plot.maxCol {PAICE}

Plot asymptotic estimators of colonization events

Description

Plots for the estimators calculated by maxCol.

Usage

## S3 method for class 'maxCol'
plot(x, xlim, ylim, col, xlabbotton, xlabtop, ylab, main,
     pch = 16, lty = 1, lwd = 2, cex = 1, estimation = TRUE,
     legend = TRUE, ...)

Arguments

x

an object of class "maxCol" returned by maxCol function.

xlim, ylim

numeric vector containing limits of x and y axis of the plot (min, max).

col

character vector containing colour of both estimation: genetic and field.

xlabbotton

a title of the x axis at the bottom of the plot. It correspond with genetic estimation.

xlabtop

a title of the x axis at the top of the plot. It correponds with field estimation.

ylab

a title of the y axis of the plot.

main

an overall title for the plot.

pch

indicate symbol used for points of the plot (by default pch = 16). See par for additional information.

lty

type of lines used in the plot for curve fitting (by default lty = 1). See par for additional information.

lwd

width of lines used in the plot for curve fitting (by default lwd = 2). See par for additional information.

cex

size of elements in the plot.

estimation

logical. If it is TRUE an estimation of estimation of number of colonization events is plotted at the right size of the plot.

legend

logial. If it is TRUE the legend is added.

...

aditional graphical parameters (see par) for aditional information.

Details

Genetic and field estimation are fitted to Michaelis-Menten equation following Coello et al. (2022).

Value

Plot returned by this function represent estimations calculated by maxCol. The two curves representing both estimators: genetic and field. Each point represent the mean of number of colonization events inferred by all replicates at this sampling level. Curves represent Michaelis-Menten equation fitted to this dataset. If it is plotted, right side of the plot represent the number of colonization events estimated by this fitting curve for each estimation, including the conficende interval of this estimation.

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

maxCol to fit the accumulation curve of colonization events and estimate the number of colonization events.

Examples

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