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'.

AuthorPaul Staab [aut, cre], Dirk Metzler [aut, ths], Jorge E. Amaya Romero [ctb]
Date of publication2016-12-29 16:17:25
MaintainerPaul Staab <develop@paulstaab.de>
LicenseMIT + file LICENSE
Version0.5.0
https://github.com/statgenlmu/coala

View on CRAN

Man pages

as.segsites: Convert genetic data to coala's internal format

as.segsites.GENOME: Convert PopGenome Data into Coala's Format

calc_jsfs: Calculates the Joint Site Frequency Spectrum

calc_sumstats_from_data: Calculate summary statistics for biological data

check_model: Check which simulator can simulate a model

coala-package: A Framework for Coalescent Simulation in R

coal_model: Create a Coalescent Model

conv_to_ms_arg: Generate command line arguments for features

create_abc_param: Convert Simulation Results to abc's Parameter Format

create_abc_sumstat: Convert Simulation Results to abc's Summary Statistic Format

feat_growth: Feature: Exponential population size growth/decline

feat_ignore_singletons: Feature: Ignore Singletons

feat_migration: Feature: Migration/Gene Flow

feat_mutation: Feature: Mutation

feat_outgroup: Feature: Outgroup

feat_pop_merge: Feature: Population Merge

feat_recombination: Feature: Recombination

feat_sample: Creates a feature that represents the sampling from one...

feat_selection: Feature: Selection

feat_size_change: Feature: Instantaneous Size Change

feat_unphased: Feature: Unphased Sequences

get_features: Getters for coalescent models

list_simulators: Returns the available simulators

locus: Loci

locus_trio: Locus Trios

parameter: Model Parameters

par_variation: Variable Parameters

par_zero_inflation: Zero Inflation for Parameters

plus-.coalmodelpart: Add a feature or parameter to a model

scale_model: Function that downscales a coalescent model

search_executable: Search the working directory and the run path for an...

