coala: A Framework for Coalescent Simulation
Version 0.5.0

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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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
URL https://github.com/statgenlmu/coala
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("coala")

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

+.coalmodelpart Man page
activate_ms Man page Source code
activate_msms Man page Source code
activate_scrm Man page Source code
activate_seqgen Man page Source code
add_to_model Source code
add_to_model.default Source code
add_to_model.feature Source code
add_to_model.locus Source code
add_to_model.named_par Source code
add_to_model.parameter Source code
add_to_model.partial_model Source code
add_to_model.sumstat Source code
add_to_model.variation_par Source code
add_variation Source code
as.matrix.segsites Source code
as.segsites Man page Source code
as.segsites.GENOME Man page Source code
as.segsites.default Source code
as.segsites.list Source code
cache Source code
calc_four_gamete_stat Source code
calc_jsfs Man page Source code
calc_mcmf Source code
calc_nucleotide_div Source code
calc_sumstats Source code
calc_sumstats_from_data Man page Source code
calc_sumstats_from_sim Source code
check_model Man page Source code
coal_model Man page Source code
coala Man page
coala-package Man page
combine_results Source code
conv_for_trios Source code
conv_middle_to_trio_pos Source code
conv_to_ms_arg Man page Source code
conv_to_ms_arg.default Man page Source code
conv_to_ms_arg.files_feat Man page
conv_to_ms_arg.growth Man page Source code
conv_to_ms_arg.ign_singletons Man page
conv_to_ms_arg.migration Man page Source code
conv_to_ms_arg.mutation Man page Source code
conv_to_ms_arg.outgroup Man page Source code
conv_to_ms_arg.pop_merge Man page Source code
conv_to_ms_arg.recombination Man page Source code
conv_to_ms_arg.sample Man page Source code
conv_to_ms_arg.seg_sites_feat Man page Source code
conv_to_ms_arg.selection Man page Source code
conv_to_ms_arg.size_change Man page Source code
conv_to_ms_arg.trees_feat Man page Source code
conv_to_ms_arg.unphased Man page
conv_to_ms_output Source code
conv_to_msms_arg Source code
conv_to_msms_arg.default Man page Source code
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 Source code
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 Source code
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 Source code
conv_to_scrm_arg.default Man page Source code
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 Source code
conv_to_scrm_arg.outgroup Man page Source code
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 Source code
conv_to_seqgen_arg.default Man page Source code
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 Source code
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 Source code
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 Source code
conv_to_seqgen_arg.unphased Man page
create_abc_param Man page Source code
create_abc_sumstat Man page Source code
create_empty_segsites Source code
create_group_model Source code
create_locus_trio Man page Source code
create_par_env Source code
create_popgenome_test_data Source code
create_segsites Man page Source code
create_sim_task Source code
create_sumstat_container Source code
create_test_segsites Source code
create_zero_frac_func Source code
dim.segsites Source code
feat_growth Man page Source code
feat_ignore_singletons Man page Source code
feat_migration Man page Source code
feat_mutation Man page Source code
feat_outgroup Man page Source code
feat_pop_merge Man page Source code
feat_recombination Man page Source code
feat_sample Man page Source code
feat_selection Man page Source code
feat_size_change Man page Source code
feat_unphased Man page Source code
fill_cmd_template Source code
generate_sim_tasks Source code
generate_tree_model Source code
generate_trio_trees Source code
get_cmd Source code
get_feature_unphased Source code
get_features Man page Source code
get_id Source code
get_loci Source code
get_locus_group Source code
get_locus_group_number Source code
get_locus_length Man page Source code
get_locus_length_matrix Man page Source code
get_locus_number Man page Source code
get_outgroup Man page Source code
get_outgroup_size Man page Source code
get_par_names Source code
get_parameter Man page Source code
get_parameter_table Man page Source code
get_ploidy Source code
get_population_individuals Man page Source code
get_populations Man page Source code
get_positions Man page Source code
get_sample_size Man page Source code
get_samples_per_ind Source code
get_simulator Source code
get_snp_positions Source code
get_snps Man page Source code
get_summary_statistics Man page Source code
get_trio_locus Man page Source code
has_ign_singletons Source code
has_ms Source code
has_msms Source code
has_omega Source code
has_seqgen Source code
has_trios Source code
has_variation Source code
ignore_par Source code
is.feature Source code
is.locus Source code
is.model Source code
is.named_par Source code
is.par Source code
is.par_variation Source code
is.prior_par Source code
is.ranged_par Source code
is.sum_stat Source code
is_feat_mutation Source code
is_feat_outgroup Source code
is_feat_sample Source code
is_feat_unphased Source code
is_partial_model Source code
is_segsites Man page Source code
is_simulation_task Source code
is_simulator Source code
is_unphased Source code
list_simulators Man page Source code
loci Man page
locus Man page
locus_averaged Man page Source code
locus_single Man page Source code
locus_trio Man page Source code
model_gtr Source code
model_hky Source code
model_theta_tau Source code
model_trios Source code
onLoad Source code
par_const Man page Source code
par_eval_func Source code
par_expr Man page Source code
par_named Man page Source code
par_print_func Source code
par_prior Man page Source code
par_range Man page Source code
par_variation Man page Source code
par_zero_inflation Man page Source code
parameter Man page
parse_ms_output Source code
parse_ms_positions Source code
parse_seqgen_output Source code
prepare_pars Source code
print.coalmodel Source code
print.partial_model Source code
print.segsites Source code
print_model_part Source code
print_par Source code
read_cache Source code
reduce_sim_tasks Source code
register_simulator Source code
remove_singletons Source code
require_package Source code
requires_files Source code
requires_segsites Source code
requires_trees Source code
reset_cache Source code
sample_par_priors Source code
sample_seed Source code
scale_model Man page Source code
search_executable Man page Source code
segsites Man page
select_simprog Source code
set_positions Man page Source code
set_trio_locus Man page Source code
sg_generate_opts Source code
simulate.coalmodel Man page Source code
simulator_ms Man page
simulator_msms Man page
simulator_scrm Man page
simulator_seqgen Man page
sumstat_class Man page
sumstat_dna Man page Source code
sumstat_file Man page Source code
sumstat_four_gamete Man page Source code
sumstat_ihh Man page Source code
sumstat_jsfs Man page Source code
sumstat_mcmf Man page Source code
sumstat_nucleotide_div Man page Source code
sumstat_omega Man page Source code
sumstat_seg_sites Man page Source code
sumstat_sfs Man page Source code
sumstat_tajimas_d Man page Source code
sumstat_trees Man page Source code
tempfile Source code
test_model Source code
test_simulator Source code
unphase_segsites Source code
variation Source code
zero_inflate Source code

