# Estimation of genetic differentiation measures

### Description

`Genetics`

: Estimation allelic differentiation among subpopulations based on multiple-subpopulation
genetics data. The richness-based indices include the classic Jaccard and Sorensen dissimilarity
indices; the abundance-based indices include the conventional Gst measure, Horn, Morisita-Horn
and regional species-differentiation indices.

Only Type (1) abundance data (datatype="abundance") is supported; input data for each sub-population
include sample frequencies in an empirical sample of individuals. When there are multiple subpopulations, input data consist of an allele-by-subpopulation frequency matrix.

### Usage

1 |

### Arguments

`X` |
a matrix, or a data.frame of allele frequencies. |

`q` |
a specified order to use to compute pairwise dissimilarity measures. If |

`nboot` |
an integer specifying the number of bootstrap replications. |

### Value

a list of ten objects:

`$info`

for summarizing data information.

`$Empirical_richness`

for showing the observed values of the richness-based dis-similarity indices
including the classic Jaccard and Sorensen indices.

`$Empirical_relative`

for showing the observed values of the equal-weighted dis-similarity
indices for comparing allele relative abundances including Gst, Horn, Morisita-Horn and regional differentiation measures.

`$Empirical_WtRelative`

for showing the observed value of the dis-similarity index for
comparing size-weighted allele relative abundances, i.e., Horn size-weighted measure based on Shannon-entropy under equal-effort sampling.

The corresponding three objects for showing the estimated dis-similarity indies are:

`$estimated_richness`

, `$estimated_relative`

and `$estimated_WtRelative`

.

`$pairwise`

and `$dissimilarity.matrix`

for showing respectively the pairwise dis-similarity
estimates (with related statistics) and the dissimilarity matrix for various measures depending on
the diversity order `q`

specified in the function argument.

`$q`

for showing which diversity order `q`

to compute pairwise dissimilarity.

### References

Chao, A., and Chiu, C. H. (2016). Bridging the variance and diversity decomposition approaches to beta diversity via similarity and differentiation measures. Methods in Ecology and Evolution, 7, 919-928.

Chao, A., Jost, L., Hsieh, T. C., Ma, K. H., Sherwin, W. B. and Rollins, L. A. (2015). Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model. Plos One, 10:e0125471.

Jost, L. (2008). *G_{ST}* and its relatives do not measure differentiation. Molecular Ecology, 17, 4015-4026.

### Examples

1 2 3 4 5 6 | ```
## Not run:
# Type (1) abundance data
data(GeneticsDataAbu)
Genetics(GeneticsDataAbu,q=2,nboot=200)
## End(Not run)
``` |