test_replen: Test repeat length consistency.

In poppr: Genetic Analysis of Populations with Mixed Reproduction

Test repeat length consistency.

Description

This function will test for consistency in the sense that all alleles are able to be represented as discrete units after division and rounding.

Usage

test_replen(gid, replen)

Arguments

gid	a genind or genclone object
replen	a numeric vector of repeat motif lengths.

Details

This function is modified from the version used in \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.13007")}.

Value

a logical vector indicating whether or not the repeat motif length is consistent.

Author(s)

Zhian N. Kamvar

References

Zhian N. Kamvar, Meg M. Larsen, Alan M. Kanaskie, Everett M. Hansen, & Niklaus J. Grünwald. Sudden_Oak_Death_in_Oregon_Forests: Spatial and temporal population dynamics of the sudden oak death epidemic in Oregon Forests. ZENODO, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.13007")}, 2014.

Kamvar, Z. N., Larsen, M. M., Kanaskie, A. M., Hansen, E. M., & Grünwald, N. J. (2015). Spatial and temporal analysis of populations of the sudden oak death pathogen in Oregon forests. Phytopathology 105:982-989. doi: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1094/PHYTO-12-14-0350-FI")}

Ruzica Bruvo, Nicolaas K. Michiels, Thomas G. D'Souza, and Hinrich Schulenburg. A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Molecular Ecology, 13(7):2101-2106, 2004.

See Also

fix_replen bruvo.dist bruvo.msn bruvo.boot

Examples

data(Pram)
(Pram_replen <- setNames(c(3, 2, 4, 4, 4), locNames(Pram)))
test_replen(Pram, Pram_replen)

poppr documentation built on May 29, 2024, 5:54 a.m.