Files

inst
inst/CITATION
inst/example_fasta_files
inst/example_fasta_files/sample.fasta
inst/doc
inst/doc/coala-install.html
inst/doc/coala-abc.Rmd
inst/doc/coala-data-import.Rmd
inst/doc/coala-abc.R
inst/doc/coala-data-import.R
inst/doc/coala-examples.html
inst/doc/coala-install.R
inst/doc/coala-extend.Rmd
inst/doc/coala-data-import.html
inst/doc/coala-extend.html
inst/doc/coala-examples.R
inst/doc/coala-abc.html
inst/doc/coala-examples.Rmd
inst/doc/coala-intro.Rmd
inst/doc/coala-intro.html
inst/doc/coala-intro.R
inst/doc/coala-extend.R
inst/doc/coala-install.Rmd
inst/include
inst/include/coala.h
tests
tests/testthat.R
tests/testthat
tests/testthat/test-tempfile.R
tests/testthat/test-interface-abc.R
tests/testthat/test-parameter-class.R
tests/testthat/test-parameter-zero-inflation.R
tests/testthat/test-simulator-scrm.R
tests/testthat/test-simulation-tasks.R
tests/testthat/test-sumstat-mcmf.R
tests/testthat/test-simulator-class.R
tests/testthat/test-feature-outgroup.R
tests/testthat/test-feature-selection.R
tests/testthat/test-feature-samples.R
tests/testthat/test-sumstat-dna.R
tests/testthat/test-feature-pop-merge.R
tests/testthat/test-sumstat-trees.R
tests/testthat/test-sumstat-omega.R
tests/testthat/test-travis-setup.R
tests/testthat/test-sumstat-class.R
tests/testthat/test-tools.R
tests/testthat/test-sumstat-sfs.R
tests/testthat/test-sumstat-pi.R
tests/testthat/test-sumstat-iHH.R
tests/testthat/test-model-class.R
tests/testthat/test-model-simulation.R
tests/testthat/test-sumstat-jsfs.R
tests/testthat/test-feature-size-change.R
tests/testthat/test-segsites-class.R
tests/testthat/test-feature-growth.R
tests/testthat/test-simulator-ms.R
tests/testthat/test-feature-class.R
tests/testthat/test-sumstat-segsites.R
tests/testthat/test-sumstat-fpc.R
tests/testthat/test-search-executables.R
tests/testthat/test-parameter-variation.R
tests/testthat/test-simulator-seqgen.R
tests/testthat/test-feature-unphased.R
tests/testthat/test-sumstat-file.R
tests/testthat/test-feature-migration.R
tests/testthat/test-feature-mutation.R
tests/testthat/test-feature-ign-singletons.R
tests/testthat/test-model-cache.R
tests/testthat/test-locus.R
tests/testthat/test-sumstat-tajimas-d.R
tests/testthat/test-import-popgenome.R
tests/testthat/test-simulator-msms.R
tests/testthat/test-parameter-priors.R
tests/testthat/test-simulators.R
tests/testthat/test-feature-recombination.R
src
src/stat_jsfs.cpp
src/stat_mcmf.cpp
src/seg_sites.cpp
src/parse_trees.cpp
src/parse_ms_output.cpp
src/stat_fpc.cpp
src/RcppExports.cpp
