{ "_id": "6a17fc5facfb0bcc41daa63a", "Package": "MixSIAR", "Title": "Bayesian Mixing Models in R", "Version": "3.1.12", "Authors@R": "c(\nperson(\"Brian\", \"Stock\", email = \"bstock09@gmail.com\", role = c(\"cre\",\"aut\")),\nperson(\"Brice\", \"Semmens\", email = \"semmens@ucsd.edu\", role = \"aut\"),\nperson(\"Eric\", \"Ward\", role = \"ctb\"),\nperson(\"Andrew\", \"Parnell\", role = \"ctb\"),\nperson(\"Andrew\", \"Jackson\", role = \"ctb\"),\nperson(\"Donald\", \"Phillips\", role = \"ctb\"))", "Description": "Creates and runs Bayesian mixing models to analyze\nbiological tracer data (i.e. stable isotopes, fatty acids),\nwhich estimate the proportions of source (prey) contributions\nto a mixture (consumer). 'MixSIAR' is not one model, but a\nframework that allows a user to create a mixing model based on\ntheir data structure and research questions, via options for\nfixed/ random effects, source data types, priors, and error\nterms. 'MixSIAR' incorporates several years of advances since\n'MixSIR' and 'SIAR'.", "SystemRequirements": "JAGS (>= 4.3)", "URL": "https://github.com/brianstock/MixSIAR", "BugReports": "https://github.com/brianstock/MixSIAR/issues", "Encoding": "UTF-8", "License": "GPL-3", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 08:23:46 UTC", "User": "root" }, "Author": "Brian Stock [cre, aut], Brice Semmens [aut], Eric Ward [ctb],\nAndrew Parnell [ctb], Andrew Jackson [ctb], Donald Phillips\n[ctb]", "Maintainer": "Brian Stock ", "Config/pak/sysreqs": "jags", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2020-10-20 06:00:44 UTC", "RemoteUrl": "https://github.com/cran/MixSIAR", "RemoteRef": "HEAD", "RemoteSha": "01ee546e4207a6aa5a873fe3fdbbf7f18bf2b231", "MD5sum": "2455d16f5202c33184962dc4241a750c", "_user": "cran", "_type": "src", "_file": "MixSIAR_3.1.12.tar.gz", "_fileid": 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"author": "Brian Stock ", "committer": "cran-robot ", "message": "version 3.1.12\n", "time": 1603173644 }, "_maintainer": { "name": "Brian Stock", "email": "bstock09@gmail.com", "login": "brianstock", "description": "", "uuid": 5124211 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "ggplot2", "version": ">= 3.3.0", "role": "Imports" }, { "package": "R2jags", "version": ">= 0.5-7", "role": "Imports" }, { "package": "MASS", "version": ">= 7.3", "role": "Imports" }, { "package": "RColorBrewer", "version": ">= 1.1", "role": "Imports" }, { "package": "reshape", "version": ">= 0.8.7", "role": "Imports" }, { "package": "reshape2", "version": ">= 1.4.3", "role": "Imports" }, { "package": "lattice", "version": ">= 0.20-35", "role": "Imports" }, { "package": "MCMCpack", "version": ">= 1.4-2", "role": "Imports" }, { "package": "ggmcmc", "version": ">= 1.1", "role": "Imports" }, { "package": "coda", "version": ">= 0.19-1", 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"extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MixSIAR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/brianstock/mixsiar", "_realowner": "brianstock", "_cranurl": false, "_releases": [ { "version": "3.1.6", "date": "2016-06-25" }, { "version": "3.1.7", "date": "2016-08-23" }, { "version": "3.1.9", "date": "2018-03-30" }, { "version": "3.1.10", "date": "2018-04-13" }, { "version": "3.1.11", "date": "2020-05-13" }, { "version": "3.1.12", "date": "2020-10-20" } ], "_exports": [ "calc_area", "combine_sources", "compare_models", "load_discr_data", "load_mix_data", "load_source_data", "output_JAGS", "plot_continuous_var", "plot_data", "plot_data_one_iso", "plot_data_two_iso", "plot_intervals", "plot_prior", "run_model", "summary_stat", "write_JAGS_model" ], "_help": [ { "page": "calc_area", "title": "Calculate the normalized surface area of the source convex hull", "topics": [ "calc_area" ] }, { "page": "combine_sources", "title": "Combine sources from a finished MixSIAR model (_a posteriori_)", "topics": [ "combine_sources" ] }, { "page": "compare_models", "title": "Compare the predictive accuracy of 2 or more MixSIAR models", "topics": [ "compare_models" ] }, { "page": "load_discr_data", "title": "Load trophic discrimination factor (TDF) data", "topics": [ "load_discr_data" ] }, { "page": "load_mix_data", "title": "Load mixture data", "topics": [ "load_mix_data" ] }, { "page": "load_source_data", "title": "Load source data", "topics": [ "load_source_data" ] }, { "page": "mixsiar_env", "title": "mixsiar", "topics": [ "mixsiar_env" ] }, { "page": "output_JAGS", "title": "Process mixing model output from JAGS", "topics": [ "output_JAGS" ] }, { "page": "plot_continuous_var", "title": "Plot proportions by a continuous covariate", "topics": [ "plot_continuous_var" ] }, { "page": "plot_data", "title": "Plot biotracer data", "topics": [ "plot_data" ] }, { "page": "plot_data_one_iso", "title": "Plot biotracer data (1-D)", "topics": [ "plot_data_one_iso" ] }, { "page": "plot_data_two_iso", "title": "Plot biotracer data (2-D)", "topics": [ "plot_data_two_iso" ] }, { "page": "plot_intervals", "title": "Plot posterior uncertainty intervals from a MixSIAR model", "topics": [ "plot_intervals" ] }, { "page": "plot_prior", "title": "Plot prior", "topics": [ "plot_prior" ] }, { "page": "run_model", "title": "Run the JAGS model", "topics": [ "run_model" ] }, { "page": "summary_stat", "title": "Summary statistics from posterior of MixSIAR model", "topics": [ "summary_stat" ] }, { "page": "write_JAGS_model", "title": "Write the JAGS model file", "topics": [ "write_JAGS_model" ] } ], "_readme": "https://github.com/cran/MixSIAR/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "bayesplot", "boot", "checkmate", "cli", "coda", "cpp11", "crayon", "distributional", "dplyr", "farver", "forcats", "generics", "GGally", "ggmcmc", "ggplot2", "ggridges", "ggstats", "glue", "gtable", "hms", "isoband", "labeling", "lattice", "lifecycle", "loo", "magrittr", "MASS", "Matrix", "MatrixModels", "matrixStats", "mcmc", "MCMCpack", "numDeriv", "patchwork", "pillar", "pkgconfig", "plyr", "posterior", "prettyunits", "progress", "purrr", "quantreg", "R2jags", "R2WinBUGS", "R6", "RColorBrewer", "Rcpp", "reshape", "reshape2", "rjags", "rlang", "S7", "scales", "sp", "SparseM", "splancs", "stringi", "stringr", "survival", "tensorA", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libjags", "package": "jags", "headers": "jags", "source": "jags", "version": "4.3.2-2.2404.0", "name": "jags", "homepage": "https://mcmc-jags.sourceforge.io", "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary\nJAGS is Just Another Gibbs Sampler. It is a program for analysis of\nBayesian hierarchical models using Markov Chain Monte Carlo (MCMC)\nsimulation not wholly unlike BUGS.\n\nJAGS was written with three aims in mind:\n* To have an engine for the BUGS language that runs on Unix\n* To be extensible, allowing users to write their own functions,\ndistributions and samplers.