A Framework for Coalescent Simulation

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Documentation for package ‘coala’ version 0.7.1

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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