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  "Package": "Sibyl",
  "Title": "Sibyl",
  "Version": "1.0",
  "Authors@R": "c(\nperson(\"Lorenzo\", \"Assentato\", email = \"assentato.lorenzo@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3699-0483\")),\nperson(\"Magdalena\", \"Polder\", email = \"polder.magdalena@gmail.com\",\nrole = c(\"aut\"))\n)",
  "Description": "The Sibyl package provides a convenient way of testing a\nrange of thresholds for rarefation, evaluating the effect of\ndifferent values on ordination results, integrating with\ncommonly used packages in microbial ecology. You provide\nphyloseq data with count data and sample information.",
  "License": "GPL (>= 3)",
  "Language": "en-US",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "biocViews": "",
  "SystemRequirements": "libcurl, OpenSSL, XML2, LAPACK, Fortran, zlib,\nOpenGL, GLU, X11, JPEG, PNG",
  "LazyData": "true",
  "Config/testthat/edition": "3",
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  "Repository": "https://headonpillow.r-universe.dev",
  "Date/Publication": "2026-07-20 11:12:40 UTC",
  "RemoteUrl": "https://github.com/Headonpillow/Sibyl",
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  "Packaged": {
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  "Author": "Lorenzo Assentato [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3699-0483>),\nMagdalena Polder [aut]",
  "Maintainer": "Lorenzo Assentato <assentato.lorenzo@gmail.com>",
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    "id": "af8f183b3c92dc48999d9d720a2ad9cfe02b4c3a",
    "author": "Headonpillow <85705350+Headonpillow@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #4 from Headonpillow/probabilities\n\nSibyl currently evaluates ordination uncertainty by repeatedly rarefying count data. This PR adds a second uncertainty-generation workflow: Dirichlet Monte Carlo sampling through ALDEx2 that estimates the same kind of uncertainty without discarding reads via subsampling.\nBoth workflows now share the same downstream pipeline (ordinate → align by Procrustes → consensus coordinates → uncertainty clouds), so results from the two are directly comparable within a common framework.\n\nNew public API\n\n    dirichlet_ordination() (exported): runs repeated Monte Carlo sampling from the Dirichlet posterior via ALDEx2::aldex.clr(), ordinates each realization using Aitchison distances, and produces the same consensus-coordinate/cloud visualization as repeated_rarefaction().\n    New internal helper rep_mc_draws() (mirrors rep_raref()) extracts the Dirichlet Monte Carlo instances from ALDEx2.\n    New dependency: ALDEx2 (added to DESCRIPTION Imports).\n    Refactor: shared ordination core\n    ord_and_mean() (previously duplicated as ord_and_mean2() in a separate file) now takes a distance argument (\"bray\" for rarefaction, \"aitchison\" for the Dirichlet workflow) and is the single implementation used by repeated_rarefaction(), dirichlet_ordination(), and test_threshold(). The old duplicate file/function is gone.\n    Fixed a couple of naming leftovers from this consolidation: an internal validation message in rep_mc_draws() referenced \"repeats\" instead of \"draws,\" and rep_mc_draws()'s cores argument is now actually wired to ALDEx2's useMC option (previously accepted but unused).\n\nTests\n\n    tests/testthat/test-dirichlet_ordination.R: covers the cloud/ellipse/color option combinations for dirichlet_ordination() on both bundled datasets, return-value structure, and the \"too few draws to draw an ellipse\" warning path.\n\nDocs\n\n    dirichlet_ordination() and rep_mc_draws() are now fully roxygen-documented; dirichlet_ordination() is exported",
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      "name": "v1.1.0",
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