calculateJsfs

DNA sequence data of multiple individuals from two populations
and an optional outgroup sequence. It should be in a
format as returned by ape's 'read.dna' function. Please
refer to ape's manual for further details.

ape.data

A numeric vector indicating which individuals of your
dataset belong to the first population. The individuals
are revered by their position in the dataset/their row
number in 'ape.data'.

pop1.rows

Same as 'pop1.rows', but for the individuals of the second
population.

pop2.rows

Same as 'pop1.rows', but for the individuals of the
outgroup (if any). The outgroup can consist of more than
one individual to account for ancestral
misidentification. In this case, only positions in which
all outgroup sequences are identically are consid

outgroup.rows

The function 'read.dna' of package 'ape' allows you do import DNA data from
various formats into R. This function calculates the JSFS of such imported
data which can then be used as input for a Jaatha search. Please note that
the data must be aligned.

Jaatha is a composite likelihood method for inferring evolutionary
    parameters using genetic data. Given a model of the evolutionary history of
    two biological populations as well as SNP data from multiple individuals
    from each population, it estimates model parameters like the time of
    separation of both species.

calculateJsfs: Calculates the JSFS for data imported with ape

Description

Usage

Arguments

Value