Package: gadget3 0.12-1-999
Jamie Lentin
gadget3: Globally-Applicable Area Disaggregated General Ecosystem Toolbox V3
A framework to assist creation of marine ecosystem models, generating either 'R' or 'C++' code which can then be optimised using the 'TMB' package and standard 'R' tools. Principally designed to reproduce gadget2 models in 'TMB', but can be extended beyond gadget2's capabilities. Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.". Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".
Authors:
gadget3_0.12-1-999.tar.gz
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gadget3_0.12-1-999.tgz(r-4.4-any)gadget3_0.12-1-999.tgz(r-4.3-any)
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gadget3_0.12-1-999.tgz(r-4.4-emscripten)gadget3_0.12-1-999.tgz(r-4.3-emscripten)
gadget3.pdf |gadget3.html✨
gadget3/json (API)
NEWS
| # Install 'gadget3' in R: |
| install.packages('gadget3', repos = c('https://gadget-framework.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gadget-framework/gadget3/issues
Last updated 23 hours agofrom:41fb3bb8c7. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 21 2024 |
| R-4.5-win | OK | Nov 21 2024 |
| R-4.5-linux | OK | Nov 21 2024 |
| R-4.4-win | NOTE | Nov 21 2024 |
| R-4.4-mac | NOTE | Nov 21 2024 |
| R-4.3-win | NOTE | Nov 21 2024 |
| R-4.3-mac | NOTE | Nov 21 2024 |
Exports:g3_action_orderg3_areasg3_array_aggg3_distribution_previewg3_envg3_evalg3_fleetg3_formulag3_global_formulag3_init_valg3_is_stockg3_nativeg3_parameterizedg3_stepg3_stockg3_stock_defg3_stock_instanceg3_suitability_anderseng3_suitability_andersenfleetg3_suitability_constantg3_suitability_exponentialg3_suitability_exponentiall50g3_suitability_gammag3_suitability_richardsg3_suitability_straightlineg3_timeareadatag3_timevariableg3_tmb_adfung3_tmb_lowerg3_tmb_parg3_tmb_parscaleg3_tmb_relistg3_tmb_upperg3_to_descg3_to_rg3_to_tmbg3a_ageg3a_grow_impl_bbinomg3a_grow_length_multspecg3a_grow_length_weightjonesg3a_grow_lengthvbsimpleg3a_grow_weight_multspecg3a_grow_weight_weightjonesg3a_grow_weightsimpleg3a_growmatureg3a_initialconditionsg3a_initialconditions_normalcvg3a_initialconditions_normalparamg3a_matureg3a_mature_constantg3a_mature_continuousg3a_migrateg3a_migrate_normalizeg3a_naturalmortalityg3a_naturalmortality_expg3a_otherfoodg3a_otherfood_normalcvg3a_otherfood_normalparamg3a_predateg3a_predate_catchability_effortfleetg3a_predate_catchability_linearfleetg3a_predate_catchability_numberfleetg3a_predate_catchability_predatorg3a_predate_catchability_quotafleetg3a_predate_catchability_totalfleetg3a_predate_fleetg3a_predate_maxconsumptiong3a_predate_tagreleaseg3a_predate_totalfleetg3a_renewalg3a_renewal_initabundg3a_renewal_normalcvg3a_renewal_normalparamg3a_renewal_vonbg3a_renewal_vonb_reclg3a_renewal_vonb_t0g3a_report_detailg3a_report_historyg3a_report_stockg3a_spawng3a_spawn_recruitment_bevertonholtg3a_spawn_recruitment_bevertonholt_ss3g3a_spawn_recruitment_fecundityg3a_spawn_recruitment_hockeystickg3a_spawn_recruitment_rickerg3a_spawn_recruitment_simplessbg3a_spmodelg3a_spmodel_logisticg3a_tag_sheddingg3a_timeg3a_weightlossg3l_abundancedistributiong3l_bounds_penaltyg3l_catchdistributiong3l_distribution_multinomialg3l_distribution_multivariateg3l_distribution_sumofsquaredlogratiosg3l_distribution_sumofsquaresg3l_distribution_surveyindices_linearg3l_distribution_surveyindices_logg3l_random_dnormg3l_random_walkg3l_sparsesampleg3l_sparsesample_linregg3l_sparsesample_sumsquaresg3l_tagging_ckmrg3l_understockingg3s_ageg3s_agegroupg3s_areagroupg3s_cloneg3s_livesonareasg3s_tagg3s_timeg3s_time_convert
Incorporating observation data into models
Rendered fromincorporating-observation-data.Rmdusingknitr::rmarkdownon Nov 21 2024.Last update: 2024-07-19
Started: 2024-01-26
Introduction to gadget3: A single stock model
Rendered fromintroduction-single-stock.Rmdusingknitr::rmarkdownon Nov 21 2024.Last update: 2024-11-11
Started: 2024-01-26
Model customisation
Rendered frommodel-customisation.Rmdusingknitr::rmarkdownon Nov 21 2024.Last update: 2024-01-26
Started: 2024-01-26
Debugging a gadget3 model
Rendered frommodel-debugging.Rmdusingknitr::rmarkdownon Nov 21 2024.Last update: 2024-01-26
Started: 2021-02-18
