rankSlidWin: Rank a 'slidWin' object.
In spider: Species Identity and Evolution in R

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

Display the highest ranking windows measured by slideAnalyses.

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

`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.

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.

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

Samuel Brown <s_d_j_brown@hotmail.com>

slideAnalyses.

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)