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

criteria 
Name of criteria to sort by. Can be any of the following:

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 <[email protected]>
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)

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