src/stat_nucleotide_div.cpp
src/parse_seqgen_output.cpp
src/unphase_segsites.cpp
NAMESPACE
NEWS.md
R
R/coala.R
R/sumstat_trees.R
R/sumstat_sfs.R
R/simulator_scrm.R
R/simulator_class.R
R/parameter_zero_inflation.R
R/segsites.R
R/interface_abc.R
R/locus.R
R/model_build.R
R/feature_outgroup.R
R/model_check.R
R/feature_ignore_singletons.R
R/onLoad.R
R/model.R
R/sumstat_seg_sites.R
R/parameter_variation.R
R/sumstat_tajimas_d.R
R/feature_size_change.R
R/model_print.R
R/feature_recombination.R
R/sumstat_file.R
R/sumstat_nucleotide_div.R
R/feature_migration.R
R/feature_selection.R
R/feature_sample.R
R/sumstat_jsfs.R
R/feature_sumstats.R
R/sumstat_omega.R
R/feature_mutation.R
R/import_popgenome.R
R/sumstat_mcmf.R
R/simulator_seqgen.R
R/cache.R
R/sumstat.R
R/RcppExports.R
R/tools.R
R/feature.R
R/model_simulate.R
R/simulator_msms.R
R/sumstat_ihh.R
R/simulation_tasks.R
R/model_getters.R
R/sumstat_four_gamete.R
R/simulator_ms.R
R/model_examples.R
R/feature_pop_merge.R
R/feature_unphased.R
R/sumstat_dna.R
R/search_executable.R
R/model_scale.R
R/feature_growth.R
R/parameter.R
R/parameter_prior.R
vignettes
vignettes/coala-abc.Rmd
vignettes/coala-data-import.Rmd
vignettes/img
vignettes/img/abc_posterior.jpeg
vignettes/coala-extend.Rmd
vignettes/coala-examples.Rmd
vignettes/coala-intro.Rmd
vignettes/coala-install.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/feat_outgroup.Rd
man/feat_growth.Rd
man/simulate.coalmodel.Rd
man/sumstat_class.Rd
man/plus-.coalmodelpart.Rd
man/create_abc_param.Rd
man/feat_ignore_singletons.Rd
man/calc_jsfs.Rd
man/as.segsites.GENOME.Rd
man/conv_to_ms_arg.Rd
man/get_features.Rd
man/simulator_msms.Rd
man/scale_model.Rd
man/segsites.Rd
man/sumstat_file.Rd
man/par_variation.Rd
man/sumstat_ihh.Rd
man/feat_recombination.Rd
man/simulator_ms.Rd
man/sumstat_four_gamete.Rd
man/sumstat_nucleotide_div.Rd
man/feat_size_change.Rd
man/sumstat_mcmf.Rd
man/feat_selection.Rd
man/coal_model.Rd
man/sumstat_dna.Rd
man/as.segsites.Rd
man/create_abc_sumstat.Rd
man/coala-package.Rd
man/list_simulators.Rd
man/sumstat_seg_sites.Rd
man/check_model.Rd
man/sumstat_jsfs.Rd
man/feat_migration.Rd
man/simulator_seqgen.Rd
man/feat_unphased.Rd
man/parameter.Rd
man/locus.Rd
man/sumstat_trees.Rd
man/feat_sample.Rd
man/calc_sumstats_from_data.Rd
man/sumstat_omega.Rd
man/sumstat_sfs.Rd
man/simulator_scrm.Rd
man/feat_mutation.Rd
man/search_executable.Rd
man/sumstat_tajimas_d.Rd
man/locus_trio.Rd
man/feat_pop_merge.Rd
man/par_zero_inflation.Rd
LICENSE
coala documentation built on May 19, 2017, 6:31 p.m.