{ "_id": "6a495054f6c47c441949abc8", "Type": "Package", "Package": "BayesGrowth", "Title": "Estimate Fish Growth Using MCMC Analysis", "Date": "2023-11-13", "Version": "1.0.0.9000", "Authors@R": "person(\"Jonathan\", \"Smart\", \nemail = \"jonsmartphd@gmail.com\",\nrole = c(\"aut\", \"cre\", \"ctb\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-2070-3208\"))", "Maintainer": "Jonathan Smart ", "Description": "Estimate fish length-at-age models using MCMC analysis\nwith 'rstan' models. This package allows a multimodel approach\nto growth fitting to be applied to length-at-age data and is\nsupported by further analyses to determine model selection and\nresult presentation. The core methods of this package are\npresented in Smart and Grammer (2021) \"Modernising fish and\nshark growth curves with Bayesian length-at-age models\". PLOS\nONE 16(2): e0246734 .", "License": "GPL-3", "URL": "https://github.com/jonathansmart/BayesGrowth", "BugReports": "https://github.com/jonathansmart/BayesGrowth/issues", "SystemRequirements": "GNU make", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "Biarch": "true", "Config/pak/sysreqs": "make libicu-dev libxml2-dev libx11-dev", "Repository": "https://jonathansmart.r-universe.dev", "Date/Publication": "2026-06-30 02:29:42 UTC", "RemoteUrl": "https://github.com/jonathansmart/bayesgrowth", "RemoteRef": "HEAD", "RemoteSha": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-30 03:43:18 UTC", "User": "root" }, "Author": "Jonathan Smart [aut, cre, ctb, cph] (ORCID:\n)", "_user": "jonathansmart", "_type": "src", "_file": "BayesGrowth_1.0.0.9000.tar.gz", "_fileid": "https://r2.ropensci.org/9328485a524ed84db02ce3bd41c824d7a2156d3d6786a3e49dd1394034212809", "_filesize": 1648227, "_sha256": "9328485a524ed84db02ce3bd41c824d7a2156d3d6786a3e49dd1394034212809", "_expires": "2026-10-12T18:26:26.000Z", "_created": "2026-06-30T03:43:18.000Z", "_published": "2026-07-04T18:26:28.060Z", "_jobs": [ { "job": 85156205889, "time": 381, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7970553107" }, { "job": 85156206070, "time": 444, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7970564489" }, { "job": 85156205996, "time": 394, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "7970555400" }, { "job": 85156205991, "time": 395, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "7970555231" }, { "job": 85156206022, "time": 319, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7970534145" }, { "job": 85156205982, "time": 816, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7970629279" }, { "job": 85156206047, "time": 413, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "7970551150" }, { "job": 85156205960, "time": 667, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "7970601418" }, { "job": 85156205866, "time": 495, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "7970475459" }, { "job": 85156205892, "time": 175, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 85156205855, "time": 445, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7970564927" }, { "job": 85156206074, "time": 427, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7970561470" }, { "job": 85156206082, "time": 470, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "7970569935" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180", "_status": "success", "_upstream": "https://github.com/jonathansmart/bayesgrowth", "_commit": { "id": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "author": "Jonathan Smart ", "committer": "Jonathan Smart ", "message": "test push\n", "time": 1782786582 }, "_maintainer": { "name": "Jonathan Smart", "email": "jonsmartphd@gmail.com", "login": "jonathansmart", "description": "", "uuid": 20293486, "orcid": "0000-0003-2070-3208" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4.0", "role": "Depends" }, { "package": "BH", "version": ">= 1.66.0", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "LinkingTo" }, { "package": "RcppEigen", "version": ">= 0.3.3.3.0", "role": "LinkingTo" }, { "package": "RcppParallel", "version": ">= 