\n* To be a plaftorm for experimentation with ideas in Bayesian modelling\n\nThis package contains the 'jags' binary as well as the associated\nshared library modules loaded by the binary." }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "wolves_ex.Rmd", "filename": "wolves_ex.html", "title": "Ex 1: Wolves", "engine": "knitr::rmarkdown", "headings": [ "Wolves Example", "Load MixSIAR package", "Load mixture data", "Load source data", "Load discrimination data", "Plot data", "Calculate convex hull area", "Plot prior", "Write JAGS model file", "Run model", "Analyze diagnostics and output" ], "created": "2016-06-25 19:07:27", "modified": "2020-10-20 06:00:44", "commits": 4 }, { "source": "geese_ex.Rmd", "filename": "geese_ex.html", "title": "Ex 2: Geese", "engine": "knitr::rmarkdown", "headings": [ "Geese Example", "Load MixSIAR package", "Load mixture data", "Load source data", "Load discrimination data", "Plot data", "Calculate convex hull area", "Plot prior", "Write JAGS model file", "Run model", "Analyze diagnostics and output" ], "created": "2016-06-25 19:07:27", "modified": "2020-10-20 06:00:44", "commits": 4 }, { "source": "lake_ex.Rmd", "filename": "lake_ex.html", "title": "Ex 3: Lake", "engine": "knitr::rmarkdown", "headings": [ "Lake Example", "Load MixSIAR package", "Load mixture data", "Load source data", "Load discrimination data", "Plot data", "Calculate convex hull area", "Plot prior", "Write JAGS model file", "Run model", "Analyze diagnostics and output" ], "created": "2016-06-25 19:07:27", "modified": "2020-10-20 06:00:44", "commits": 4 }, { "source": "killerwhale_ex.Rmd", "filename": "killerwhale_ex.html", "title": "Ex 4: Killer Whale", "engine": "knitr::rmarkdown", "headings": [ "Killer Whale Example", "Load MixSIAR package", "Load mixture data", "Load source data", "Load discrimination data", "Plot data", "Run the model with uninformative prior", "Run the model with informative prior" ], "created": "2016-06-25 19:07:27", "modified": "2020-10-20 06:00:44", "commits": 4 }, { "source": "isopod_ex.Rmd", "filename": "isopod_ex.html", "title": "Ex 5: Isopod", "engine": "knitr::rmarkdown", "headings": [ "Isopod Example", "Load MixSIAR package", "Load mixture data", "Load source data", "Load discrimination data", "Plot data", "Plot prior", "Write JAGS model file", "Run model", "Analyze diagnostics and output" ], "created": "2016-06-25 19:07:27", "modified": "2020-10-20 06:00:44", "commits": 4 }, { "source": "cladocera_ex.Rmd", "filename": "cladocera_ex.html", "title": "Ex 6: Cladocera", "engine": "knitr::rmarkdown", "headings": [ "Cladocera Example", "Load MixSIAR package", "Load mixture data", "Load source data", "Load discrimination data", "Plot data", "Plot prior", "Write JAGS model file", "Run model", "Analyze diagnostics and output" ], "created": "2016-06-25 19:07:27", "modified": "2020-10-20 06:00:44", "commits": 5 } ], "_score": 5.707570176097937, "_indexed": false, "_nocasepkg": "mixsiar", "_universes": [ "cran" ], "_indexurl": "https://brianstock.r-universe.dev/MixSIAR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.1.12", "date": "2026-05-28T08:26:13.000Z", "distro": "noble", "commit": "01ee546e4207a6aa5a873fe3fdbbf7f18bf2b231", "fileid": "43e6d19f9fd12dd04aeafb1793964fd5b19935b798b3874c096fb7ae2d42d1dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26563331148" }, { "r": "4.6.0", "os": "linux", "version": "3.1.12", "date": "2026-05-28T08:26:18.000Z", "distro": "noble", "commit": "01ee546e4207a6aa5a873fe3fdbbf7f18bf2b231", "fileid": "5a6c12810e0a603f710dce7022c7f72396051eae4a92d5a6ca74753662f4d493", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26563331148" }, { "r": "4.6.0", "os": "wasm", "version": "3.1.12", "date": "2026-05-28T08:26:48.000Z", "commit": "01ee546e4207a6aa5a873fe3fdbbf7f18bf2b231", "fileid": "06f07e5c3414da1cd6574f64bd1183d8ac5f0ceeb316c9078a51ccdc8b5e8053", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26563331148" } ] }