slideBoxplots: Boxplots across windows

In spider: Species Identity and Evolution in R

Description

Calculates boxplots of genetic distances using sliding windows.

Usage

slideBoxplots(DNAbin, sppVector, width, interval = 1, method = "nonCon")

Arguments

DNAbin	A DNA alignment of class ‘DNAbin’.
sppVector	A species vector (see sppVector).
width	Width of windows.
interval	Distance between each window in number of base pairs. Default of 1. Giving the option of "codons" sets the size to 3.
method	Options of "overall", "interAll" or "nonCon" (the default).

Details

Giving method="overall" calculates the boxplot for the distance matrix of each window.

Giving method="interAll" calculates boxplots for the inter- and intra-specific distances of each window, showing the result for ALL inter-specific distances.

Giving method="nonCon" calculates boxplots for the inter- and intra-specific distances of each window, showing the result for only the nearest-conspecific distances for each individual.

Value

A list with

treeMeasures	Logical. Tree measures calculated? Always FALSE.
distMeasures	Logical. Distance measures calculated? Always FALSE.
bp_out	If method="overall", contains the boxplot objects of each window.
bp_InterSpp_out	If method!="overall", contains the boxplot objects of the interspecific distances of each window.
bp_IntraSpp_out	If method!="overall", contains the boxplot objects of the intraspecific distances of each window.
bp_range_out	range of y-axis values.
pos_out	x-axis values.
boxplot_out	Logical. Boxplots calculated? Always TRUE.
method	The method used for calculating boxplots. "overall", "interAll" or "nonCon".

Author(s)

Samuel Brown <[e-mail]>

See Also

boxplot, plot.slidWin, slideAnalyses, slidingWindow.

Examples

data(dolomedes)
doloDist <- dist.dna(dolomedes)
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)

doloNonCon <- slideBoxplots(dolomedes, doloSpp, 200, interval=10)
plot(doloNonCon)

doloOverall <- slideBoxplots(dolomedes, doloSpp, 200, interval=10, method="overall")
plot(doloOverall)

doloInterall <- slideBoxplots(dolomedes, doloSpp, 200, interval=10, method="interAll")
plot(doloInterall)

spider documentation built on May 2, 2019, 5:16 p.m.