gl.evanno {dartR.popgen}

Creates an Evanno plot from a STRUCTURE run object

Description

This function takes a genlight object and runs a STRUCTURE analysis based on functions from strataG

Usage

gl.evanno(sr, plot.out = TRUE)

Arguments

sr

structure run object from gl.run.structure [required].

plot.out

TRUE: all four plots are shown. FALSE: all four plots are returned as a ggplot but not shown [default TRUE].

Details

The function is basically a convenient wrapper around the beautiful strataG function evanno (Archer et al. 2016). For a detailed description please refer to this package (see references below).

Value

An Evanno plot is created and a list of all four plots is returned.

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

References

• Pritchard, J.K., Stephens, M., Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959.

• Archer, F. I., Adams, P. E. and Schneiders, B. B. (2016) strataG: An R package for manipulating, summarizing and analysing population genetic data. Mol Ecol Resour. doi:10.1111/1755-0998.12559

• Evanno, G., Regnaut, S., and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611-2620.

See Also

gl.run.structure, clumpp,

Examples

# examples need structure to be installed on the system (see above)
## Not run: 
 bc <- bandicoot.gl[,1:100]
 sr <- gl.run.structure(bc, k.range = 2:5, num.k.rep = 3, exec = './structure.exe')
 ev <- gl.evanno(sr)
 ev
 qmat <- gl.plot.structure(sr, K=3)
 head(qmat)
 gl.map.structure(qmat, bc, K=3, scalex=1, scaley=0.5)

## End(Not run)