Package: coala Version: 0.7.2 License: MIT + file LICENSE Title: A Framework for Coalescent Simulation Authors@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')) Author: Paul Staab [aut], Dirk Metzler [aut, ths, cre], Jorge E. Amaya Romero [ctb] BugReports: https://github.com/statgenlmu/coala/issues URL: https://github.com/statgenlmu/coala Description: 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 ). 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 (). Depends: R (>= 3.1.0) Imports: assertthat (>= 0.1), digest, methods, parallel, R6 (>= 2.0.1), Rcpp (>= 0.11.0), rehh (>= 3.0.0), scrm (>= 1.6.0-2), stats, utils Suggests: abc (>= 2.0), knitr, PopGenome (>= 2.1.0), phyclust (>= 0.1-16), rmarkdown, testthat (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo (>= 0.3.810.0) VignetteBuilder: knitr Collate: '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' 'import_popgenome.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' Encoding: UTF-8 RoxygenNote: 7.3.1 NeedsCompilation: yes Packaged: 2024-03-04 14:51:03 UTC; dirk Maintainer: Dirk Metzler Repository: CRAN Date/Publication: 2024-03-04 16:20:17 UTC