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spider (version 1.5.1)

rankSlidWin: Rank a 'slidWin' object.

Description

Display the highest ranking windows measured by slideAnalyses.

Usage

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

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.

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.

Author

Samuel Brown <s_d_j_brown@hotmail.com>

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.

See Also

slideAnalyses.

Examples

Run this code

data(dolomedes)
doloDist <- ape::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)

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