Sliding window analyses

Description

Wraps a number of measures used in sliding window analyses into one easy-to-use function.

Usage

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slideAnalyses(DNAbin, sppVector, width, interval = 1, 
    distMeasures = TRUE, treeMeasures = FALSE)

Arguments

DNAbin

A DNA alignment of class ‘DNAbin’.

sppVector

Species vector (see sppVector).

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 tree-based measures be calculated? Default of FALSE.

Details

Distance measures include the following: proportion of zero non-conspecific distances, number of diagnostic nucleotides, number of zero-length distances, and overall mean distance.

Tree-based 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".

Tree-based measures are a lot more time-intensive 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.

Value

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 tree-based analyses.

noncon_out

Proportion of zero non-conspecific distances.

nd_out

The sum of diagnostic nucleotides for each species.

zero_out

The number of zero-length distances.

dist_mean_out

Overall mean K2P distance of each window.

pos_out

Index of window position.

dat_zero_out

Number of zero inter-specific distances in the full dataset.

boxplot_out

Always FALSE. Required for plot.slidWin.

distMeasures

Value of argument. Required for plot.slidWin.

treeMeasures

Value of argument. Required for plot.slidWin.

Author(s)

Samuel Brown <s_d_j_brown@hotmail.com>

See Also

dist.dna, plot.slidWin, rankSlidWin, slideNucDiag.

Examples

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## Not run: 
data(dolomedes)
doloDist <- dist.dna(dolomedes)
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)

slideAnalyses(dolomedes, doloSpp, 200, interval=10, treeMeasures=TRUE)

## End(Not run)

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