spider (version 1.2-0)

slideBoxplots: Boxplots across windows

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).

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".

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.

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)