abc (>= 2.0), knitr, phyclust (>= 0.1-16), rmarkdown,
testthat (>= 0.11.0)
'RcppExports.R' 'cache.R' 'coala.R' 'model.R' 'feature.R'
'feature_growth.R' 'feature_ignore_singletons.R'
'feature_migration.R' 'feature_mutation.R' 'feature_outgroup.R'
'feature_pop_merge.R' 'feature_recombination.R'
'feature_sample.R' 'feature_selection.R'
'feature_size_change.R' 'feature_sumstats.R'
'feature_unphased.R' 'interface_abc.R' 'locus.R'
'model_build.R' 'model_check.R' 'model_examples.R'
'model_getters.R' 'model_print.R' 'model_scale.R'
'model_simulate.R' 'onLoad.R' 'parameter.R' 'parameter_prior.R'
'parameter_variation.R' 'parameter_zero_inflation.R'
'search_executable.R' 'segsites.R' 'simulation_tasks.R'
'simulator_class.R' 'simulator_ms.R' 'simulator_msms.R'
'simulator_scrm.R' 'simulator_seqgen.R' 'sumstat.R'
'sumstat_dna.R' 'sumstat_file.R' 'sumstat_four_gamete.R'
'sumstat_ihh.R' 'sumstat_jsfs.R' 'sumstat_mcmf.R'
'sumstat_nucleotide_div.R' 'sumstat_omega.R'
'sumstat_seg_sites.R' 'sumstat_sfs.R' 'sumstat_tajimas_d.R'
'sumstat_trees.R' 'tools.R'

c(
person('Paul', 'Staab', , 'develop@paulstaab.de', role=c('aut')),
person('Dirk', 'Metzler', , 'metzler@bio.lmu.de', role=c('aut', 'ths', 'cre')),
person('Jorge E.', 'Amaya Romero', role = 'ctb'))
Paul Staab [aut],
Dirk Metzler [aut, ths, cre],
Jorge E. Amaya Romero [ctb]
Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results (Staab, Metzler,
2016 <doi:10.1093/bioinformatics/btw098>).
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.

coalescentMCMC provides a flexible framework for
coalescent analyses in R. It includes a main function running
the MCMC algorithm, auxilliary functions for tree
rearrangement, and some functions to compute population genetic
parameters.