Man pages for coala
A Framework for Coalescent Simulation
| as.segsites | Convert genetic data to coala's internal format |
| as.segsites.GENOME | Convert PopGenome Data into Coala's Format |
| calc_jsfs | Calculates the Joint Site Frequency Spectrum |
| calc_sumstats_from_data | Calculate summary statistics for biological data |
| check_model | Check which simulator can simulate a model |
| coala-package | A Framework for Coalescent Simulation in R |
| coal_model | Create a Coalescent Model |
| conv_to_ms_arg | Generate command line arguments for features |
| create_abc_param | Convert Simulation Results to abc's Parameter Format |
| create_abc_sumstat | Convert Simulation Results to abc's Summary Statistic Format |
| 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_sample | Creates a feature that represents the sampling from one... |
| feat_selection | Feature: Selection |
| feat_size_change | Feature: Instantaneous Size Change |
| feat_unphased | Feature: Unphased Sequences |
| get_features | Getters for coalescent models |
| list_simulators | Returns the available simulators |
| locus | Loci |
| locus_trio | Locus Trios |
| parameter | Model Parameters |
| par_variation | Variable Parameters |
| par_zero_inflation | Zero Inflation for Parameters |
| plus-.coalmodelpart | Add a feature or parameter to a model |
| scale_model | Function that downscales a coalescent model |
| search_executable | Search the working directory and the run path for an... |
| segsites | 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_class | Base Class for Summary Statistics |
| 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 |
