Package: MetaEntropy
Title: Functional Shannon Entropy for Virome Mutational Analysis
Version: 1.4
Date: 2026-08-31
Authors@R: c( person("Leandro Roberto", "Jones", email = "lrj000@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5877-4194")),
    person("Julieta Marina", "Manrique", role = c("aut"), comment = c(ORCID = "0000-0001-8712-6666")))
Description: Estimates Shannon entropy, per gene and per genomic
        position, associated with non-synonymous mutation frequencies
        in viral populations, such as wastewater samples. The package
        uses codon translations for functional insights. Each amino
        acid can be treated as an individual state, resulting in a
        20-state entropy computation, or grouped into one of six
        physicochemical classes, adding further functional context.
        Provides normalized values (0-1 scale) to facilitate the direct
        comparison of different genomic positions or total functional
        entropy across multiple metagenomes. Designed to analyze
        mutational data using tabular 'Single Nucleotide Variant' (SNV)
        frequency tables generated by variant callers (e.g., 'iVar' or
        'LoFreq'), operating independently of consensus sequence
        estimation and multiple sequence alignment.
Encoding: UTF-8
Depends: R (>= 4.1.0)
LazyData: true
Suggests: rmarkdown, tidyr
Imports: ggplot2, patchwork, beeswarm, ggbeeswarm, knitr, dplyr,
        grDevices, rlang
VignetteBuilder: knitr
License: MIT + file LICENSE
Config/roxygen2/version: 8.1.0
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-10-26 10:44:14 UTC; root
Author: Leandro Roberto Jones [aut, cre] (ORCID:
        <https://orcid.org/0000-0002-5877-4194>), Julieta Marina
        Manrique [aut] (ORCID: <https://orcid.org/0000-0001-8712-6666>)
Maintainer: Leandro Roberto Jones <lrj000@gmail.com>
Repository: https://jones-lr.r-universe.dev
Date/Publication: 2026-09-03 14:10:02 UTC
RemoteUrl: https://github.com/cran/MetaEntropy
RemoteRef: HEAD
RemoteSha: 9fdb9ebe35fb97535f2e19510fcae516c9e59466