Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/slideAnalyses.R
Wraps a number of measures used in sliding window analyses into one easytouse function.
1 2  slideAnalyses(DNAbin, sppVector, width, interval = 1,
distMeasures = TRUE, treeMeasures = FALSE)

DNAbin 
A DNA alignment of class ‘DNAbin’. 
sppVector 
Species vector (see 
width 
Desired width of windows in number of nucleotides. 
interval 
Distance between each window in number of nucleotides. Default of 1. Giving the option of 'codons' sets the size to 3. 
distMeasures 
Logical. Should distance measures be calculated? Default of TRUE. 
treeMeasures 
Logical. Should treebased measures be calculated? Default of FALSE. 
Distance measures include the following: proportion of zero nonconspecific distances, number of diagnostic nucleotides, number of zerolength distances, and overall mean distance.
Treebased measures include the following: proportion of species that are
monophyletic, proportion of clades that are identical between the neighbour
joining tree calculated for the window and the tree calculated for the full
dataset, and the latter with method="shallow"
.
Treebased measures are a lot more timeintensive than distance measures. When dealing with lots of taxa and short windows, this part of the function can take hours.
Both distance and tree measures are calculated from a K2P distance matrix
created from the data with the option pairwise.deletion = TRUE
. When
sequences with missing data are compared with other sequences, a NA
distance results. These are ignored in the calculation of
slideAnalyses
distance metrics. However, the tree measures cannot
cope with this missing data, and so no result is returned for windows where
some sequences solely contain missing data.
An object of class 'slidWin' which is a list containing the following elements:
win_mono_out 
Proportion of species that are monophyletic. 
comp_out 
Proportion of clades that are identical between the NJ tree calculated for the window and the tree calculated for the full dataset. 
comp_depth_out 
Proportion of shallow clades that are identical. 
pos_tr_out 
Index of window position for treebased analyses. 
noncon_out 
Proportion of zero nonconspecific distances. 
nd_out 
The sum of diagnostic nucleotides for each species. 
zero_out 
The number of zerolength distances. 
dist_mean_out 
Overall mean K2P distance of each window. 
pos_out 
Index of window position. 
dat_zero_out 
Number of zero interspecific distances in the full dataset. 
boxplot_out 
Always
FALSE. Required for 
distMeasures 
Value
of argument. Required for 
treeMeasures 
Value of argument. Required for

Samuel Brown <[email protected]>
dist.dna
, plot.slidWin
,
rankSlidWin
, slideNucDiag
.
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