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. 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'.

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Description file content

Package
coala
Version
0.5.3
License
MIT + file LICENSE
Title
A Framework for Coalescent Simulation
BugReports
https://github.com/statgenlmu/coala/issues
URL
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. 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'.
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'
RoxygenNote
6.1.1
NeedsCompilation
yes
Packaged
2019-07-09 19:30:39 UTC; paul
Author
Paul Staab [aut, cre], Dirk Metzler [aut, ths], Jorge E. Amaya Romero [ctb]
Maintainer
Paul Staab
Repository
CRAN
Date/Publication
2019-07-09 20:11:56 UTC

install.packages('coala')

0.5.3

8 days ago

https://github.com/statgenlmu/coala

Paul Staab

MIT + file LICENSE

Depends on

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)

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