{ "_id": "6a1f29b7b401979e73424182", "Type": "Package", "Package": "raretrans", "Title": "Bayesian Priors for Matrix Population Models", "Version": "1.0.5", "Authors@R": "c(person(given = \"Raymond\",\nfamily = \"Tremblay\",\nrole = c(\"aut\",\"cre\",\"cph\"),\nemail = \"raymond.tremblay@upr.edu\",\ncomment = c(ORCID = \"0000-0002-8588-4372\")),\nperson(given = \"Andrew\",\nfamily = \"Tyre\",\nrole = c(\"aut\",\"cph\"),\nemail = \"atyre2@gmail.com\",\ncomment = c(ORCID = \"0000-0001-9736-641X\")),\nperson(given = \"Maria-Eglee\",\nfamily = \"Perez\",\nrole = \"aut\",\nemail = \"mariaeglee@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8641-8405\")),\nperson(given = \"Sasha\",\nfamily = \"Tenhumberg\",\nrole = \"ctb\"))", "Description": "Provides functions to correct biased transition and\nfertility estimates in population projection matrices caused by\nsmall sample sizes. Small or short-term studies frequently\nproduce structural zeros (biologically possible transitions\nnever observed) and structural ones (transitions estimated at\n100% survival, stasis, or mortality that are biologically\nimplausible). Both distort matrix structure and bias estimates\nof population growth. Implements a multinomial-Dirichlet\nBayesian prior for transition probabilities and a Gamma-Poisson\nprior for reproduction, allowing analysts to incorporate prior\nbiological knowledge and regularise estimates from rare or\nunobserved events. Includes functions to compute marginal\nposterior credible intervals for all transition probabilities\n(transition_CrI()), visualise those intervals as point-range\nplots (plot_transition_CrI()), and display the full posterior\nbeta density for each matrix entry (plot_transition_density()).\nMethods are described in Tremblay et al. (2021)\n.", "URL": "https://atiretoo.github.io/raretrans/,\nhttps://github.com/atiretoo/raretrans", "BugReports": "https://github.com/atiretoo/raretrans/issues", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Config/roxygen2/version": "8.0.0", "Repository": "https://atiretoo.r-universe.dev", "Date/Publication": "2026-05-15 21:24:34 UTC", "RemoteUrl": "https://github.com/atiretoo/raretrans", "RemoteRef": "HEAD", "RemoteSha": "b1f2e5c4265ab96c495986ab7c63fb0e2acd161b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 22:00:20 UTC", "User": "root" }, "Author": "Raymond Tremblay [aut, cre, cph] (ORCID:\n),\nAndrew Tyre [aut, cph] (ORCID: ),\nMaria-Eglee Perez [aut] (ORCID:\n),\nSasha Tenhumberg [ctb]", "Maintainer": "Raymond Tremblay ", "MD5sum": "47fed09e06b9aecd01a67cf38e32f90d", "_user": "atiretoo", "_type": "src", "_file": "raretrans_1.0.5.tar.gz", "_fileid": "ea864c04a11458a9ef40f3aaa061e1e90fda737645ab284170090a29b8d9051b", "_filesize": 3250357, "_sha256": "ea864c04a11458a9ef40f3aaa061e1e90fda737645ab284170090a29b8d9051b", "_created": "2026-05-15T22:00:20.000Z", "_published": "2026-06-02T19:06:31.006Z", "_distro": "noble", "_jobs": [ { "job": 79150488142, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7027337747" }, { "job": 79150488691, "time": 132, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7027335379" }, { "job": 79150488290, "time": 106, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7027329835" }, { "job": 79150488218, "time": 79, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7027323812" }, { "job": 79150487652, "time": 306, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7027305843" }, { "job": 79150487216, "time": 114, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367283883" }, { "job": 79150488264, "time": 91, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7027326705" }, { "job": 79150488428, "time": 83, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7027324597" }, { "job": 79150488004, "time": 88, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7027325902" } ], "_buildurl": "https://github.com/r-universe/atiretoo/actions/runs/25943299659", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/atiretoo/raretrans", "_commit": { "id": "b1f2e5c4265ab96c495986ab7c63fb0e2acd161b", "author": "Raymond Tremblay ", "committer": "Raymond Tremblay ", "message": "cran: remove MultinomialCI overlay from vignette\n\nWin-builder reported MultinomialCI is no longer in CRAN's mainstream\n repositories. Removed the dependency entirely:\n\n - DESCRIPTION: remove MultinomialCI from Suggests\n - vignettes/transition_priors.Rmd: comment out the multinomial CI\n computation and the corresponding plot layers; preserve the original\n code as inline documentation so it can be restored from a non-CRAN\n source or replaced