the rarefaction curves produced by rarecol.

Usage

## S3 method for class 'rarecol'
plot(x, xlim1, xlim2, ylim, ylim1, ylim2, palette1, palette2, main1,
    main2, xlab1, xlab2, ylab1, ylab2, las1 = 1, las2 = 1,
    cextText = 0.75, legendbar = TRUE, ...)

Arguments

x

an object generated by the rarecol function.

xlim1, xlim2

x limits (min, max) of the two plots.

ylim1, ylim2

y limits (min, max) of the two plots.

ylim

y limits (min, max) of the two plots simultaneously. If ylim is defined, the function does not consider ylim1 and ylim2.

palette1, palette2

vector of color for lines in plot 1 and plot 2.

main1, main2

overall title of plot 1 and plot 2.

xlab1, xlab2

label of x axis of plot 1 and plot 2.

ylab1, ylab2

label of y axis of plot 1 and plot 2

las1, las2

numeric. Corresponds to the style of axis labels in plot 1 and plot 2. Values: 0 (always parallel to the axis), 1 (always horizontal), 2 (always perpendicular to the axis), 3 (always vertical). See par for more information.

cextText

size of legend text.

legendbar

logical. If TRUE, it shows a legend bar indicating the color value of each variable position.

...

aditional graphical parameters (see par) for additional information.

Details

The first plot corresponds to the genetic estimation. This plot shows accumulation of colonization events as a function of population number. Each curve was created for each number of variable positions in the dataset.

The second plot corresponds to the field estimation. This plot shows accumulation of colonization events as a function of the number of variable positions. Each curve is created for each number of populations in the dataset.

Value

This function returns two plots corresponding to the two resampling methods used in rarecol. The first curve corresponds to the "genetic estimation" in which a genetic resampling of every possible number of variable position is done and, for each resample, a complete resampling of population is done. The second curve represents the opposite method corresponding to the "field estimation": it first resamples every possible number of populations and, for each case, a complete resampling of variable positions is done.

References

Coello, A.J., Fernandez-Mazuecos, M., Heleno, R.H., Vargas, P. (2022). PAICE: A new R package to estimate the number of inter-island colonizations considering haplotype data and sample size. Journal of Biogeography, 49(4), 577-589.DOI: 10.1111/jbi.14341

See Also

rarecol to build a rarefection curve of colonization events.

Examples

# Use 'CmonsRare' data, a dataset generated using 25 replicates
# in both genetic and field sampling
data(CmonsRare)
plot(CmonsRare)