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Principally\ndesigned to reproduce gadget2 models in 'TMB', but can be\nextended beyond gadget2's capabilities. Kasper Kristensen,\nAnders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell\n(2016) \"TMB: Automatic\nDifferentiation and Laplace Approximation.\". Begley, J., &\nHowell, D. (2004) \"An overview\nof Gadget, the globally applicable area-disaggregated general\necosystem toolbox. 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"concept": [ "G3 action" ], "topics": [ "g3a_initialconditions_normalcv", "g3a_initialconditions_normalparam", "g3a_otherfood", "g3a_otherfood_normalcv", "g3a_otherfood_normalparam", "g3a_renewal_initabund", "g3a_renewal_normalcv", "g3a_renewal_normalparam", "g3a_renewal_vonb", "g3a_renewal_vonb_recl", "g3a_renewal_vonb_t0" ] }, { "page": "action_report", "title": "Gadget3 report actions", "concept": [ "G3 action" ], "topics": [ "g3a_report_detail", "g3a_report_history", "g3a_report_stock" ] }, { "page": "action_spawn", "title": "Gadget3 spawning action", "concept": [ "G3 action" ], "topics": [ "g3a_spawn", "g3a_spawn_recruitment_bevertonholt", "g3a_spawn_recruitment_bevertonholt_ss3", "g3a_spawn_recruitment_fecundity", "g3a_spawn_recruitment_hockeystick", "g3a_spawn_recruitment_ricker", "g3a_spawn_recruitment_simplessb" ] }, { "page": "action_spmodel", "title": "Gadget3 surplus production model", "concept": [ "G3 action" ], "topics": [ "g3a_spmodel", "g3a_spmodel_logistic" ] }, { 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"page": "formula_utils", "title": "Gadget3 formula helpers", "concept": [ "G3 utilities" ], "topics": [ "g3_formula" ] }, { "page": "init_val", "title": "Gadget3 parameter value setter", "concept": [ "G3 compilation" ], "topics": [ "g3_init_val" ] }, { "page": "language", "title": "G3 language extensions to R", "concept": [ "G3 internals" ], "topics": [ "g3_idx", "g3_param", "g3_param_table", "g3_param_vector", "g3_with" ] }, { "page": "likelihood_bounds", "title": "Gadget3 likelihood bounds_penalty action", "concept": [ "G3 action" ], "topics": [ "g3l_bounds_penalty" ] }, { "page": "likelihood_distribution", "title": "Gadget3 likelihood actions", "concept": [ "G3 action" ], "topics": [ "g3l_abundancedistribution", "g3l_catchdistribution", "g3l_distribution_multinomial", "g3l_distribution_multivariate", "g3l_distribution_sumofsquaredlogratios", "g3l_distribution_sumofsquares", "g3l_distribution_surveyindices_linear", "g3l_distribution_surveyindices_log", "g3_distribution_preview" ] }, 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"g3_suitability_exponential", "g3_suitability_exponentiall50", "g3_suitability_gamma", "g3_suitability_richards", "g3_suitability_straightline" ] }, { "page": "timedata", "title": "Gadget3 time-based data", "concept": [ "G3 utilities" ], "topics": [ "g3_timeareadata" ] }, { "page": "timevariable", "title": "Gadget3 time-based formulas", "concept": [ "G3 utilities" ], "topics": [ "g3_timevariable" ] } ], "_readme": "https://github.com/gadget-framework/gadget3/raw/HEAD/README.md", "_rundeps": [ "digest", "lattice", "Matrix", "Rcpp", "RcppEigen", "rlang", "TMB" ], "_vignettes": [ { "source": "incorporating-observation-data.Rmd", "filename": "incorporating-observation-data.html", "title": "Incorporating observation data into models", "engine": "knitr::rmarkdown", "headings": [ "length column: Length distribution data", "age column: Age-Length distribution data", "area column", "stock column: Maturity stage distribution", "fleet column", "predator column" ], "created": "2024-01-26 15:12:54", "modified": "2025-04-14 17:32:44", "commits": 3 }, { "source": "introduction-single-stock.Rmd", "filename": "introduction-single-stock.html", "title": "Introduction to gadget3: A single stock