with DescTools::MultinomCI() in a future release\n - NEWS.md: update 1.0.5 bullets to reflect the change\n - cran-comments.md: note win-builder Status: OK\n\n Local check: 0 errors, 0 warnings, 0 notes\n Win-builder R-devel: Status OK\n", "time": 1778880274 }, "_maintainer": { "name": "Raymond Tremblay", "email": "raymond.tremblay@upr.edu", "orcid": "0000-0002-8588-4372" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "bslib", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "formatR", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "huxtable", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "popdemo", "role": "Suggests" }, { "package": "popbio", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" } ], "_owner": "atiretoo", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-12", "n": 3 }, { "week": "2026-13", "n": 14 }, { "week": "2026-14", "n": 1 }, { "week": "2026-15", "n": 15 }, { "week": "2026-16", "n": 1 }, { "week": "2026-20", "n": 5 } ], "_tags": [ { "name": "v1.0.3", "date": "2026-04-11" } ], "_stars": 0, "_contributors": [ { "user": "atyre2", "count": 212, "uuid": 2787883 }, { "user": "stenhumberg", "count": 11, "uuid": 17917214 }, { "user": "raymondltremblay", "count": 11, "uuid": 29467955 }, { "user": "trashbirdecology", "count": 4, "uuid": 9939381 }, { "user": "atiretoo", "count": 2, "uuid": 124002781 } ], "_userbio": { "uuid": 124002781, "type": "user", "name": "Drew Tyre", "description": "I'm currently a Resistance Modeler at Bayer Crop Science. In a past life I was a professor of wildlife ecology. I'm a dad, dog dad, and maker. " }, "_downloads": { "count": 429, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/raretrans" }, "_devurl": "https://github.com/atiretoo/raretrans", "_pkgdown": "https://atiretoo.github.io/raretrans/", "_searchresults": 24, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/raretrans.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/atiretoo/raretrans", "_realowner": "atiretoo", "_cranurl": true, "_releases": [ { "version": "1.0.4", "date": "2026-04-21" } ], "_exports": [ "fill_fertility", "fill_transitions", "get_state_vector", "plot_transition_CrI", "plot_transition_density", "rdirichlet", "run_app", "sim_transitions", "transition_CrI" ], "_datasets": [ { "name": "L_elto", "title": "Transition and recruitment data for _Lepanthes eltoroensis_", "object": "L_elto", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "POPNUM", "year", "seedlings", "adults", "fertility", "IND_NUM", "stage", "next_stage", "first_year", "last_year", "recruited", "died", "lifespan" ], "rows": 5233, "table": true, "tojson": true } ], "_help": [ { "page": "raretrans-package", "title": "raretrans: Bayesian Priors for Matrix Population Models", "topics": [ "raretrans-package", "raretrans" ] }, { "page": "fill_fertility", "title": "Combine prior and data for fertility matrix", "topics": [ "fill_fertility" ] }, { "page": "fill_transitions", "title": "Combine prior and data for transition matrix", "topics": [ "fill_transitions" ] }, { "page": "get_state_vector", "title": "Helper functions for generating different priors", "topics": [ "get_state_vector" ] }, { "page": "L_elto", "title": "Transition and recruitment data for _Lepanthes eltoroensis_", "topics": [ "L_elto" ] }, { "page": "plot_transition_CrI", "title": "Plot beta credible intervals for transition matrix entries", "topics": [ "plot_transition_CrI" ] }, { "page": "plot_transition_density", "title": "Plot posterior beta density curves for all transition matrix entries", "topics": [ "plot_transition_density" ] }, { "page": "rdirichlet", "title": "Dirichlet distributed random numbers", "topics": [ "rdirichlet" ] }, { "page": "run_app", "title": "Run the interactive Shiny application for Bayesian transition priors", "topics": [ "run_app" ] }, { "page": "sim_transitions", "title": "Simulate population projection matrices", "topics": [ "sim_transitions" ] }, { "page": "transition_CrI", "title": "Calculate beta credible intervals for all transition matrix entries", "topics": [ "transition_CrI" ] } ], "_readme": "https://github.com/atiretoo/raretrans/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "quick_start.Rmd", "filename": "quick_start.html", "title": "01 Quick start: credible intervals for transition probabilities", "author": "Raymond Tremblay", "engine": "knitr::rmarkdown", "headings": [ "What this vignette shows", "The data", "Build the input matrices", "Compute credible intervals", "Visualise", "Including the dead fate", "Excluding the dead fate", "Next steps", "Reference" ], "created": "2026-03-25 