A Framework for Coalescent Simulation

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Documentation for package ‘coala’ version 0.7.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

coala-package	A Framework for Coalescent Simulation in R
activate_ms	Simulator: ms
activate_msms	Simulator: msms
activate_scrm	Simulator: scrm
activate_seqgen	Simulator: seq-gen
as.segsites	Convert genetic data to coala's internal format
as.segsites.GENOME	Convert PopGenome Data into Coala's Format
calc_sumstats_from_data	Calculate summary statistics for biological data
check_model	Check which simulator can simulate a model
coala	A Framework for Coalescent Simulation in R
coalmodelpart	Create a Coalescent Model
coal_model	Create a Coalescent Model
create_abc_param	Convert Simulation Results to abc's Parameter Format
create_abc_sumstat	Convert Simulation Results to abc's Summary Statistic Format
create_locus_trio	Segregating Sites
create_segsites	Segregating Sites
feat_growth	Feature: Exponential population size growth/decline
feat_ignore_singletons	Feature: Ignore Singletons
feat_migration	Feature: Migration/Gene Flow
feat_mutation	Feature: Mutation
feat_outgroup	Feature: Outgroup
feat_pop_merge	Feature: Population Merge
feat_recombination	Feature: Recombination
feat_selection	Feature: Selection
feat_size_change	Feature: Instantaneous Size Change
feat_unphased	Feature: Unphased Sequences
get_positions	Segregating Sites
get_snps	Segregating Sites
get_trio_locus	Segregating Sites
is_segsites	Segregating Sites
list_simulators	Returns the available simulators
loci	Loci
locus	Loci
locus_averaged	Loci
locus_single	Loci
locus_trio	Locus Trios
parameter	Model Parameters
par_const	Model Parameters
par_expr	Model Parameters
par_named	Model Parameters
par_prior	Model Parameters
par_range	Model Parameters
par_variation	Variable Parameters
par_zero_inflation	Zero Inflation for Parameters
scale_model	Function that downscales a coalescent model
segsites	Segregating Sites
set_positions	Segregating Sites
set_trio_locus	Segregating Sites
simulate.coalmodel	Simulate Data According to a Demographic Model
simulator_ms	Simulator: ms
simulator_msms	Simulator: msms
simulator_scrm	Simulator: scrm
simulator_seqgen	Simulator: seq-gen
sumstat_dna	Summary Statistic: DNA
sumstat_file	Summary Statistic: Files
sumstat_four_gamete	Summary Statistic: Four-Gamete-Condition
sumstat_ihh	Summary Statistic: Integrated Extended Haplotype Homozygosity
sumstat_jsfs	Summary Statistic: Joint Site Frequency Spectrum
sumstat_mcmf	Summary Statistic: Most Common Mutation's Frequency
sumstat_nucleotide_div	Summary Statistic: Nucleotide Diversity
sumstat_omega	Summary Statistic: Omega
sumstat_seg_sites	Summary Statistic: Segregating Sites
sumstat_sfs	Summary Statistic: Site Frequency Spectrum
sumstat_tajimas_d	Summary Statistic: Tajima's D
sumstat_trees	Summary Statistic: Ancestral Trees