model", "engine": "knitr::rmarkdown", "headings": [ "Creating a (single species) model", "Actions", "Create time definitions", "Stocks", "Create stock definition for fish", "Stock actions", "Fleet actions", "Landings data", "Landings data: For each year/step/area", "Length distribution data", "Aggregate .raw data", "Group into length bins", "Report count in each length bin", "Save into ldist_f_surv", "Age-length distribution data", "Fleet definition", "Survey indices", "Generate random data", "fish.init.scalar & fish.rec.scalar: Overall scalar for recruitment/initial conditions, see g3a_renewal_normalcv()", "fish.rec.(age): Per-age recriutment scalar, see g3a_renewal_normalcv()", "fish.rec.(year): Recruitment level year-on-year, see g3a_renewal_normalcv()", "init.F: Offset for initial M, see g3a_renewal_initabund()", "fish.M.(age): per-age M for our species, see g3a_naturalmortality()", "fish.Linf, fish.K, fish.t0: VonB parameters for our species, see g3a_renewal_vonb_t0(), g3a_grow_lengthvbsimple()", "fish.walpha, fish.wbeta: Age/weight relationship for initialconditions, renewal, see g3a_renewal_normalcv()", "fish.f_surv.alpha, fish.f_surv.l50: Curve/l50 for fishing suitability, see g3_suitability_exponentiall50()", "fish.bbin: Beta for beta-binomial distribution for fish growth, see g3a_grow_impl_bbinom()", "identity() is a do-nothing function, but it lets us finish on a new line", "Appendix: Full model script" ], "created": "2024-01-26 15:12:54", "modified": "2025-09-18 18:10:53", "commits": 14 }, { "source": "model-customisation.Rmd", "filename": "model-customisation.html", "title": "Model customisation", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-01-26 15:12:54", "modified": "2024-01-26 15:12:54", "commits": 1 }, { "source": "model-debugging.Rmd", "filename": "model-debugging.html", "title": "Debugging a gadget3 model", "engine": "knitr::rmarkdown", "headings": [ "Viewing & editing model code", "NaN in likelihood / reports", "\"Error in optim(...): initial value in 'vmmin' is not finite\"", "Increasing objective function verbosity", "TMB model crashes your R session", "Interactive debugging of TMB models", "Random effects", "Tracing inner model", "Logging messages", "Missing value for m", "Missing value par - parold", "Separate netwton optimisation" ], "created": "2021-02-18 17:49:31", "modified": "2025-08-28 15:25:13", "commits": 7 }, { "source": "model-structure.Rmd", "filename": "model-structure.html", "title": "Structure of a gadget3 model", "engine": "knitr::rmarkdown", "headings": [ "R formula, or the tilde operator", "Actions", "Stocks", "Model parameterization", "Combining actions", "Ordering of actions" ], "created": "2024-01-26 15:12:54", "modified": "2025-04-14 17:32:44", "commits": 2 }, { "source": "multiple-substocks.Rmd", "filename": "multiple-substocks.html", "title": "Modelling maturity & sex with multiple stocks", "engine": "knitr::rmarkdown", "headings": [ "Stocks", "Fleet actions", "Landings data: For each year/step/area", "Length distribution data: Generate 1000 random samples in each year/step/area", "Generate random lengths for these samples", "Save unagggregated data into ldist_f_surv.raw", "Aggregate .raw data", "Group into length bins", "Report count in each length bin", "Save into ldist_f_surv", "Assume 100 * 100 samples in each year/step/area", "Generate random whole numbers for age", "Group into length/age bins", "Map maturity stage data to stocks", "Generate random maturity stage data from age data, our stock matures between 3..5", "Map maturity stage to the stock name: Note we don't have to use the full stock name", "Remove redundant columns", "Survey indices", "Generate random data", "Treat maturity alpha/l50 separately", "Appendix: Full model script" 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