{ "_id": "6a4dedd1e691af43f13de49f", "Package": "ecostate", "Type": "Package", "Title": "State-Space Mass-Balance Model for Marine Ecosystems", "Version": "0.3.0", "Date": "2025-09-08", "Authors@R": "c(\nperson(c(\"James\", \"T.\"), \"Thorson\", , \"James.Thorson@noaa.gov\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7415-1010\"))\n)", "Maintainer": "James T. Thorson ", "Description": "Fits a state-space mass-balance model for marine\necosystems, which implements dynamics derived from 'Ecopath\nwith Ecosim' ('EwE') while fitting to\ntime-series of fishery catch, biomass indices, age-composition\nsamples, and weight-at-age data. 'Ecostate' fits biological\nparameters (e.g., equilibrium mass) and measurement parameters\n(e.g., catchability coefficients) jointly with residual\nvariation in process errors, and can include Bayesian priors\nfor parameters.", "License": "GPL-3", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "LazyData": "true", "URL": "https://james-thorson-noaa.github.io/ecostate/", "BugReports": "https://github.com/James-Thorson-NOAA/ecostate/issues", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://james-thorson-noaa.r-universe.dev", "Date/Publication": "2025-12-10 11:21:50 UTC", "RemoteUrl": "https://github.com/james-thorson-noaa/ecostate", "RemoteRef": "HEAD", "RemoteSha": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-08 06:23:45 UTC", "User": "root" }, "Author": "James T. Thorson [aut, cre] (ORCID:\n)", "_user": "james-thorson-noaa", "_type": "src", "_file": "ecostate_0.3.0.tar.gz", "_fileid": "https://r2.ropensci.org/fdedf06cd54f1d5ae831559839e3e22552c662f2221ad8d23194a7a881e22f67", "_filesize": 299094, "_sha256": "fdedf06cd54f1d5ae831559839e3e22552c662f2221ad8d23194a7a881e22f67", "_expires": "2026-10-16T06:27:27.000Z", "_created": "2026-07-08T06:23:45.000Z", "_published": "2026-07-08T06:27:28.926Z", "_jobs": [ { "job": 85801748937, "time": 163, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8159950584" }, { "job": 85801748933, "time": 178, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8159955203" }, { "job": 85801748941, "time": 113, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8159935702" }, { "job": 85801748926, "time": 122, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8159938887" }, { "job": 85801206489, "time": 233, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8159901519" }, { "job": 85801748919, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8159936659" }, { "job": 85801748955, "time": 126, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8159940196" }, { "job": 85801749029, "time": 117, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8159937155" }, { "job": 85801748946, "time": 126, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8159940547" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487", "_status": "success", "_upstream": "https://github.com/james-thorson-noaa/ecostate", "_commit": { "id": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "author": "James Thorson ", "committer": "James Thorson ", "message": "Update surplus_production.Rmd\n", "time": 1765365710 }, "_maintainer": { "name": "James T. Thorson", "email": "james.thorson@noaa.gov", "login": "james-thorson-noaa", "orcid": "0000-0001-7415-1010", "description": "", "uuid": 50178738 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "RTMB", "version": ">= 1.5.0", "role": "Depends" }, { "package": "TMB", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "checkmate", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggnetwork", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "james-thorson-noaa", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-32", "n": 8 }, { "week": "2025-35", "n": 1 }, { "week": "2025-37", "n": 1 }, { "week": "2025-50", "n": 1 } ], "_tags": [ { "name": "0.2.0", "date": "2025-08-06" } ], "_stars": 13, "_contributors": [ { "user": "james-thorson", "count": 51, "uuid": 7989837 }, { "user": "james-thorson-noaa", "count": 19, "uuid": 50178738 } ], "_userbio": { "uuid": 50178738, "type": "user", "name": "James T. Thorson", "followers": 116 }, "_downloads": { "count": 517, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ecostate" }, "_devurl": "https://github.com/james-thorson-noaa/ecostate", "_pkgdown": "https://james-thorson-noaa.github.io/ecostate/", "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ecostate.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/james-thorson-noaa/ecostate", "_realowner": "james-thorson-noaa", "_cranurl": true, "_releases": [ { "version": "0.2.0", "date": "2024-11-25" }, { "version": "0.3.0", "date": "2025-09-08" } ], "_exports": [ "abm3pc_sys", "add_equilibrium", "compute_nll", "compute_tracer", "dBdt", "ddirmult", "ecostate", "ecostate_control", "ode23", "plot_foodweb", "print_ecopars", "rk4sys", "stanza_settings" ], "_datasets": [ { "name": "eastern_bering_sea", "title": "eastern Bering Sea ecosystem data", "object": "eastern_bering_sea", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "gulf_of_alaska", "title": "eastern Gulf of Alaska data", "object": "gulf_of_alaska", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "whitehouse_2021", "title": "Full rpath inputs for eastern Bering