rankSlidWin: Rank a 'slidWin' object.

In spider: Species Identity and Evolution in R

Description

Display the highest ranking windows measured by slideAnalyses.

Usage

rankSlidWin(slidWin, criteria="mean_distance", num = 10)

Arguments

slidWin	An object of class ‘slidWin’, made using slideAnalyses.
criteria	Name of criteria to sort by. Can be any of the following: "mean_distance", "monophyly", "clade_comparison", "clade_comp_shallow", "zero_noncon", "zero_distances", "diag_nuc" or "all". Default of "mean_distance" if distance measures have been calculated, otherwise "monophyly".
num	Number of windows to return. Default of 10.

Details

The criteria for rankSlidWin correspond to the variables outputted by slideAnalyses and are sorted in the following manner:

rankSlidWin criterion:	slideAnalyses output:	Sorting method:
"mean_distance"	"dist_mean_out"	Ascending
"monophyly"	"win_mono_out"	Ascending
"clade_comparison"	"comp_out"	Ascending
"clade_comp_shallow"	"comp_depth_out"	Ascending
"zero_noncon"	"noncon_out"	Descending
"zero_distances"	"zero_out"	Descending
"diag_nuc"	"nd_out"	Ascending

Given a sequence of 1:10, the ascending method of sorting considers 10 as high. The descending method considers 1 as high.

The "all" criterion returns the windows that have the highest cumulative total score over all criteria.

Value

A data frame giving the values of the measures calculated by slideAnalyses, ranked to show the top 10 positions based on the criterion given.

Author(s)

Samuel Brown <[e-mail]>

See Also

slideAnalyses.

Examples

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

doloSlide <- slideAnalyses(dolomedes, doloSpp, 200, interval = 10, treeMeasures = TRUE)

rankSlidWin(doloSlide)
rankSlidWin(doloSlide, criteria = "zero_distances")

doloSlide2 <- slideAnalyses(dolomedes, doloSpp, 200, interval = 10, treeMeasures = FALSE)
rankSlidWin(doloSlide2)

doloSlide3 <- slideAnalyses(dolomedes, doloSpp, 200, interval = 10, distMeasures = FALSE, 
    treeMeasures = TRUE)
rankSlidWin(doloSlide3)

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