{ "_id": "6a103d07acfb0bcc41c9c1e8", "Package": "mpmsim", "Title": "Simulation of Matrix Population Models with Defined Life History\nCharacteristics", "Version": "3.3.0", "Authors@R": "person(\"Owen\", \"Jones\", , \"jones@biology.sdu.dk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5720-4686\"))", "Description": "Allows users to simulate matrix population models with\nparticular characteristics based on aspects of life history\nsuch as mortality trajectories and fertility trajectories. Also\nallows the exploration of sampling error due to small sample\nsize.", "License": "CC BY-SA 4.0", "URL": "https://jonesor.github.io/mpmsim/", "BugReports": "https://github.com/jonesor/mpmsim/issues/", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-GB", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libx11-dev", "Repository": "https://jonesor.r-universe.dev", "Date/Publication": "2026-04-28 21:15:30 UTC", "RemoteUrl": "https://github.com/jonesor/mpmsim", "RemoteRef": "HEAD", "RemoteSha": "40c5b0a4c414263a282ff644b83a39151429a02d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 09:57:43 UTC", "User": "root" }, "Author": "Owen Jones [aut, cre] (ORCID: )", "Maintainer": "Owen Jones ", "MD5sum": "fd13c569426879344e59a47cfda88694", "_user": "jonesor", "_type": "src", "_file": "mpmsim_3.3.0.tar.gz", "_fileid": "0e97e0ad25a1740540742291224818ec56bd01a9a088f2c3d3b4153c1de498be", "_filesize": 797930, "_sha256": "0e97e0ad25a1740540742291224818ec56bd01a9a088f2c3d3b4153c1de498be", "_created": "2026-05-11T09:57:43.000Z", "_published": "2026-05-22T11:24:55.775Z", "_distro": "noble", "_jobs": [ { "job": 77369943358, "time": 186, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6915552500" }, { "job": 77369942984, "time": 185, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6915554558" }, { "job": 77369943184, "time": 102, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6915526686" }, { "job": 77369942992, "time": 153, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6915541942" }, { "job": 77369942288, "time": 221, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6915492633" }, { "job": 77369942333, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159334173" }, { "job": 77369942913, "time": 133, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6915535768" }, { "job": 77369943274, "time": 136, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6915537476" }, { "job": 77369943484, "time": 141, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6915538448" } ], "_buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jonesor/mpmsim", "_commit": { "id": "40c5b0a4c414263a282ff644b83a39151429a02d", "author": "Owen Jones ", "committer": "GitHub ", "message": "Merge pull request #30 from jonesor/claude/check-r-package-errors-AzD5h\n\nReduce GitHub Actions usage", "time": 1777410930 }, "_maintainer": { "name": "Owen Jones", "email": "jones@biology.sdu.dk", "login": "jonesor", "uuid": 2965464, "orcid": "0000-0001-5720-4686" }, "_registered": true, "_dependencies": [ { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "popbio", "role": "Imports" }, { "package": "popdemo", "role": "Imports" }, { "package": "Rage", "role": "Imports" }, { "package": "Rcompadre", "role": "Imports" }, { "package": "reshape", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "jonesor", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-21", "n": 3 }, { "week": "2025-23", "n": 11 }, { "week": "2025-27", "n": 2 }, { "week": "2026-17", "n": 10 }, { "week": "2026-18", "n": 2 } ], "_tags": [ { "name": "v3.3.0", "date": "2026-04-24" }, { "name": "v3.1.0", "date": "2026-04-28" }, { "name": "v3.2.1", "date": "2026-04-28" } ], "_stars": 5, "_contributors": [ { "user": "jonesor", "count": 430, "uuid": 2965464 }, { "user": "claude", "count": 6, "uuid": 81847 } ], "_userbio": { "uuid": 2965464, "type": "user", "name": "Owen Jones", "description": "I'm an Associate Professor working on life history evolution, senescence/aging and population dynamics at the University of Southern Denmark." }, "_downloads": { "count": 401, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mpmsim" }, "_devurl": "https://github.com/jonesor/mpmsim", "_pkgdown": "https://jonesor.github.io/mpmsim/", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mpmsim.