5.0.1", "role": "LinkingTo" }, { "package": "rstan", "version": ">= 2.18.1", "role": "LinkingTo" }, { "package": "StanHeaders", "version": ">= 2.18.0", "role": "LinkingTo" }, { "package": "AquaticLifeHistory", "role": "Imports" }, { "package": "bayesplot", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "loo", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "Imports" }, { "package": "RcppParallel", "version": ">= 5.0.1", "role": "Imports" }, { "package": "rstan", "version": ">= 2.18.1", "role": "Imports" }, { "package": "rstantools", "version": ">= 2.3.1.1", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidybayes", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "jonathansmart", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-27", "n": 1 } ], "_tags": [], "_stars": 13, "_userbio": { "uuid": 20293486, "type": "user", "name": "Jonathan Smart", "followers": 25 }, "_downloads": { "count": 256, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BayesGrowth" }, "_devurl": "https://github.com/jonathansmart/bayesgrowth", "_searchresults": 9, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/BayesGrowth.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jonathansmart/bayesgrowth", "_realowner": "jonathansmart", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2023-11-21" } ], "_exports": [ "Calc_Gompertz_LAA", "Calc_Logistic_LAA", "Calc_VBGF_LAA", "Calculate_MCMC_growth_curve", "Compare_Growth_Models", "Estimate_MCMC_Growth", "Get_MCMC_parameters" ], "_datasets": [ { "name": "example_data", "title": "Example length-at-age data", "object": "example_data", "class": [ "data.frame" ], "fields": [ "Length", "Age" ], "rows": 789, "table": true, "tojson": true }, { "name": "Looic_example_results", "title": "Example MCMC model comparison outputs outputs", "object": "Looic_example_results", "class": [ "data.frame" ], "fields": [ "Model", "elpd_diff", "se_diff", "elpd_loo", "se_elpd_loo", "p_loo", "se_p_loo", "looic", "se_looic", "looic_Weight" ], "rows": 3, "table": true, "tojson": true }, { "name": "MCMC_example_results", "title": "Example MCMC model outputs", "object": "MCMC_example_results", "class": [ "stanfit" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "BayesGrowth", "title": "BayesGrowth", "topics": [ "BayesGrowth" ] }, { "page": "Calc_Gompertz_LAA", "title": "Calc_Gompertz_LAA", "topics": [ "Calc_Gompertz_LAA" ] }, { "page": "Calc_Logistic_LAA", "title": "Calc_Logistic_LAA", "topics": [ "Calc_Logistic_LAA" ] }, { "page": "Calc_VBGF_LAA", "title": "Calc_VBGF_LAA", "topics": [ "Calc_VBGF_LAA" ] }, { "page": "Calculate_MCMC_growth_curve", "title": "Calculate_MCMC_growth_curve", "topics": [ "Calculate_MCMC_growth_curve" ] }, { "page": "Compare_Growth_Models", "title": "Compare_Growth_Models", "topics": [ "Compare_Growth_Models" ] }, { "page": "Estimate_MCMC_Growth", "title": "Estimate_MCMC_Growth", "topics": [ "Estimate_MCMC_Growth" ] }, { "page": "example_data", "title": "Example length-at-age data", "topics": [ "example_data" ] }, { "page": "Get_MCMC_parameters", "title": "Get_MCMC_parameters", "topics": [ "Get_MCMC_parameters" ] }, { "page": "Looic_example_results", "title": "Example MCMC model comparison outputs outputs", "topics": [ "Looic_example_results" ] }, { "page": "MCMC_example_results", "title": "Example MCMC model outputs", "topics": [ "MCMC_example_results" ] } ], "_readme": "https://github.com/jonathansmart/bayesgrowth/raw/HEAD/README.md", "_rundeps": [ "abind", "AquaticLifeHistory", "arrayhelpers", "backports", "bayesplot", "BH", "bit", "bit64", "broom", "callr", "checkmate", "cli", "clipr", "coda", "cpp11", "crayon", "data.table", "desc", "distributional", "dplyr", "farver", "generics", "ggdist", "ggplot2", "ggridges", "glue", "gridExtra", "gtable", "hms", "inline", "insight", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "loo", "magrittr", "MASS", "Matrix", "matrixStats", "minpack.lm", "MuMIn", "nlme", "numDeriv", "otel", "pillar", "pkgbuild", "pkgconfig", "plyr", "posterior", "prettyunits", "processx", "progress", "ps", "purrr", "quadprog", "QuickJSR", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "readr", "reshape2", "rlang", "rlist", "rstan", "rstantools", "S7", "scales", "StanHeaders", "stringi", "stringr", "svUnit", "tensorA", "tibble", "tidybayes", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "XML", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "MCMC-example.Rmd", "filename": "MCMC-example.html", "title": "Estimate