Man pages for coala
A Framework for Coalescent Simulation

as.segsitesConvert genetic data to coala's internal format
as.segsites.GENOMEConvert PopGenome Data into Coala's Format
calc_jsfsCalculates the Joint Site Frequency Spectrum
calc_sumstats_from_dataCalculate summary statistics for biological data
check_modelCheck which simulator can simulate a model
coala-packageA Framework for Coalescent Simulation in R
coal_modelCreate a Coalescent Model
conv_to_ms_argGenerate command line arguments for features
create_abc_paramConvert Simulation Results to abc's Parameter Format
create_abc_sumstatConvert Simulation Results to abc's Summary Statistic Format
feat_growthFeature: Exponential population size growth/decline
feat_ignore_singletonsFeature: Ignore Singletons
feat_migrationFeature: Migration/Gene Flow
feat_mutationFeature: Mutation
feat_outgroupFeature: Outgroup
feat_pop_mergeFeature: Population Merge
feat_recombinationFeature: Recombination
feat_sampleCreates a feature that represents the sampling from one...
feat_selectionFeature: Selection
feat_size_changeFeature: Instantaneous Size Change
feat_unphasedFeature: Unphased Sequences
get_featuresGetters for coalescent models
list_simulatorsReturns the available simulators
locus_trioLocus Trios
parameterModel Parameters
par_variationVariable Parameters
par_zero_inflationZero Inflation for Parameters
plus-.coalmodelpartAdd a feature or parameter to a model
scale_modelFunction that downscales a coalescent model
search_executableSearch the working directory and the run path for an...
segsitesSegregating Sites
simulate.coalmodelSimulate Data According to a Demographic Model
simulator_msSimulator: ms
simulator_msmsSimulator: msms
simulator_scrmSimulator: scrm
simulator_seqgenSimulator: seq-gen
sumstat_classBase Class for Summary Statistics
sumstat_dnaSummary Statistic: DNA
sumstat_fileSummary Statistic: Files
sumstat_four_gameteSummary Statistic: Four-Gamete-Condition
sumstat_ihhSummary Statistic: Integrated Extended Haplotype Homozygosity
sumstat_jsfsSummary Statistic: Joint Site Frequency Spectrum
sumstat_mcmfSummary Statistic: Most Common Mutation's Frequency
sumstat_nucleotide_divSummary Statistic: Nucleotide Diversity
sumstat_omegaSummary Statistic: Omega
sumstat_seg_sitesSummary Statistic: Segregating Sites
sumstat_sfsSummary Statistic: Site Frequency Spectrum
sumstat_tajimas_dSummary Statistic: Tajima's D
sumstat_treesSummary Statistic: Ancestral Trees
coala documentation built on May 29, 2024, 11:14 a.m.