Example.Data: Example dataset for package Demerelate to calculate inter...

Description Usage Details Author(s) See Also Examples

Description

The dataset gives randomized loci information of populations with differently related individuals. Pop-FS-HS consists of 10 full siblings (45 pairs) combined of 10 half siblings (45 pairs). Pop-FS-Non consists of 10 full sibilings (45 pairs) and 10 random individuals (45 pairs). Pop-Non is a population of 20 random drawn individuals (180 pairs). Datasets are based on information of 8 diploid loci with total number in alleles indicated by column names, i.e. number of alleles = 5, 10, 15, 20, 25, 30, 35, 40.
The dataset demerelref gives randomized loci information of a population with 1000 individuals. Dataset is based on information of 8 diploid loci with total number in alleles indicated by column names, i.e. number of alleles = 5, 10, 15, 20, 25, 30, 35, 40.
The dataset demereldist gives randomized relative positions for each individual in the dataset.

Usage

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Details

Standard inputformat is given for all applications in a similar way. Table is formatted as dataframe with headers set as TRUE. Headernames are not necessary but recommended.
First column contains sample IDs (mode=character), which must be unique. However, no proofreading is implemented yet, but double named individuals may lead to errors or strange results. Column two contains population information (mode=factor). Pairwise relatedness is only calculated within populations. If you want to compare pairwise individual comparisons of several populations you need to build a new fictive population. You should do that with caution, since hidden population structures may produce strange results. Column three and four containing two alleles of a diploid marker for the sample defined in column one. Each marker should be appended in pairwise columns from then on.
Allele size should be sorted in columns with the small allele in the odd numbered column and the bigger in even numbered column for convenience. However, Demerelate will take care of not sorted allele sizes and handle it correctly. The same inputformat is used for reference populations.
All populations of inputdata are used as reference if no reference is defined by reference.pop. Additionally, the distance data are given (tab.dist) by the same inputformat. In column three and four you will need to define the x and y coordinate of each individual either by relative x-y coordinates or by decimal degrees of geographic coordinates.

Example input. Every dataframe in Demerelate should be organized in this way.

Sample-ID Population locus.1.a locus.1.b locus.2.a locus.2.b ...
Ind.Norway.01 Norway 001 002 001 002 ...
Ind.Norway.02 Norway 001 003 002 005 ...
Ind.Norway.03 Norway 001 004 003 004 ...
Ind.Norway.04 Norway 002 005 006 008 ...
Ind.Germany.01 Germany 001 001 001 006 ...
Ind.Germany.02 Germany 002 002 001 007 ...
Ind.Germany.03 Germany 001 006 001 004 ...
Ind.Germany.04 Germany 003 004 001 002 ...

Author(s)

Philipp Kraemer, <[email protected]>

See Also

Demerelate Emp.calc Loci.test

Examples

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# Please consult examples from Demerelate   
     
     

Demerelate documentation built on May 30, 2017, 8:14 a.m.