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coala (version 0.3.0)

A Framework for Coalescent Simulation

Description

Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. You can use this package to specify such models, to conduct the simulations and to calculate additional statistics from the results. It relies on existing simulators for doing the simulation, and currently supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites mutation models by combining the simulators with the program 'seq-gen'.

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Install

install.packages('coala')

Monthly Downloads

325

Version

0.3.0

License

MIT + file LICENSE

Issues

6

Pull Requests

0

Stars

23

Forks

4

Maintainer

Paul Staab

Last Published

December 21st, 2015

Functions in coala (0.3.0)

create_segsites

Segregating Sites
activate_ms

Active the simulator ms
get_outgroup

Getters for coalescent models
scale_model

Function that downscales a coalescent model
as.segsites

Convert genetic data to coala's internal format
list_simulators

Returns the available simulators
check_model

Check which simulator can simulate a model
feat_size_change

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

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

Feature: Mutation
feat_outgroup

Adds an outgroup to a demographic model
calc_sumstats_from_data

Calculate summary statistics for biological data
sumstat_class

Base Class for Summary Statistics
par_zero_inflation

Zero inflation for Parameters
activate_msms

Use the simulator msms
sumstat_seg_sites

Returns the Segregation Sites Statistics from simulations
feat_selection

Adds positive selection to a model
create_locus_trio

Combines three segregating sites to a locus trio
locus_single

Add one locus or multiple loci to a Model
coala-package

A Framework for Coalescent Simulation in R
sumstat_nucleotide_div

Calculates the Nucleodite Diversity Pi
sumstat_file

Returns files with the raw results of simulations
feat_sample

Creates a feature that represents the sampling from one population
as.segsites.GENOME

Convert PopGenome Data into Coala's Format
feat_unphased

Feature: Unphased
sumstat_jsfs

Calculates the Joint Site Frequency Spectrum from simulations
+.coalmodel

Add a feature or parameter to a model
sumstat_ihh

Integrated Extended Haplotype Homozygosity
search_executable

Search the working directory and the run path for an executable
conv_to_ms_arg.growth

Generate command line arguments for features
feat_ignore_singletons

Feature: Ignore Singletons
feat_recombination

Feature: Recombination
feat_growth

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

Adds a trio of loci to a group
sumstat_sfs

Calculates the Site Frequency Spectrum from simulations
feat_pop_merge

Feature: Population Merge
par_expr

Define Model parameters
sumstat_tajimas_d

Tajima's D
calc_jsfs

Calculates the JSFS
sumstat_omega

Calculates the Omega Statistic from Simulations
sumstat_dna

Returns the Segregation Sites Statistics from simulations
par_variation

Let the parameter values vary between different loci
sumstat_four_gamete

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

Returns ancestral tress in NEWICK format from simulations
simulate.coalmodel

Simulates data according to a demographic model
activate_seqgen

Use seq-gen for simulating finite sites mutation models
coal_model

Creates a coalescent model
sumstat_mcmf

The MCMF Summary Statistic