Package: strainspy
Type: Package
Title: Strain Level Microbiome Wide Association Studies
Version: 0.99.3
Depends: R (>= 4.1.0)
Authors@R: c(
    person(given = "Gerry", family = "Tonkin-Hill",
        role = "aut", email = "g.tonkinhill@gmail.com"),
    person(given = "Sudaraka", family = "Mallawaarachchi",
        role = c("aut", "cre"), email = "smallawaarachchi@gmail.com",
        comment = c(ORCID = "0000-0001-8899-3323"))
    )
Description: Fits statistical models to detect microbial strains
        associated with a phenotype. For small sample sizes, models can
        be fitted using empirical Bayes maximum a posteriori (MAP)
        priors to improve detection power. Supports various
        experimental design scenarios, including repeated measures.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/gtonkinhill/strainspy,
        https://sudaraka88.r-universe.dev/strainspy
BugReports: https://github.com/gtonkinhill/strainspy/issues
biocViews: Software, Microbiome, Metagenomics, MicrobialStrain,
        DifferentialExpression, Regression, ExperimentalDesign,
        Sequencing
Imports: ape, BiocParallel, data.table, dplyr, ggforce, ggplot2,
        ggrepel, ggthemes, ggtree, glmmTMB, graphics, grDevices,
        harmonicmeanp, lmerTest, magrittr, Matrix, methods, patchwork,
        purrr, R.utils (>= 2.13.0), S4Vectors, stats, stringr,
        SummarizedExperiment, rlang, tibble, tidyr, tools, utils,
        viridis
Suggests: betareg, BiocStyle, compositions, fastglm, future, gamlss,
        gamlss.dist, knitr, mgcv, rmarkdown, testthat (>= 3.0.0),
        vegan, emmeans
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev make libicu-dev libpng-dev libuv1-dev
        zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-14 00:47:49 UTC
RemoteUrl: https://github.com/BiocStaging/strainspy
RemoteRef: HEAD
RemoteSha: a961691294dad5448b7fd0087a47f5f0c55bd21d
NeedsCompilation: no
Packaged: 2026-10-14 07:56:02 UTC; root
Author: Gerry Tonkin-Hill [aut],
  Sudaraka Mallawaarachchi [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8899-3323>)
Maintainer: Sudaraka Mallawaarachchi <smallawaarachchi@gmail.com>