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jonesor/mpmsim", "_realowner": "jonesor", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2023-04-18" }, { "version": "1.1.0", "date": "2023-09-29" }, { "version": "2.0.0", "date": "2024-01-15" }, { "version": "3.0.0", "date": "2024-07-01" }, { "version": "3.1.0", "date": "2024-10-12" }, { "version": "3.2.0", "date": "2025-03-06" }, { "version": "3.2.1", "date": "2025-06-05" }, { "version": "3.3.0", "date": "2026-04-24" } ], "_exports": [ "add_mpm_error", "calculate_errors", "compute_ci", "compute_ci_U", "driven_vital_rate", "make_leslie_mpm", "model_fecundity", "model_fertility", "model_mortality", "model_reproduction", "model_survival", "plot_matrix", "rand_lefko_mpm", "rand_lefko_set", "rand_leslie_set", "reorganise_matrices", "summarise_mpms" ], "_help": [ { "page": "add_mpm_error", "title": "Add sampling error to matrix population models (MPMs) based on expected values of transition rates and sample sizes", "concept": [ "errors" ], "topics": [ "add_mpm_error" ] }, { "page": "calculate_errors", "title": "Calculate error (standard error or 95%CI) in elements of a matrix population model.", "concept": [ "errors" ], "topics": [ "calculate_errors" ] }, { "page": "compute_ci", "title": "Compute 95% confidence intervals for derived estimates from a matrix population model", "concept": [ "errors" ], "topics": [ "compute_ci" ] }, { "page": "compute_ci_U", "title": "Compute 95% confidence intervals for derived estimates from the U submatrix of a matrix population model", "concept": [ "errors" ], "topics": [ "compute_ci_U" ] }, { "page": "driven_vital_rate", "title": "Calculate driven vital rates", "concept": [ "drivers" ], "topics": [ "driven_vital_rate" ] }, { "page": "make_leslie_mpm", "title": "Create a Leslie matrix population model", "concept": [ "Leslie matrices" ], "topics": [ "make_leslie_mpm" ] }, { "page": "model_fecundity", "title": "Model reproductive output with age using set functional forms", "concept": [ "trajectories" ], "topics": [ "model_fecundity", "model_fertility", "model_reproduction" ] }, { "page": "model_survival", "title": "Model mortality hazard, survivorship and age-specific survival probability using a mortality model", "concept": [ "trajectories" ], "topics": [ "model_mortality", "model_survival" ] }, { "page": "plot_matrix", "title": "Plot a matrix as a heatmap", "concept": [ "utility" ], "topics": [ "plot_matrix" ] }, { "page": "rand_lefko_mpm", "title": "Generate random Lefkovitch matrix population models (MPMs) based on life history archetypes", "concept": [ "Lefkovitch matrices" ], "topics": [ "rand_lefko_mpm" ] }, { "page": "rand_lefko_set", "title": "Generate lists of Lefkovitch matrix population models (MPMs) based on life history archetypes", "concept": [ "Lefkovitch matrices" ], "topics": [ "rand_lefko_set" ] }, { "page": "rand_leslie_set", "title": "Generate a set of random Leslie Matrix Population Models", "concept": [ "Leslie matrices" ], "topics": [ "rand_leslie_set" ] }, { "page": "reorganise_matrices", "title": "Reorganise Matrix Population Models", "concept": [ "Leslie matrices" ], "topics": [ "reorganise_matrices" ] }, { "page": "summarise_mpms", "title": "Summarise Matrix Population Models", "concept": [ "utility" ], "topics": [ "summarise_mpms" ] } ], "_readme": "https://github.com/jonesor/mpmsim/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bit", "bit64", "bslib", "cachem", "cli", "clipr", "coda", "cpp11", "crayon", "DiagrammeR", "digest", "dplyr", "evaluate", "expm", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "igraph", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixModels", "mcmc", "MCMCpack", "memoise", "mime", "pillar", "pkgconfig", "plyr", "popbio", "popdemo", "prettyunits", "progress", "purrr", "quantreg", "R6", "Rage", "rappdirs", "RColorBrewer", "Rcompadre", "Rcpp", "readr", "reshape", "rlang", "rmarkdown", "rstudioapi", "S7", "sass", "scales", "SparseM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "utf8", "vctrs", "viridisLite", "visNetwork", "vroom", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "generating_lefkovitch_models.Rmd", "filename": "generating_lefkovitch_models.html", "title": "Generating