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 <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>).
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 <metzler@bio.lmu.de>
Repository: CRAN
Date/Publication: 2024-03-04 16:20:17 UTC
Built: R 4.4.3; x86_64-w64-mingw32; 2025-12-29 17:25:49 UTC; windows
Archs: x64
