satPlot: Saturation plots

In spiderDev: Species Identity and Evolution in R--development

Description

Two methods for creating plots to guage the amount of sequence saturation within an alignment.

Usage

satPlot(DNAbin)

satPlot2(DNAbin)

Arguments

DNAbin

An object of class DNAbin

Details

satPlot compares the uncorrected p-distance matrix with a model-corrected distance based on an arbitrary model. In the current implementation, the model-corrected distances are based on a NJ-tree with branch lengths (but not topology) optimised under an HKY + I + G model.

satPlot2 merely plots the uncorrected p-distances and indicates the 10% mark, above which point distances tend to require model-correction.

Value

Both functions create a saturation plot. In addition, satPlot also invisibly returns a list with the following elements:

Pdist	The pairwise uncorrected p-distance matrix.
MLdist	The pairwise uncorrect p-distance matrix.

Author(s)

Samuel Brown <[e-mail]>

References

Collins, R. A., Boykin, L. M., Cruickshank, R. H., \& Armstrong, K. F. (2012). Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification. _Methods in Ecology and Evolution_, *3* , 457-465.

See Also

pml, cophenetic

Examples

data(carpophilus)

satPlot(carpoCOI)
satPlot(carpo28S)
satPlot(carpoITS)

satPlot2(carpoCOI)
satPlot2(carpo28S)
satPlot2(carpoITS)

spiderDev documentation built on May 2, 2019, 5:23 p.m.