dispersalDiversity-package: Analyse individual and genetic diversity of dispersal...

In douglasgscofield/dispersalDiversity: Analyse individual and genetic diversity of dispersal processes in biological populations

Description

A collection of R functions to analyse individual and genetic diversity in biological populations, primarily in the context of studying dispersal processes. The basic data format is a sites-by-counts matrix. Functions are provided for calculating alpha, beta, delta/omega and gamma diversity using a variety of measures; calculating alpha, beta, delta/omega and gamma diversity of allelic variation; and comparing diversity measures between samples.

Details

A similar set of functions provides analyses for either of two types of data sets. The first is sites-by-counts data, with sites representing some form of aggregation including groupings, hosts, seed caches, etc., and counts being of species, parents, haplotypes, etc. Sites-by-counts data is held within a table of class divtable. The methods underlying these analyses are derived from classical biodiversity measures and are described in Scofield et al. (2012).

The second data set accepted describes similar patterns but for genetic diversity coded as alleles. An object of class allele_divtables is a list of tables of class divtable, one table per locus under study. Each such table contains sites-by-alleles counts for individual loci. These data are analysed with extensions of the Scofield et al. (2012) methods as described in Sork et al. (in press).

The function createAlleleTables accepts an argument of class genalex or of a class and format convertable to class genalex using as.genalex.

Note

Due to their mathematical structure, the functions testing structure in diversity cannot accept data sets with rows (sites) containing a single item. The functions will generate an error if given such data. The as.divtable function will produce a warning if given such data. Descriptive functions such as diversity and the plotting functions will accept such data without warning or error, though some estimators may produce NA or NaN.

These statistical tools were developed in collaboration with Peter E. Smouse (Rutgers University) and Victoria L. Sork (UCLA) and were funded in part by U.S. National Science Foundation awards NSF-DEB-0514956 and NSF-DEB-0516529.

References

Grivet, D., Smouse, P. E. and Sork, V. L. (2005) A novel approach to an old problem: tracking dispersed seeds. Molecular Ecology 14:3585-3595.

Nielsen, R., Tarpy, D. R. and Reeve, H. K. (2003) Estimating effective paternity number in social insects and the effective number of alleles in a population. Molecular Ecology 12:3157-3164.

Scofield, D. G., Sork, V. L. and Smouse, P. E. (2010) Influence of acorn woodpecker social behaviour on transport of coast live oak (Quercus agrifolia) acorns in a southern California oak savanna. Journal of Ecology 98:561-572.

Scofield, D. G., Alfaro, V. R., Sork, V. L., Grivet, D., Martinez, E., Papp, J., Pluess, A. R., Koenig, W. D. and Smouse, P. E. (2011) Foraging patterns of acorn woodpeckers (Melanerpes formicivorus) on valley oak (Quercus lobata N\'ee) in two California oak savanna-woodlands. Oecologia 166:187-196.

Scofield, D. G., Smouse, P. E., Karubian, J. and Sork, V. L. (2012) Use of alpha, beta and gamma diversity measures to characterize seed dispersal by animals. American Naturalist 180:719-732.

Sork, V. L., Smouse, P. E., Grivet, D. and Scofield, D. G. (In press) Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata N\'ee). Evolutionary Ecology.

https://github.com/douglasgscofield/dispersalDiversity

douglasgscofield/dispersalDiversity documentation built on March 30, 2021, 9:50 a.m.