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

Functions

activate_ms Man page
activate_msms Man page
activate_scrm Man page
activate_seqgen Man page
as.segsites Man page
as.segsites.GENOME Man page
calc_jsfs Man page
calc_sumstats_from_data Man page
check_model Man page
coala Man page
coala-package Man page
coal_model Man page
+.coalmodelpart Man page
conv_to_ms_arg Man page
conv_to_ms_arg.default Man page
conv_to_ms_arg.files_feat Man page
conv_to_ms_arg.growth Man page
conv_to_ms_arg.ign_singletons Man page
conv_to_ms_arg.migration Man page
conv_to_ms_arg.mutation Man page
conv_to_ms_arg.outgroup Man page
conv_to_ms_arg.pop_merge Man page
conv_to_ms_arg.recombination Man page
conv_to_ms_arg.sample Man page
conv_to_ms_arg.seg_sites_feat Man page
conv_to_ms_arg.selection Man page
conv_to_ms_arg.size_change Man page
conv_to_ms_arg.trees_feat Man page
conv_to_ms_arg.unphased Man page
conv_to_msms_arg.default Man page
conv_to_msms_arg.files_feat Man page
conv_to_msms_arg.growth Man page
conv_to_msms_arg.ign_singletons Man page
conv_to_msms_arg.migration Man page
conv_to_msms_arg.mutation Man page
conv_to_msms_arg.outgroup Man page
conv_to_msms_arg.pop_merge Man page
conv_to_msms_arg.recombination Man page
conv_to_msms_arg.sample Man page
conv_to_msms_arg.seg_sites_feat Man page
conv_to_msms_arg.selection Man page
conv_to_msms_arg.size_change Man page
conv_to_msms_arg.trees_feat Man page
conv_to_msms_arg.unphased Man page
conv_to_scrm_arg.default Man page
conv_to_scrm_arg.files_feat Man page
conv_to_scrm_arg.growth Man page
conv_to_scrm_arg.ign_singletons Man page
conv_to_scrm_arg.migration Man page
conv_to_scrm_arg.mutation Man page
conv_to_scrm_arg.outgroup Man page
conv_to_scrm_arg.pop_merge Man page
conv_to_scrm_arg.recombination Man page
conv_to_scrm_arg.sample Man page
conv_to_scrm_arg.seg_sites_feat Man page
conv_to_scrm_arg.selection Man page
conv_to_scrm_arg.size_change Man page
conv_to_scrm_arg.trees_feat Man page
conv_to_scrm_arg.unphased Man page
conv_to_seqgen_arg.default Man page
conv_to_seqgen_arg.files_feat Man page
conv_to_seqgen_arg.growth Man page
conv_to_seqgen_arg.ign_singletons Man page
conv_to_seqgen_arg.migration Man page
conv_to_seqgen_arg.mutation Man page
conv_to_seqgen_arg.outgroup Man page
conv_to_seqgen_arg.pop_merge Man page
conv_to_seqgen_arg.recombination Man page
conv_to_seqgen_arg.sample Man page
conv_to_seqgen_arg.seg_sites_feat Man page
conv_to_seqgen_arg.selection Man page
conv_to_seqgen_arg.size_change Man page
conv_to_seqgen_arg.trees_feat Man page
conv_to_seqgen_arg.unphased Man page
create_abc_param Man page
create_abc_sumstat Man page
create_locus_trio Man page
create_segsites Man page
feat_growth Man page
feat_ignore_singletons Man page
feat_migration Man page
feat_mutation Man page
feat_outgroup Man page
feat_pop_merge Man page
feat_recombination Man page
feat_sample Man page
feat_selection Man page
feat_size_change Man page
feat_unphased Man page
get_features Man page
get_locus_length Man page
get_locus_length_matrix Man page
get_locus_number Man page
get_outgroup Man page
get_outgroup_size Man page
get_parameter Man page
get_parameter_table Man page
get_population_individuals Man page
get_populations Man page
get_positions Man page
get_sample_size Man page
get_snps Man page
get_summary_statistics Man page
get_trio_locus Man page
is_segsites Man page
list_simulators Man page
loci Man page
locus Man page
locus_averaged Man page
locus_single Man page
locus_trio Man page
parameter Man page
par_const Man page
par_expr Man page
par_named Man page
par_prior Man page
par_range Man page
par_variation Man page
par_zero_inflation Man page
scale_model Man page
search_executable Man page
segsites Man page
set_positions Man page
set_trio_locus Man page
simulate.coalmodel Man page
simulator_ms Man page
simulator_msms Man page
simulator_scrm Man page
simulator_seqgen Man page
sumstat_class Man page
sumstat_dna Man page
sumstat_file Man page
sumstat_four_gamete Man page
sumstat_ihh Man page
sumstat_jsfs Man page
sumstat_mcmf Man page
sumstat_nucleotide_div Man page
sumstat_omega Man page
sumstat_seg_sites Man page
sumstat_sfs Man page
sumstat_tajimas_d Man page
sumstat_trees Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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