segsites: Segregating Sites

simulate.coalmodel: Simulate Data According to a Demographic Model

simulator_ms: Simulator: ms

simulator_msms: Simulator: msms

simulator_scrm: Simulator: scrm

simulator_seqgen: Simulator: seq-gen

sumstat_class: Base Class for Summary Statistics

sumstat_dna: Summary Statistic: DNA

sumstat_file: Summary Statistic: Files

sumstat_four_gamete: Summary Statistic: Four-Gamete-Condition

sumstat_ihh: Summary Statistic: Integrated Extended Haplotype Homozygosity

sumstat_jsfs: Summary Statistic: Joint Site Frequency Spectrum

sumstat_mcmf: Summary Statistic: Most Common Mutation's Frequency

sumstat_nucleotide_div: Summary Statistic: Nucleotide Diversity

sumstat_omega: Summary Statistic: Omega

sumstat_seg_sites: Summary Statistic: Segregating Sites

sumstat_sfs: Summary Statistic: Site Frequency Spectrum

sumstat_tajimas_d: Summary Statistic: Tajima's D

sumstat_trees: Summary Statistic: Ancestral Trees

Files in this package

coala
coala/inst
coala/inst/CITATION
coala/inst/example_fasta_files
coala/inst/example_fasta_files/sample.fasta
coala/inst/doc
coala/inst/doc/coala-install.html
coala/inst/doc/coala-abc.Rmd
coala/inst/doc/coala-data-import.Rmd
coala/inst/doc/coala-abc.R
coala/inst/doc/coala-data-import.R
coala/inst/doc/coala-examples.html
coala/inst/doc/coala-install.R
coala/inst/doc/coala-extend.Rmd
coala/inst/doc/coala-data-import.html
coala/inst/doc/coala-extend.html
coala/inst/doc/coala-examples.R
coala/inst/doc/coala-abc.html
coala/inst/doc/coala-examples.Rmd
coala/inst/doc/coala-intro.Rmd
coala/inst/doc/coala-intro.html
coala/inst/doc/coala-intro.R
coala/inst/doc/coala-extend.R
coala/inst/doc/coala-install.Rmd
coala/inst/include
coala/inst/include/coala.h
coala/tests
coala/tests/testthat.R
coala/tests/testthat
coala/tests/testthat/test-tempfile.R
coala/tests/testthat/test-interface-abc.R
coala/tests/testthat/test-parameter-class.R
coala/tests/testthat/test-parameter-zero-inflation.R
coala/tests/testthat/test-simulator-scrm.R
coala/tests/testthat/test-simulation-tasks.R
coala/tests/testthat/test-sumstat-mcmf.R
coala/tests/testthat/test-simulator-class.R
coala/tests/testthat/test-feature-outgroup.R
coala/tests/testthat/test-feature-selection.R
coala/tests/testthat/test-feature-samples.R
coala/tests/testthat/test-sumstat-dna.R
coala/tests/testthat/test-feature-pop-merge.R
coala/tests/testthat/test-sumstat-trees.R
coala/tests/testthat/test-sumstat-omega.R
coala/tests/testthat/test-travis-setup.R
coala/tests/testthat/test-sumstat-class.R
coala/tests/testthat/test-tools.R
coala/tests/testthat/test-sumstat-sfs.R
coala/tests/testthat/test-sumstat-pi.R
coala/tests/testthat/test-sumstat-iHH.R
coala/tests/testthat/test-model-class.R
coala/tests/testthat/test-model-simulation.R
coala/tests/testthat/test-sumstat-jsfs.R
coala/tests/testthat/test-feature-size-change.R
coala/tests/testthat/test-segsites-class.R
coala/tests/testthat/test-feature-growth.R
coala/tests/testthat/test-simulator-ms.R
coala/tests/testthat/test-feature-class.R
coala/tests/testthat/test-sumstat-segsites.R
coala/tests/testthat/test-sumstat-fpc.R
coala/tests/testthat/test-search-executables.R
coala/tests/testthat/test-parameter-variation.R
coala/tests/testthat/test-simulator-seqgen.R
coala/tests/testthat/test-feature-unphased.R
coala/tests/testthat/test-sumstat-file.R
coala/tests/testthat/test-feature-migration.R
coala/tests/testthat/test-feature-mutation.R
coala/tests/testthat/test-feature-ign-singletons.R
coala/tests/testthat/test-model-cache.R
coala/tests/testthat/test-locus.R
coala/tests/testthat/test-sumstat-tajimas-d.R
coala/tests/testthat/test-import-popgenome.R
coala/tests/testthat/test-simulator-msms.R
coala/tests/testthat/test-parameter-priors.R
coala/tests/testthat/test-simulators.R
coala/tests/testthat/test-feature-recombination.R
coala/src
coala/src/stat_jsfs.cpp
coala/src/stat_mcmf.cpp
coala/src/seg_sites.cpp
coala/src/parse_trees.cpp
coala/src/parse_ms_output.cpp
coala/src/stat_fpc.cpp
coala/src/RcppExports.cpp
coala/src/stat_nucleotide_div.cpp
coala/src/parse_seqgen_output.cpp
coala/src/unphase_segsites.cpp
coala/NAMESPACE
coala/NEWS.md
coala/R
coala/R/coala.R coala/R/sumstat_trees.R coala/R/sumstat_sfs.R coala/R/simulator_scrm.R coala/R/simulator_class.R coala/R/parameter_zero_inflation.R coala/R/segsites.R coala/R/interface_abc.R coala/R/locus.R coala/R/model_build.R coala/R/feature_outgroup.R coala/R/model_check.R coala/R/feature_ignore_singletons.R coala/R/onLoad.R coala/R/model.R coala/R/sumstat_seg_sites.R coala/R/parameter_variation.R coala/R/sumstat_tajimas_d.R coala/R/feature_size_change.R coala/R/model_print.R coala/R/feature_recombination.R coala/R/sumstat_file.R coala/R/sumstat_nucleotide_div.R coala/R/feature_migration.R coala/R/feature_selection.R coala/R/feature_sample.R coala/R/sumstat_jsfs.R coala/R/feature_sumstats.R coala/R/sumstat_omega.R coala/R/feature_mutation.R coala/R/import_popgenome.R coala/R/sumstat_mcmf.R coala/R/simulator_seqgen.R coala/R/cache.R coala/R/sumstat.R coala/R/RcppExports.R coala/R/tools.R coala/R/feature.R coala/R/model_simulate.R coala/R/simulator_msms.R coala/R/sumstat_ihh.R coala/R/simulation_tasks.R coala/R/model_getters.R coala/R/sumstat_four_gamete.R coala/R/simulator_ms.R coala/R/model_examples.R coala/R/feature_pop_merge.R coala/R/feature_unphased.R coala/R/sumstat_dna.R coala/R/search_executable.R coala/R/model_scale.R coala/R/feature_growth.R coala/R/parameter.R coala/R/parameter_prior.R
coala/vignettes
coala/vignettes/coala-abc.Rmd
coala/vignettes/coala-data-import.Rmd
coala/vignettes/img
coala/vignettes/img/abc_posterior.jpeg
coala/vignettes/coala-extend.Rmd
coala/vignettes/coala-examples.Rmd
coala/vignettes/coala-intro.Rmd
coala/vignettes/coala-install.Rmd
coala/README.md
coala/MD5
coala/build
coala/build/vignette.rds
coala/DESCRIPTION
coala/man
coala/man/feat_outgroup.Rd coala/man/feat_growth.Rd coala/man/simulate.coalmodel.Rd coala/man/sumstat_class.Rd coala/man/plus-.coalmodelpart.Rd coala/man/create_abc_param.Rd coala/man/feat_ignore_singletons.Rd coala/man/calc_jsfs.Rd coala/man/as.segsites.GENOME.Rd coala/man/conv_to_ms_arg.Rd coala/man/get_features.Rd coala/man/simulator_msms.Rd coala/man/scale_model.Rd coala/man/segsites.Rd coala/man/sumstat_file.Rd coala/man/par_variation.Rd coala/man/sumstat_ihh.Rd coala/man/feat_recombination.Rd coala/man/simulator_ms.Rd coala/man/sumstat_four_gamete.Rd coala/man/sumstat_nucleotide_div.Rd coala/man/feat_size_change.Rd coala/man/sumstat_mcmf.Rd coala/man/feat_selection.Rd coala/man/coal_model.Rd coala/man/sumstat_dna.Rd coala/man/as.segsites.Rd coala/man/create_abc_sumstat.Rd coala/man/coala-package.Rd coala/man/list_simulators.Rd coala/man/sumstat_seg_sites.Rd coala/man/check_model.Rd coala/man/sumstat_jsfs.Rd coala/man/feat_migration.Rd coala/man/simulator_seqgen.Rd coala/man/feat_unphased.Rd coala/man/parameter.Rd coala/man/locus.Rd coala/man/sumstat_trees.Rd coala/man/feat_sample.Rd coala/man/calc_sumstats_from_data.Rd coala/man/sumstat_omega.Rd coala/man/sumstat_sfs.Rd coala/man/simulator_scrm.Rd coala/man/feat_mutation.Rd coala/man/search_executable.Rd coala/man/sumstat_tajimas_d.Rd coala/man/locus_trio.Rd coala/man/feat_pop_merge.Rd coala/man/par_zero_inflation.Rd
coala/LICENSE

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All documentation is copyright its authors; we didn't write any of that.