Package: scoup
Version: 1.6.0
Date: 2026-03-17
License: GPL (>= 2)
Authors@R: c(person("Hassan", "Sadiq", role=c("aut","cre","cph"),
                    email="hassan.t.sadiq@gmail.com",
                    comment=c(ORCID="0000-0003-0192-7134")))
Title: Simulate Codons with Darwinian Selection Modelled as an OU
        Process
Description: An elaborate molecular evolutionary framework that facilitates
             straightforward simulation of codon genetic sequences
             subjected to different degrees and/or patterns of Darwinian
             selection. The model is built upon the fitness landscape
             paradigm of Sewall Wright, as popularised by the
             mutation-selection model of Halpern and Bruno. This
             enables realistic evolutionary process of living organisms
             to be reproducible seamlessly. For example, an
             Ornstein-Uhlenbeck fitness update algorithm is incorporated
             herein. Consequently, otherwise complex biological processes,
             such as the effect of the interplay between genetic drift
             and fitness landscape fluctuations on the inference of
             diversifying selection, may now be investigated with minimal
             effort. Frequency-dependent and stochastic fitness landscape
             update techniques are available.
Depends: R (>= 4.4), Matrix
Imports: Biostrings, methods
Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat
        (>= 3.0.0), yaml
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Alignment, Classification, ComparativeGenomics, DataImport,
        Genetics, MathematicalBiology, ResearchField, Sequencing,
        SequenceMatching, Software, StatisticalMethod, WorkflowStep
Contact: <hassan.t.sadiq@gmail.com>
URL: https://github.com/thsadiq/scoup
BugReports: https://github.com/thsadiq/scoup/issues
Packaged: 2026-04-28 23:26:47 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/scoup
git_branch: RELEASE_3_23
git_last_commit: d96f7cd
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Author: Hassan Sadiq [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-0192-7134>)
Maintainer: Hassan Sadiq <hassan.t.sadiq@gmail.com>
Built: R 4.6.0; ; 2026-04-29 04:59:57 UTC; unix
