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 |