satPlot: Saturation plots

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/satPlot.R

Description

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

Usage

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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 <s_d_j_brown@hotmail.com>

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

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

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