diss.dist uses the same discrete dissimilarity matrix utilized by the index
of association (see ia
for details). By default, it returns a
distance reflecting the number of allelic differences between two
individuals. When percent = TRUE
, it returns a ratio of the number of
observed differences by the number of possible differences. Eg. two
individuals who share half of the same alleles will have a distance of 0.5.
This function can analyze distances for any marker system.
Arguments
- x
a
genind
object.- percent
logical
. Should the distance be represented as a percent? If set toFALSE
(default), the distance will be reflected as the number of alleles differing between to individuals. When set toTRUE
, These will be divided by the ploidy multiplied by the number of loci.- mat
logical
. Return a matrix object. Default set toFALSE
, returning a dist object.TRUE
returns a matrix object.
Details
The distance calculated here is quite simple and goes by many names, depending on its application. The most familiar name might be the Hamming distance, or the number of differences between two strings.
Note
When percent = TRUE
, this is exactly the same as
provesti.dist
, except that it performs better for large
numbers of individuals (n > 125) at the cost of available memory.
See also
prevosti.dist
,
bitwise.dist
(for SNP data)