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coala
View on CRAN: Click
here
Download and install coala package within the R console
Install from CRAN:
install.packages("coala")
Install from Github:
library("remotes")
install_github("cran/coala")
Install by package version:
library("remotes")
install_version("coala", "0.7.2")
Attach the package and use:
library("coala")
Maintained by
Dirk Metzler
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-07-14
Latest Update: 2023-01-05
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 (Staab, Metzler,
2016 ).
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'.
Coala provides functions for calculating certain summary statistics, which
can also be applied to actual biological data.
One possibility to import data is through the 'PopGenome' package
().
How to cite:
Dirk Metzler (2015). coala: A Framework for Coalescent Simulation. R package version 0.7.2, https://cran.r-project.org/web/packages/coala. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.1.0 (2015-07-14 20:40), 0.1.1 (2015-07-17 12:44), 0.2.0 (2015-11-11 16:34), 0.2.1 (2015-11-17 15:25), 0.3.0 (2015-12-21 12:16), 0.4.0 (2016-02-06 12:17), 0.4.1 (2016-08-04 00:59), 0.5.0 (2016-12-29 16:17), 0.5.2 (2017-10-30 16:56), 0.5.3 (2019-07-09 22:13), 0.6.0 (2020-01-19 18:40), 0.6.1 (2022-02-14 16:40), 0.7.0 (2022-08-05 18:30), 0.7.1 (2023-01-05 16:20)
Other packages that cited coala R package
View coala citation profile
Other R packages that coala depends,
imports, suggests or enhances
Complete documentation for coala
Functions, R codes and Examples using
the coala R package
Some associated functions: as.segsites.GENOME . as.segsites . calc_jsfs . calc_sumstats_from_data . check_model . coal_model . coala-package . conv_to_ms_arg . create_abc_param . create_abc_sumstat . feat_growth . feat_ignore_singletons . feat_migration . feat_mutation . feat_outgroup . feat_pop_merge . feat_recombination . feat_sample . feat_selection . feat_size_change . feat_unphased . get_features . list_simulators . locus . locus_trio . par_variation . par_zero_inflation . parameter . plus-.coalmodelpart . scale_model . search_executable . segsites . simulate.coalmodel . simulator_ms . simulator_msms . simulator_scrm . simulator_seqgen . sumstat_class . sumstat_dna . sumstat_file . sumstat_four_gamete . sumstat_ihh . sumstat_jsfs . sumstat_mcmf . sumstat_nucleotide_div . sumstat_omega . sumstat_seg_sites . sumstat_sfs . sumstat_tajimas_d . sumstat_trees .
Some associated R codes: RcppExports.R . cache.R . coala.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.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 . Full coala package functions and examples
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