Learn R Programming
⚠️There's a newer version (0.7.2) of this package.Take me there.

coala (version 0.2.0)

A Framework for Coalescent Simulation

Description

Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. This package allows to specify such models, transparently calls a suitable simulator, parses the results and calculates additional summary statistics. It supports the simulators 'ms', 'msms' and 'scrm' and can simulate finite-sites mutation models by combining the simulators with the program 'seq-gen'.

Copy Link

Version

Install

install.packages('coala')

Monthly Downloads

349

Version

0.2.0

License

MIT + file LICENSE

Issues

6

Pull Requests

0

Stars

23

Forks

4

Maintainer

Paul Staab

Last Published

November 11th, 2015

Functions in coala (0.2.0)

list_simulators

Returns the available simulators
feat_size_change

Adds an instantaneous change of the population size of one population to a model.
feat_recombination

Feature: Recombination
simulate.coalmodel

Simulates data according to a demographic model
sumstat_four_gamete

A Summary Statistic based on the Four-Gamete-Condition
sumstat_trees

Returns ancestral tress in NEWICK format from simulations
par_zero_inflation

Zero inflation for Parameters
locus_single

Add one locus or multiple loci to a Model
feat_pop_merge

Feature: Population Merge
sumstat_seg_sites

Returns the Segregation Sites Statistics from simulations
locus_trio

Adds a trio of loci to a group
feat_outgroup

Adds an outgroup to a demographic model
feat_growth

Adds an exponential growth or decline of the size of one population to a model.
feat_migration

Add migration/gene flow between two populations to a demographic model
feat_unphased

Feature: Unphased
sumstat_mcmf

The MCMF Summary Statistic
par_variation

Let the parameter values vary between different loci
sumstat_ihh

Integrated Extended Haplotype Homozygosity
sumstat_omega

Calculates the Omega Statistic from Simulations
coala

A Framework for Coalescent Simulation in R
+.coalmodel

Add a feature or parameter to a model
calc_jsfs

Calculates the JSFS for two populations
activate_msms

Use the simulator msms
check_model

Check which simulator can simulate a model
coal_model

Creates a coalescent model
sumstat_tajimas_d

Tajima's D
get_outgroup

Getters for coalescent models
sumstat_file

Returns files with the raw results of simulations
sumstat_dna

Returns the Segregation Sites Statistics from simulations
scale_model

Function that downscales a coalescent model
activate_ms

Use the simulator ms
par_expr

Define Model parameters
activate_seqgen

Use seq-gen for simulating finite sites mutation models
feat_mutation

Feature: Mutation
sumstat_sfs

Calculates the Site Frequency Spectrum from simulations
conv_to_ms_arg.growth

Generate command line arguments for features
sumstat_nucleotide_div

Calculates the Nucleodite Diversity Pi
sumstat_jsfs

Calculates the Joint Site Frequency Spectrum from simulations
sumstat_class

Base Class for Summary Statistics
feat_sample

Creates a feature that represents the sampling from one population
feat_selection

Adds positive selection to a model
search_executable

Search the working directory and the run path for an executable