slideAnalyses {spider} | R Documentation |
Sliding window analyses
Description
Wraps a number of measures used in sliding window analyses into one easy-to-use function.
Usage
slideAnalyses(DNAbin, sppVector, width, interval = 1, distMeasures = TRUE,
treeMeasures = FALSE)
Arguments
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 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 |
distMeasures |
Value
of argument. Required for |
treeMeasures |
Value of argument. Required for
|
Author(s)
Samuel Brown <s_d_j_brown@hotmail.com>
See Also
dist.dna
, plot.slidWin
,
rankSlidWin
, slideNucDiag
.
Examples
## Not run:
data(dolomedes)
doloDist <- ape::dist.dna(dolomedes)
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)
slideAnalyses(dolomedes, doloSpp, 200, interval=10, treeMeasures=TRUE)
## End(Not run)