{ "_id": "6a267b5c794753ddbc3ee6f5", "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": "2026-06-08 08:16:45 UTC", "User": "root" }, "Author": "James T. Thorson [aut, cre] (ORCID:\n)", "MD5sum": "b46de21d509bd149712c2f2cfeb32def", "_user": "james-thorson-noaa", "_type": "src", "_file": "ecostate_0.3.0.tar.gz", "_fileid": "3b2b7c8d02ef0075ce2c824450c444bf705926655693c53201e94f0f373d64f6", "_filesize": 293511, "_sha256": "3b2b7c8d02ef0075ce2c824450c444bf705926655693c53201e94f0f373d64f6", "_created": "2026-06-08T08:16:45.000Z", "_published": "2026-06-08T08:20:44.943Z", "_distro": "noble", "_jobs": [ { "job": 80050486680, "time": 171, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7474863833" }, { "job": 80050486748, "time": 169, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7474863116" }, { "job": 80050486695, "time": 125, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7474848858" }, { "job": 80050486798, "time": 136, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7474852519" }, { "job": 80049867825, "time": 219, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7474809503" }, { "job": 80050486783, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7474847999" }, { "job": 80050486804, "time": 129, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7474850567" }, { "job": 80050486842, "time": 118, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7474847230" }, { "job": 80050486950, "time": 128, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7474850308" } ], "_buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314", "_status": "failure", "_host": "GitHub-Actions", "_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 }, "_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" }, "_downloads": { "count": 505, "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": "4.6.0", "_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", "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": "2026-06-08T08:19:24.000Z", "distro": "noble", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "ea5501b8ec384c73d4b79faa62f21c65f049fe6c8452830b7ba69d658cca692c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314" }, { "r": "4.6.0", "os": "linux", "version": "0.3.0", "date": "2026-06-08T08:19:23.000Z", "distro": "noble", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "28fdd67289319683b319552f883591a12b78f111dee448de20055cb8c1e66749", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0", "date": "2026-06-08T08:18:54.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "4c637fe62fc5ac51d42333886319a35f5b7eccac3520c83108d5b45321a63c74", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314" }, { "r": "4.6.0", "os": "mac", "version": "0.3.0", "date": "2026-06-08T08:19:01.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "7cde6301992091d003b1082f47e95036dec46ef43e9ed3f86d0be071112a02d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.0", "date": "2026-06-08T08:19:26.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "fafb23fe8cbc7c8cd1fe5914885c6f05e5a8e8ead227b6ddc95635f857c1739c", "status": "success", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314" }, { "r": "4.7.0", "os": "win", "version": "0.3.0", "date": "2026-06-08T08:18:38.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "2a81bb27321d0ad42d62be3aab26eec50645d46b0363024d56457f37c3eab313", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314" }, { "r": "4.5.3", "os": "win", "version": "0.3.0", "date": "2026-06-08T08:18:30.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "59c2140d30bdd0f439039be4f558ea3ad6e8df3d04e0f90cf36029f9c0a5f6c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314" }, { "r": "4.6.0", "os": "win", "version": "0.3.0", "date": "2026-06-08T08:18:37.000Z", "commit": "77c4c3a889e1366dfc54be2bc1dc8c2f2d45c070", "fileid": "bb15cae9fc9d039895960e0776a3a62eb732255ceba54662ffb006c9102cffc0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/james-thorson-noaa/actions/runs/27124603314" } ] }