observed.sumstat: Observed summary statistics

In gehara/PipeMaster: Building and Simulating Coalescent models.

Observed summary statistics

Description

This function calculates the observed summary statistics from an empirical data. This summary statistics are the same as those simulated by the sim.sumstat function. It is optimized for sanger data.

Usage

observed.sumstat(
  model,
  path.to.fasta,
  fasta.files = list.files(),
  overall.SS = T,
  perpop.SS = T,
  get.moments = T
)

Arguments

model	A model object bult by the main.menu function.
path.to.fasta	Path to the folder containing all fastas to be included in the calculation.
list.files	A list of fasta files to be included in the calculation. By default all fastas present in the folder are included.
moments	Logical. If TRUE computes the four moments (mean, variance, kurtosis, skewness) of each summary statistics across loci. If False only mean is computed. Defalt is FALSE.
pop.assign	A two-column data frame with sample names in the first column and the corresponding population membership as numbers in the second column. The numbers should match the population number in the model object.
msABC.call	String. Path to the msABC executable. msABC binaries for Mac's and Linux are included in the package and should work in most computers. There is no need to change that unless you want to compile the program yourself and point the function to it.

Value

A list of vectors containing the observed summary stats.

Note

This function does not work on Windows systems.

Author(s)

Marcelo Gehara

gehara/PipeMaster documentation built on April 19, 2024, 8:14 a.m.