R: A Framework for Coalescent Simulation

# A Framework for Coalescent Simulation

## Documentation for package ‘coala’ version 0.7.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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