Demerelate (version 0.9-2)

Emp.calc: Function to calculate pairwise relatedness within populations based on allele sharing.

Description

Allele sharing and relatedness estimators can be calculated for one population as a mean over several loci.

Usage

Emp.calc(tab.pop.pop, value="NA", ref.pop="NA")

Arguments

tab.pop.pop

Object with information for one population and loci. Object needs to be formatted according to inputformat.

value

String defining method to calculate allele sharing or similarity estimates. Can be set as "Bxy", "Sxy", "Mxy", "Li", "lxy", "rxy", "loiselle", "wang.fin", "wang", "ritland", "morans.fin" or "morans" allele.sharing.

ref.pop

Reference population needs to be specified for several calculations.

Value

Details

The function calculates pairwise relatedness for all individuals in the dataframe. The output is a matrix of similarities by relatedness values in the population.

References

Armstrong, W. (2012) fts: R interface to tslib (a time series library in c++). by R package version 0.7.7. Blouin, M., Parsons, M., Lacaille, V. and Lotz, S. (1996) Use of microsatellite loci to classify indi- viduals by relatedness. Molecular Ecology, 5, 393-401. Hardy, O.J. and Vekemans, X. (1999) Isolation by distance in a contiuous population: reconciliation between spatial autocorrelation analysis and population genetics models. Heredity, 83, 145-154. Li, C.C., Weeks, D.E. and Chakravarti, A. (1993) Similarity of DNA fingerprints due to chance and relatedness. Human Heredity, 43, 45-52. Li, C.C. and Horvitz, D.G. (1953) Some methods of estimating the inbreeding coefficient. Ameri- can Journal of Human Genetics, 5, 107-17. Loiselle, B.A., Sork, V.L., Nason, J. and Graham, C. (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). American Journal of Botany, 82, 1420-1425. Lynch, M. (1988) Estimation of relatedness by DNA fingerprinting. Molecular Biology and Evolu- tion, 5(5), 584-599. Lynch, M. and Ritland, K. (1999) Estimation of pairwise relatedness with molecular markers. Ge- netics, 152, 1753-1766. Oliehoek, P. A. et al. (2006) Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. Genetics, 173, 483-496. Queller, D.C. and Goodnight, K.F. (1989) Estimating relatedness using genetic markers. Evolution, 43, 258-275. Ritland, K. (1999) Estimators for pairwise relatedness and individual inbreeding coefficients. Ge- netics Research, 67, 175-185. Wang, J. (2002) An estimator for pairwise relatedness using molecular markers. Genetics, 160, 1203-1215.

See Also

allele.sharing Bxy Sxy Mxy Li rxy lxy loiselle wang.fin wang ritland morans.fin

Examples

     ## demerelpop needs to be an object of class data.frame formatted
     ## according to inputformat. For each pairwise comparison in
     ## in the data.frame empirical estimates of relatedness are
     ## calculated omitting statistics.

      data(demerelpop)
      
      # As example Mxy is calculated for one population of demerelpop
      
      demerelpop.sp <- split(demerelpop,demerelpop[,2])

      empirical.result <- Emp.calc(demerelpop.sp[[1]], value="Mxy", 
                                   ref.pop="NA")