growth using MCMC", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Usage", "Outputs and compatibility with rstan and bayesplot packages", "Summaries", "Chain convergence", "Autocorrelation", "Other useful BayesGrowth functions", "Model comparison and selection" ], "created": "2020-11-10 01:03:12", "modified": "2023-11-17 02:11:08", "commits": 5 } ], "_score": 4.812913356642856, "_indexed": true, "_nocasepkg": "bayesgrowth", "_universes": [ "jonathansmart" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0.9000", "date": "2026-06-30T03:48:38.000Z", "distro": "resolute", "arch": "aarch64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/89eb625b5646f6b813dcee765701e09bebaed85534847553af53c5e0baf6ca1e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.7.0", "os": "linux", "version": "1.0.0.9000", "date": "2026-06-30T03:48:59.000Z", "distro": "resolute", "arch": "x86_64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/cc8c583256f5c8314c14cc0f768422bb655db17d04f39d0a451acd0ca48ed682", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.6.1", "os": "linux", "version": "1.0.0.9000", "date": "2026-06-30T03:48:59.000Z", "distro": "resolute", "arch": "aarch64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/70fdc4abdd0da989a63aefbf20cf8f232e77d2bfb6659b4a5b7f6a355b617249", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.6.1", "os": "linux", "version": "1.0.0.9000", "date": "2026-06-30T03:48:21.000Z", "distro": "resolute", "arch": "x86_64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/afc967f09a284d616b1363a499ed39ca4c92224cf095622eddc1a6614ec22307", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0.9000", "date": "2026-06-30T03:47:42.000Z", "arch": "aarch64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/c265bc5582eb49e0592d49e336acc99beac5a296f91016a7bcd551bfaa42284a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0.9000", "date": "2026-06-30T03:51:23.000Z", "arch": "x86_64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/e92b2817b29d9a8672b9155b8fef7adf36e4ddc7e32d16bee6182f08eaaec19e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.6.1", "os": "mac", "version": "1.0.0.9000", "date": "2026-06-30T03:47:42.000Z", "arch": "aarch64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/542c15f15b20e66f6632e4ee0b999e78e9fc7824d17fa0505d8f4bfb591b1bed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.6.1", "os": "mac", "version": "1.0.0.9000", "date": "2026-06-30T03:48:43.000Z", "arch": "x86_64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/68ece1b5c8e0a7aae9dd611ce16558c0289900b11d31bb391e75423ed7d63aac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.7.0", "os": "win", "version": "1.0.0.9000", "date": "2026-06-30T03:47:08.000Z", "arch": "x86_64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/c6fc1cb7e2625d33f1d73e64489289679dc3a86b52cfddb3deb5d1728de245ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.5.3", "os": "win", "version": "1.0.0.9000", "date": "2026-06-30T03:47:17.000Z", "arch": "x86_64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/2a8520661e6a36a1c9f8a901d989fd7e8929e1db097c01e09691ff1048be017d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" }, { "r": "4.6.1", "os": "win", "version": "1.0.0.9000", "date": "2026-06-30T03:47:06.000Z", "arch": "x86_64", "commit": "9932842e6c3a2893f89ffa95e731ca530395d6bd", "fileid": "https://r2.ropensci.org/128be5938561b151fb996310d9b3c3d98a5ad0ebb8de3b535a7fe482b7714648", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jonathansmart/actions/runs/28418526180" } ] }