Package: coala 0.7.2

Dirk Metzler

coala: A Framework for Coalescent Simulation

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'. Coala provides functions for calculating certain summary statistics, which can also be applied to actual biological data. One possibility to import data is through the 'PopGenome' package (<https://github.com/pievos101/PopGenome>).

Authors:Paul Staab [aut], Dirk Metzler [aut, ths, cre], Jorge E. Amaya Romero [ctb]

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Bug tracker:https://github.com/statgenlmu/coala/issues

On CRAN:

coalescentdnaevolutionpopgensimulation

64 exports 22 stars 2.24 score 8 dependencies 86 scripts 465 downloads

Last updated 7 months agofrom:017fbc7ad8. Checks:OK: 1 NOTE: 8. Indexed: yes.

Exports:activate_msactivate_msmsactivate_scrmactivate_seqgenas.segsitescalc_sumstats_from_datacheck_modelcoal_modelcreate_abc_paramcreate_abc_sumstatcreate_segsitesfeat_growthfeat_ignore_singletonsfeat_migrationfeat_mutationfeat_outgroupfeat_pop_mergefeat_recombinationfeat_selectionfeat_size_changefeat_unphasedget_featuresget_locus_lengthget_locus_length_matrixget_locus_numberget_outgroupget_outgroup_sizeget_parameterget_parameter_tableget_population_individualsget_populationsget_positionsget_sample_sizeget_snpsget_summary_statisticsget_trio_locusis_segsiteslist_simulatorslocus_averagedlocus_singlelocus_triopar_constpar_exprpar_namedpar_priorpar_rangepar_variationpar_zero_inflationscale_modelset_positionsset_trio_locussumstat_classsumstat_dnasumstat_filesumstat_four_gametesumstat_ihhsumstat_jsfssumstat_mcmfsumstat_nucleotide_divsumstat_omegasumstat_seg_sitessumstat_sfssumstat_tajimas_dsumstat_trees

Dependencies:assertthatdigestR6RcppRcppArmadillorehhrehh.datascrm