Package: rbiom
Type: Package
Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Version: 2.2.1
Date: 2025-06-27
Authors@R: c(
    person(
      "Daniel P.", "Smith",
      email   = "dansmith01@gmail.com",
      role    = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-2479-2044")),
    person(
      "Alkek Center for Metagenomics and Microbiome Research", 
      role = c("cph", "fnd") ))
Description: 
    A toolkit for working with Biological Observation Matrix ('BIOM') files.
    Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and 
    beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. 
    Subset based on metadata. Generate visualizations and statistical analyses. 
    CPU intensive operations are coded in C for speed.
URL: https://cmmr.github.io/rbiom/, https://github.com/cmmr/rbiom
BugReports: https://github.com/cmmr/rbiom/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.2.0)
RoxygenNote: 7.3.2
Config/Needs/website: rmarkdown, phyloseq, npregfast, withr
Config/testthat/edition: 3
Imports: methods, mgcv, stats, utils, ape, dplyr, emmeans, fillpattern,
        ggbeeswarm, ggnewscale, ggplot2, ggrepel, ggtext, jsonlite,
        magrittr, parallelly, patchwork, pillar, plyr, readr, readxl,
        slam, vegan
Suggests: cli, crayon, ggdensity, glue, labeling, lifecycle, openxlsx,
        optparse, pkgconfig, prettycode, R6, rlang, scales, testthat,
        tibble, tsne, uwot
NeedsCompilation: yes
Packaged: 2025-06-27 19:52:14 UTC; Daniel
Author: Daniel P. Smith [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2479-2044>),
  Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Repository: CRAN
Date/Publication: 2025-06-27 20:10:02 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-07 11:04:27 UTC; unix
Archs: rbiom.so.dSYM