Sea", "object": "whitehouse_2021", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "abm3pc_sys", "title": "Adams-Bashford-Moulton for system of equations", "topics": [ "abm3pc_sys" ] }, { "page": "add_equilibrium", "title": "Compute equilibrium values", "topics": [ "add_equilibrium" ] }, { "page": "compute_nll", "title": "Compute negative log-likelihood for EcoState model", "topics": [ "compute_nll" ] }, { "page": "compute_tracer", "title": "Calculate tracers, e.g., trophic level", "topics": [ "compute_tracer" ] }, { "page": "dBdt", "title": "Dynamics from EcoSim", "topics": [ "dBdt" ] }, { "page": "ddirmult", "title": "Dirichlet-multinomial", "topics": [ "ddirmult" ] }, { "page": "eastern_bering_sea", "title": "eastern Bering Sea ecosystem data", "topics": [ "eastern_bering_sea" ] }, { "page": "ecostate", "title": "fit EcoState model", "topics": [ "ecostate" ] }, { "page": "ecostate_control", "title": "Detailed control for ecostate structure", "topics": [ "ecostate_control" ] }, { "page": "ginv", "title": "Penrose-Moore pseudoinverse", "topics": [ "ginv" ] }, { "page": "gulf_of_alaska", "title": "eastern Gulf of Alaska data", "topics": [ "gulf_of_alaska" ] }, { "page": "logLik.ecostate", "title": "Marginal log-likelihood", "topics": [ "logLik.ecostate" ] }, { "page": "ode23", "title": "Non-stiff (and stiff) ODE solvers", "topics": [ "ode23" ] }, { "page": "plot_foodweb", "title": "Plot foodweb", "topics": [ "plot_foodweb" ] }, { "page": "print_ecopars", "title": "Print EcoSim parameters", "topics": [ "print_ecopars" ] }, { "page": "print.ecostate", "title": "Print fitted ecostate object", "topics": [ "print.ecostate" ] }, { "page": "rk4sys", "title": "Classical Runge-Kutta for system of equations", "topics": [ "rk4sys" ] }, { "page": "stanza_settings", "title": "Detailed control for stanza structure", "topics": [ "stanza_settings" ] }, { "page": "whitehouse_2021", "title": "Full rpath inputs for eastern Bering Sea", "topics": [ "whitehouse_2021" ] } ], "_readme": "https://github.com/james-thorson-noaa/ecostate/raw/HEAD/README.md", "_rundeps": [ "backports", "checkmate", "cli", "coda", "cpp11", "farver", "ggnetwork", "ggplot2", "ggrepel", "glue", "gtable", "igraph", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "network", "pillar", "pkgconfig", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "RTMB", "S7", "scales", "sna", "statnet.common", "tibble", "TMB", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "model-description.Rmd", "filename": "model-description.html", "title": "ecostate model description", "author": "James T. Thorson", "engine": "knitr::rmarkdown", "headings": [ "Introducing ecostate", "State-space mass balance modelling", "Age- and size-structured dynamics", "Theoretical background", "Equilibrium calculation", "Projecting nonequilibrium dynamics over time", "References" ], "created": "2025-08-07 04:40:56", "modified": "2025-08-07 23:04:42", "commits": 3 } ], "_score": 5.414973347970818, "_indexed": true, "_nocasepkg": "ecostate", "_universes": [ "james-thorson-noaa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.0", "date": "2026-07-08T06:26:03.000Z", "distro": "resolute", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "https://r2.ropensci.org/438469825b23cfe5c96cc726a86b6ad75f011076ed049071448a8554737d3638", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487" }, { "r": "4.6.1", "os": "linux", "version": "0.3.0", "date": "2026-07-08T06:26:16.000Z", "distro": "resolute", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "https://r2.ropensci.org/d122b718a8e8f76e5f831372902384450d1373adee83375a74f06d678eccaf04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0", "date": "2026-07-08T06:25:32.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "https://r2.ropensci.org/211cff50fbb0dbfd436736e5bafe5a0970bda584fa0e19fc6c7a1a15333ba1ca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487" }, { "r": "4.6.1", "os": "mac", "version": "0.3.0", "date": "2026-07-08T06:25:38.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "https://r2.ropensci.org/b9d62d3c5ee36b2dc884b398dd11636ca50a5f92658a096ef6eca0f360ae477f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.0", "date": "2026-07-08T06:26:05.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "https://r2.ropensci.org/2059639645d293ce537e3dd062a9d48f40188dca277e9fbfbb74fbad22856de9", "status": "success", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487" }, { "r": "4.7.0", "os": "win", "version": "0.3.0", "date": "2026-07-08T06:25:22.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "https://r2.ropensci.org/1799e35d377f9f46e80182d6805900c615b778faaebafb8e97f8230656d9341f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487" }, { "r": "4.5.3", "os": "win", "version": "0.3.0", "date": "2026-07-08T06:25:08.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "https://r2.ropensci.org/dc3a67f962e6bb53478182a9a217fd811766e0ee77f706c078c9a1cabde094f8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487" }, { "r": "4.6.1", "os": "win", "version": "0.3.0", "date": "2026-07-08T06:25:23.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "https://r2.ropensci.org/f168b6fb181ec8b9c8d7f461d97438d86bfb64c6b2652786f853b986313bc6b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/28922029487" } ] }