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'.

Author
Paul Staab [aut, cre], Dirk Metzler [aut, ths]
Date of publication
2016-08-04 00:59:21
Maintainer
Paul Staab <develop@paulstaab.de>
License
MIT + file LICENSE
Version
0.4.1
URLs

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-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-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/sample_seed.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/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