These functions are modified from the function dist.genpop to be applicable for distances between individuals.

1 2 3 4 5 6 7 8 9 10 11 | ```
nei.dist(x, warning = TRUE)
edwards.dist(x)
rogers.dist(x)
reynolds.dist(x)
provesti.dist(x)
prevosti.dist(x)
``` |

`x` |
a genind, genclone, or matrix object. |

`warning` |
If |

It is important to be careful with the interpretation of these distances as they were originally intended for calculation of between-population distance. As Nei's distance is the negative log of 0:1, this means that it is very possible to obtain distances of infinity. When this happens, infinite values are corrected to be 10 * max(D) where D is the distance matrix without infinite values.

an object of class dist with the same number of observations as the number of individuals in your data.

Prevosti's distance is identical to `diss.dist`

, except
that `diss.dist`

is optimized for a larger number of
individuals (n > 125) at the cost of required memory. Both
`prevosti.dist`

and `provesti.dist`

are the same function,
`provesti.dist`

is a spelling error and exists for backwards
compatibility.

These distances were adapted from the adegenet function
`dist.genpop`

to work with `genind`

objects.

Zhian N. Kamvar (poppr adaptation) Thibaut Jombart (adegenet adaptation) Daniel Chessel (ade4)

Nei, M. (1972) Genetic distances between populations. American Naturalist, 106, 283-292.

Nei M. (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 23, 341-369.

Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall, London.

Edwards, A.W.F. (1971) Distance between populations on the basis of gene frequencies. Biometrics, 27, 873-881.

Cavalli-Sforza L.L. and Edwards A.W.F. (1967) Phylogenetic analysis: models and estimation procedures. Evolution, 32, 550-570.

Hartl, D.L. and Clark, A.G. (1989) Principles of population genetics. Sinauer Associates, Sunderland, Massachussetts (p. 303).

Reynolds, J. B., B. S. Weir, and C. C. Cockerham. (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics, 105, 767-779.

Rogers, J.S. (1972) Measures of genetic similarity and genetic distances. Studies in Genetics, Univ. Texas Publ., 7213, 145-153.

Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall, London.

Prevosti A. (1974) La distancia genetica entre poblaciones. Miscellanea Alcobe, 68, 109-118.

Prevosti A., Oca\~na J. and Alonso G. (1975) Distances between populations of Drosophila subobscura, based on chromosome arrangements frequencies. Theoretical and Applied Genetics, 45, 231-241.

For more information on dissimilarity indexes:

Gower J. and Legendre P. (1986) Metric and Euclidean properties of dissimilarity coefficients. Journal of Classification, 3, 5-48

Legendre P. and Legendre L. (1998) Numerical Ecology, Elsevier Science B.V. 20, pp274-288.

`aboot`

`diss.dist`

`poppr.amova`

1 2 3 4 5 6 7 | ```
data(nancycats)
(nan9 <- popsub(nancycats, 9))
(neinan <- nei.dist(nan9))
(ednan <- edwards.dist(nan9))
(rodnan <- rogers.dist(nan9))
(reynan <- reynolds.dist(nan9))
(pronan <- prevosti.dist(nan9))
``` |

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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