WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.
utils.dist.ind.snp(
x,
method = "Euclidean",
scale = FALSE,
type = "dist",
verbose = NULL
)An object of class 'dist' or 'matrix' giving distances between individuals
Name of the genlight containing the genotypes [required].
Specify distance measure [default Euclidean].
If TRUE and method='Euclidean', the distance will be scaled to fall in the range [0,1] [default FALSE].
Specify the format and class of the object to be returned, dist for a object of class dist, matrix for an object of class matrix [default "dist"].
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2].
Author(s): Arthur Georges. Custodian: Arthur Georges -- Post to https://groups.google.com/d/forum/dartr
This script calculates various distances between individuals based on SNP genotypes. The distance measure can be one of:
Euclidean -- Euclidean Distance applied to Cartesian coordinates defined by the loci, scored as 0, 1 or 2.
Simple -- simple mismatch, 0 where no alleles are shared, 1 where one allele is shared, 2 where both alleles are shared.
Absolute -- absolute mismatch, 0 where no alleles are shared, 1 where one or both alleles are shared.
Czekanowski (or Manhattan) calculates the city block metric distance by summing the scores on each axis (locus).
Other distance:
gl.dist.ind(),
gl.dist.pop(),
gl.fdsim()