relate.calc: Coordinates internally reference and empirical datasets and statistics

Description

Internal function of Demerelate to combine different populations of randomized offspring and empirical populations to calculate thresholds and statistics for later use as reference for each empirical population.

Usage

relate.calc(tab.pop, pairs, file.output, value, 
                 directory.name, ref.pop)

Arguments

tab.pop

Dataframe following format of inputformat used as reference for randomizations.

pairs

Number of pairwise comparison for each randomization.

file.output

logical. Should a cluster dendogram, histograms and .txt files be sent as standard output in your working directory. In some cases (inflating NA values) it may be necessary that this value has to be set as FALSE due to problems in calculating clu

value

String defining method to calculate allele sharing or similarity estimates. Can be set as "rxy", "Bxy" or "Mxy".

directory.name

Name of the directory results send to.

ref.pop

R object or external file to be read internally with standard Demerelate inputformat. Custom reference populations will be loaded for the analysis. Population information of reference file will be omitted so that al

Value

relate.return[[1]]Object - matrix of mean pairwise relatedness of all loci of each comparison in tab.pop.
relate.return[[2]]Object - matrix of mean pairwise relatedness of each randomized comparison of full siblings.
Random.Fullsib.relatedness.overall.txtfile - matrix of mean pairwise relatedness of each randomized comparison of full siblings.
relate.return[[3]]Object - matrix of mean pairwise relatedness of each randomized comparison of half siblings.
Random.Halfsib.relatedness.overall.txtfile - matrix of mean pairwise relatedness of each randomized comparison of half siblings.
relate.return[[4]]Object - matrix of mean pairwise relatedness of each randomized comparison of non relatives.
Random.NonRelated.relatedness.overall.txtfile - matrix of mean pairwise relatedness of each randomized comparison of non relatives.
relate.return[[5]]Object - calculated thresholds for relatedness from reference populations.

Details

The function internally calls any procedure of randomization and offspring generation. Finally, it coordinates the preparation of multinomial logistic regression for threshold calculation.

References

Blouin, M.S. et al. (1996) Use of microsatellite loci to classify individuals by relatedness. Molecular Ecology, 5, 393-401. Li C.C. and Horvitz D.G. (1953) Some methods of estimating the inbreeding coefficient. American Journal of Human Genetics 5, 107-17. 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.

Examples

Run this code

## internal function not intended for usage without Demerelate

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