Lefkovitch models", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Aims", "Preparation", "1. Life cycle archetypes and generating an MPM", "2. Generate a random Lefkovitch MPM based on an archetype", "3. Generate sets of Lefkovitch matrices", "4. Constraining the output matrices", "Conclusion" ], "created": "2024-10-12 20:13:06", "modified": "2025-03-06 11:23:51", "commits": 3 }, { "source": "generating_leslie_models.Rmd", "filename": "generating_leslie_models.html", "title": "Generating Leslie models", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Aims", "Preparation", "1. Functional forms of mortality and reproduction", "2. Trajectories of mortality and reproductive output, and production of life tables", "3. From life table to MPM", "4. Producing sets of MPMs based on defined model characteristics", "Conclusion" ], "created": "2024-10-12 20:13:06", "modified": "2025-07-01 20:43:49", "commits": 6 }, { "source": "sampling_error_propagation.Rmd", "filename": "sampling_error_propagation.html", "title": "Sampling error and its propagation", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Aims", "Estimate 95% Confidence Intervals", "Sample sizes that vary across the MPM", "Exploring the impact of sample size", "Conclusion", "Addendum" ], "created": "2024-10-12 20:13:06", "modified": "2025-03-06 11:23:51", "commits": 5 } ], "_score": 5.615423952885944, "_indexed": true, "_nocasepkg": "mpmsim", "_universes": [ "jonesor" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.3.0", "date": "2026-05-11T10:00:13.000Z", "distro": "noble", "commit": "40c5b0a4c414263a282ff644b83a39151429a02d", "fileid": "69468a8eaf2c252adee1689be907de072942d14ba51e73d7606465035bed30ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507" }, { "r": "4.6.0", "os": "linux", "version": "3.3.0", "date": "2026-05-11T10:00:19.000Z", "distro": "noble", "commit": "40c5b0a4c414263a282ff644b83a39151429a02d", "fileid": "4fb319865429974db49de3ae156edceaac26afb13eee161032247a4e351e979d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507" }, { "r": "4.5.3", "os": "mac", "version": "3.3.0", "date": "2026-05-11T09:59:15.000Z", "commit": "40c5b0a4c414263a282ff644b83a39151429a02d", "fileid": "41ec20d5805964392d11951c9f48c406e144befdb85328de9659e15706624b5d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507" }, { "r": "4.6.0", "os": "mac", "version": "3.3.0", "date": "2026-05-11T09:59:39.000Z", "commit": "40c5b0a4c414263a282ff644b83a39151429a02d", "fileid": "df546fa4ba01737033775d04158432c2e3498e7232d515cf61d9a9335e6ce72b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507" }, { "r": "4.7.0", "os": "win", "version": "3.3.0", "date": "2026-05-11T09:59:12.000Z", "commit": "40c5b0a4c414263a282ff644b83a39151429a02d", "fileid": "652be409e6d09bd049e383adbdfd7673917bcc2e6b50f742c02d867dc5f30b1e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507" }, { "r": "4.5.3", "os": "win", "version": "3.3.0", "date": "2026-05-11T09:59:22.000Z", "commit": "40c5b0a4c414263a282ff644b83a39151429a02d", "fileid": "db43f6ccafc8cb2a4f978ef43ebf6767fbfdcaec901214e94e3dbab2d37f8113", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507" }, { "r": "4.6.0", "os": "win", "version": "3.3.0", "date": "2026-05-11T09:59:17.000Z", "commit": "40c5b0a4c414263a282ff644b83a39151429a02d", "fileid": "ed814f844a0ab0f716e9360e715135859825fbfe0911e6f84979106c988c0b8a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507" }, { "r": "4.6.0", "os": "wasm", "version": "3.3.0", "date": "2026-05-22T11:24:32.000Z", "commit": "40c5b0a4c414263a282ff644b83a39151429a02d", "fileid": "15f35d4919736cdda52565c2e0f14af4c6e413a717e375d881ca12a5fecb58f8", "status": "success", "buildurl": "https://github.com/r-universe/jonesor/actions/runs/25663116507" } ] }