SimCoef {simco}R Documentation

A function to carry out the calculation of similarity coefficients from multiple Structure output files.

Description

This function takes multiple Structure files that have already been imported using the "SimCoImport()" function and calculates similarity coefficients for them.

The output is printed to the screen and includes the number of populations (K) that are assumed, the number of individuals (I), the number of Structure runs that have been analysed, the range, median, mean similariy coefficient, and standard error of the mean. Lastly, the output displays the similarity coefficients and the pairs of runs that were compared.

Usage

SimCoef(mydata)

Arguments

mydata mydata is a dataframe generated using "SimCoImport()" which is the Structure output files, appended and labelled with a capital letter.

Details

An accompanying PDF is given with this package with further details of use.

Value

Number of populations (K) The number of populations that were assumed when generating the Strucure files
Number of individuals (I) The number of individuals/samples in the datafile
Number of Structure runs The number of Structure runs that have been compared
Range The range of similarity coefficients
Median Similarity Coefficient The median similarity coefficient
Mean Similarity Coefficient The mean similarity coefficient
SEM of Similarity Coefficient The standard error of the mean similarity coefficient
The similarity coefficients a list of the similarity coefficients
Summary A table showing the pairs of runs that were compared (matches up with the list of similarity coeffiencts).

Author(s)

Owen R. Jones (owen.jones@imperial.ac.uk)

References

Rebbeck, CA, Jones, OR, & Tsai, IJ (unpublished) SimCo: A program to automate the comparison of multiple structure runs (available from owen.jones@imperial.ac.uk)

Pritchard, J. K. et al. (2000) Inference of population structure using multilocus genotype data. Genetics. 155, 945-959.

See Also

SimCoImport structureexample

Examples


#You should import the files you want to use first using the SimCoImport() command.
#In this example it is assumed that you are using a pre-imported dataset called "structureexample"

data(structureexample)
SimCoef(structureexample)


[Package simco version 1.01 Index]