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poolABC
View on CRAN: Click
here
Download and install poolABC package within the R console
Install from CRAN:
install.packages("poolABC")
Install from Github:
library("remotes")
install_github("cran/poolABC")
Install by package version:
library("remotes")
install_version("poolABC", "1.0.0")
Attach the package and use:
library("poolABC")
Maintained by
João Carvalho
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-08-08
Latest Update: 2023-08-08
Description:
Provides functions to simulate Pool-seq data under models of
demographic formation and to import Pool-seq data from real populations.
Implements two ABC algorithms for performing parameter estimation and
model selection using Pool-seq data. Cross-validation can also be
performed to assess the accuracy of ABC estimates and model choice.
Carvalho et al., (2022) .
How to cite:
João Carvalho (2023). poolABC: Approximate Bayesian Computation with Pooled Sequencing Data. R package version 1.0.0, https://cran.r-project.org/web/packages/poolABC. Accessed 21 Nov. 2024.
Previous versions and publish date:
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Complete documentation for poolABC
Functions, R codes and Examples using
the poolABC R package
Some associated functions: ABC . BTmatrix . D.stat . D.statPool . Expected_Het . Het_Between . Tmatrix . abba . baba . checkCoverage . checkMajor . checkMissing . cleanData . cmd2pops . cmdParallel . cmdSingle . createHeader . createParams . errorABC . error_modelSel . euclidean . exclusive . filterData . fixed . forceLocus . getFst . getmode . importContigs . importData . index.rejABC . indexSNPs . inverse_trans . limits . meanExpected_Het . mergepost . mode_locfit . modelSelect . multipleABC . myparams . normalise . organize.poststat . organizeSCRM . pairFST . params . pickWindows . plot_Posteriors . plot_error . plot_errorABC . plot_msel . plot_param . plot_stats . plot_weighted . poolSim . poolStats . popsFST . poststat . prepareData . prepareFile . priorsMatrix . rc1 . rc2 . regABC . rejABC . removeVar . remove_quantileReads . remove_realReads . runSCRM . scaled.migration . scaledPrior . shared . sim_modelSel . simulationABC . singleABC . statsContig . summary_modelSelect . sumstats . tranf . weighted_stats .
Some associated R codes: data.R . functions_ABC.R . functions_import.R . functions_simulations.R . functions_sumstats.R . Full poolABC package functions and examples
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