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DESCRIPTION
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DESCRIPTION
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Package: coala
Version: 0.2.0
Date: 2015-11-11
License: MIT + file LICENSE
Title: A Framework for Coalescent Simulation
Authors@R: c(
person('Paul', 'Staab', , 'develop@paulstaab.de', role=c('aut', 'cre', 'cph')),
person('Dirk', 'Metzler', role=c('ths'))
)
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.
This package allows to specify such models, transparently calls a suitable
simulator, parses the results and calculates additional summary statistics.
It supports the simulators 'ms', 'msms' and 'scrm' and can simulate
finite-sites mutation models by combining the simulators with the program
'seq-gen'.
Depends:
R (>= 3.1.0)
Imports:
assertthat (>= 0.1),
methods,
parallel,
R6 (>= 2.0.1),
Rcpp (>= 0.11.0),
rehh (>= 1.11),
scrm (>= 1.6.0-2),
stats,
utils
Suggests:
abc (>= 2.0),
knitr,
rmarkdown,
testthat (>= 0.10.0)
LinkingTo: Rcpp, RcppArmadillo (>= 0.3.810.0)
VignetteBuilder: knitr
Collate:
'RcppExports.R'
'cache.R'
'coala.R'
'feature.R'
'feature_growth.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'
'locus.R'
'model.R'
'model_build.R'
'model_check.R'
'model_examples.R'
'model_getters.R'
'model_print.R'
'model_scale.R'
'model_simulate.R'
'onLoad.R'
'par_zero_inflation.R'
'parameter.R'
'parameter_prior.R'
'parameter_variation.R'
'sample_seed.R'
'search_executable.R'
'segsites.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'
'tempfile.R'
RoxygenNote: 5.0.1