single.pop.demog: Simulation of demographic models for single populations.

In gehara/PipeMaster: Building and Simulating Coalescent models.

Simulation of demographic models for single populations.

Description

Test for constant size, population expantion and bottleneck for single population (non hiersrchical).

Usage

single.pop.demog(
  nsims,
  Ne.prior,
  time.prior,
  gene.prior,
  observed,
  alpha = F,
  tol = 0.01,
  nval = 100,
  do.ABC = F,
  do.PCA = F,
  CV = F,
  mod = cbind(c(1, 0.001, 2), c(1, 0.1, 20)),
  path = path
)

Arguments

nsims	Total number of simulations per model.
Ne.prior	Data frame with the prior values for the Ne of each population.
time.prior	Data frame with parameter values for the priors of the time of demographic change of each population.
gene.prior	Data frame with parameter values for the priors of the mutation rate of each species.
observed	Observed summary statistics calculated for the empirical data.
alpha	logical. If TRUE all demographic chages are exponential. If FALSE sudden changes. Defaut is FALSE.
tol	Tolerance level of the ABC analysis. Ignored if do.ABC = FALSE. Defaut is 0.01.
nval	Number of validations for the cross-validation of the ABC. Ignored if do.ABC = FALSE. Default is 100.
do.ABC	logical. If TRUE ABC analysis is performed. Default is FALSE.
do.PCA	logical. If TRUE PCA of the observed against the simulated data is performed. Default is FALSE.
CV	logical. If TRUE cros-validation is performed. Defaut is FALSE
mod	3 x 2 matrix of multiplyer priors (unif: min, max) for ancestral population sizes for each model. Default: cbind(c(1,0.001,2),c(1,0.1,20)). First row: constant size; min 1, max 1. Secound row: expansion; min 0.001, max 0.1. Third row: bottleneck; min 2, max 20.
path	Path to the directory to write the simulations. Defaut is the working directory.

Details

This function will take the same inputs used in the codemographic simulations and test for demographic change for each population separatelly. This test could be usefull to select which populations will be included in the codemographic model and to optimize the prior distributions.

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