rankSlidWin: Rank a 'slidWin' object.

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/rankSlidWin.R

Description

Display the highest ranking windows measured by slideAnalyses.

Usage

1
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 <[email protected]>

See Also

slideAnalyses.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
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)

boopsboops/spider documentation built on May 6, 2019, 8:49 a.m.