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: 2026-07-25 06:40:31 UTC; root
Config/pak/sysreqs: zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 13:03:51 UTC
RemoteUrl: https://github.com/bioc/scoup
RemoteRef: RELEASE_3_23
RemoteSha: d96f7cdc3bd1a28635114fe8d45aad19be6bf60a
NeedsCompilation: no
Author: Hassan Sadiq [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-0192-7134>)
Maintainer: Hassan Sadiq <hassan.t.sadiq@gmail.com>