Emp.calc: Function to calculate pairwise relatedness within populations...
In Demerelate: Functions to Calculate Relatedness on Diploid Genetic Data

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2	Emp.calc(tab.pop.pop, value="NA", ref.pop="NA")

`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.

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

empirical.list

Object containing a dataframe of mean individual pairwise relatedness. If value="NA" all available estimators are calculated in one call of function Emp.calc.

Philipp Kraemer, <philipp.kraemer@uni-oldenburg.de>

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.

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

     ## 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")