19:17:29", "modified": "2026-03-25 19:17:29", "commits": 1 }, { "source": "introduction.Rmd", "filename": "introduction.html", "title": "02 Introduction to raretrans", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Biased estimates from small samples", "The example population: Chamaedorea elegans", "Providing the stage-population vector N", "Part 1: Observed matrix and its limitations", "Part 2: Adding priors with fill_transitions()", "Uniform (non-informative) prior", "Informative (expert) prior", "Adjusting prior weight", "Part 3: Adding priors for fecundity with fill_fertility()", "Combined posterior matrix", "Part 4: Other return types", "Augmented fate matrix (TN)", "Full projection matrix A", "Alpha and beta vectors (fertility)", "Part 5: Simulating matrices and credible intervals on $\\lambda$", "Part 6: Credible intervals on individual transition probabilities", "Computing credible intervals with transition_CrI()", "Visualising credible intervals with plot_transition_CrI()", "Visualising the full posterior density with plot_transition_density()", "Summary", "References" ], "created": "2026-03-25 16:09:00", "modified": "2026-03-27 21:34:06", "commits": 3 }, { "source": "onepopperiod.Rmd", "filename": "onepopperiod.html", "title": "03 Working with a single population and transition", "engine": "knitr::rmarkdown", "headings": [ "Part I: Obtaining the projection matrix", "Step 1: Load and munge the single population data for L. elto", "Step 2: Obtain starting number of individuals per stage", "Part 2: Using priors to incorporate rare transitions", "Use uninformative priors", "Transition matrix", "Fertility matrix", "Other options for argument returnType", "Incorporate informative priors", "Part 3: Obtain Credible Intervals", "Obtain CI for indvidual matrix entries", "Credible intervals on $\\lambda$" ], "created": "2018-06-08 18:44:18", "modified": "2026-04-11 14:39:24", "commits": 24 }, { "source": "credible_intervals.Rmd", "filename": "credible_intervals.html", "title": "04 Credible intervals for transition probabilities: Cypripedium calceolus", "author": "Raymond Tremblay", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The Cypripedium calceolus transition matrix (matU)", "Computing credible intervals", "Visualising with plot_transition_CrI()", "Including the dead fate (default)", "Excluding the dead fate", "Effect of prior weight", "Visualising full posterior densities", "With uninformative prior", "Effect of prior weight on densities", "Summary", "References" ], "created": "2026-03-25 19:17:29", "modified": "2026-03-25 19:17:29", "commits": 1 }, { "source": "transition_priors.Rmd", "filename": "transition_priors.html", "title": "05 Effect of prior information on transition probabilities and fertility", "author": "Drew Tyre", "engine": "knitr::rmarkdown", "headings": [ "Borrowing strength", "The matrix", "Ignore the problem", "Fill in including constraints on transitions", "Fill in using uninformative priors on fertility", "Effects of informative priors", "Interactive Exploration", "Obtaining credible intervals on vital rates and $\\lambda$", "References" ], "created": "2017-07-16 22:00:26", "modified": "2026-05-15 21:24:34", "commits": 61 }, { "source": "animal_matrices.Rmd", "filename": "animal_matrices.html", "title": "06 Matrices of animal populations", "engine": "knitr::rmarkdown", "headings": [ "Snail kites", "Background", "Study design and data sources", "Survival values", "Why a Beta distribution?", "Moment matching: from mean and SD to $\\alpha$ and $\\beta$", "Interpreting the effective sample size", "Comparing Beta and normal priors", "Reproductive rates", "Components of reproduction", "Nest success as a Beta variable", "Young per successful nest", "Comparing prior sources", "Interpretation", "Building the matrices", "Propagating uncertainty to $\\lambda$", "Connection to raretrans", "Literature cited" ], "created": "2020-07-24 15:48:30", "modified": "2026-04-03 18:29:51", "commits": 15 } ], "_score": 6.237543738142874, "_indexed": true, "_nocasepkg": "raretrans", "_universes": [ "atiretoo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.5", "date": "2026-05-15T22:02:45.000Z", "distro": "noble", "commit": "b1f2e5c4265ab96c495986ab7c63fb0e2acd161b", "fileid": "3ee0ffe9a68f9fffed8cc853fc90115899a97f5c27133e7ba289f0747ee5bada", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/atiretoo/actions/runs/25943299659" }, { "r": "4.6.0", "os": "linux", "version": "1.0.5", "date": "2026-05-15T22:02:35.000Z", "distro": "noble", 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