Structure of a gadget3 model
Rendered frommodel-structure.Rmdusingknitr::rmarkdownon Nov 21 2024.Last update: 2024-01-26
Started: 2024-01-26
Modelling maturity & sex with multiple stocks
Rendered frommultiple-substocks.Rmdusingknitr::rmarkdownon Nov 21 2024.Last update: 2024-07-04
Started: 2024-01-26
Spawning & Random effects
Rendered fromrandom-effects.Rmdusingknitr::rmarkdownon Nov 21 2024.Last update: 2024-07-04
Started: 2024-01-26
Writing G3 Actions
Rendered fromwriting_actions.Rmdusingknitr::rmarkdownon Nov 21 2024.Last update: 2024-10-14
Started: 2020-10-08
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gadget3 language utilities | g3_global_formula g3_native |
| Gadget3 global environment | ADREPORT as.numeric assert_msg as_integer avoid_zero avoid_zero_vec bounded bounded_vec g3_env g3_matrix_vec lgamma_vec logspace_add nonconform_add nonconform_div nonconform_divavz nonconform_mult normalize_vec nvl print_array ratio_add_vec REPORT REprintf Rprintf |
| Gadget3 age action | g3a_age |
| Gadget3 growth action | g3a_growmature g3a_grow_impl_bbinom g3a_grow_lengthvbsimple g3a_grow_length_multspec g3a_grow_length_weightjones g3a_grow_weightsimple g3a_grow_weight_multspec g3a_grow_weight_weightjones |
| Gadget3 maturity action | g3a_mature g3a_mature_constant g3a_mature_continuous |
| Gadget3 migration action | g3a_migrate g3a_migrate_normalize |
| Gadget3 natural mortality action | g3a_naturalmortality g3a_naturalmortality_exp |
| Standard gadget3 order of actions | g3_action_order |
| Gadget3 predation actions | g3a_predate g3a_predate_catchability_effortfleet g3a_predate_catchability_linearfleet g3a_predate_catchability_numberfleet g3a_predate_catchability_predator g3a_predate_catchability_quotafleet g3a_predate_catchability_totalfleet g3a_predate_fleet g3a_predate_maxconsumption g3a_predate_totalfleet |
| Gadget3 renewal actions | g3a_initialconditions g3a_initialconditions_normalcv g3a_initialconditions_normalparam g3a_otherfood g3a_otherfood_normalcv g3a_otherfood_normalparam g3a_renewal g3a_renewal_initabund g3a_renewal_normalcv g3a_renewal_normalparam g3a_renewal_vonb g3a_renewal_vonb_recl g3a_renewal_vonb_t0 |
| Gadget3 report actions | g3a_report_detail g3a_report_history g3a_report_stock |
| Gadget3 spawning action | 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 |
| Gadget3 surplus production model | g3a_spmodel g3a_spmodel_logistic |
| Gadget3 tag-release action | g3a_predate_tagrelease g3a_tag_shedding |
| Gadget3 timekeeping actions | g3a_time |
| Gadget3 weightloss action | g3a_weightloss |
| Gadget3 array-handling utilities | g3_array_agg |
| g3 env: differentiable functions | dif_pmax dif_pmin dif_pminmax |
| Evaluate G3 forumulas | g3_eval |
| Gadget3 formula helpers | g3_formula |
| Gadget3 parameter value setter | g3_init_val |
| G3 language extensions to R | g3_idx g3_param g3_param_table g3_param_vector g3_with |
| Gadget3 likelihood bounds_penalty action | g3l_bounds_penalty |
| Gadget3 likelihood actions | 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 |
| Gadget3 random effects likelihood actions | g3l_random_dnorm g3l_random_walk |
| Gadget3 likelihood actions for sparse data | g3l_sparsesample g3l_sparsesample_linreg g3l_sparsesample_sumsquares |
| Gadget3 CKMR likelihood | g3l_tagging_ckmr |
| Gadget3 likelihood understocking action | g3l_understocking |
| Gadget3 parameter helpers | g3_parameterized |
| Gadget3 actions into R code | g3_to_desc |
| Gadget3 actions into R code | g3_to_r print.g3_r |
| Gadget3 actions into TMB code | g3_tmb_adfun g3_tmb_lower g3_tmb_par g3_tmb_parscale g3_tmb_relist g3_tmb_upper g3_to_tmb |
| G3 stock_* transformation functions | debug_label debug_trace g3_step stock_assert stock_interact stock_intersect stock_iterate stock_prepend stock_ss stock_ssinv stock_switch stock_with |
| Gadget3 stock storage | g3s_clone g3_fleet g3_is_stock g3_stock g3_stock_def g3_stock_instance |
| Gadget3 stock age dimensions | g3s_age g3s_agegroup |
| Gadget3 stock area dimensions | g3s_areagroup g3s_livesonareas g3_areas |
| Gadget3 tag dimension | g3s_tag |
| Gadget3 stock time dimensions | g3s_time g3s_time_convert |
| Gadget3 suitability formulae | g3_suitability_* g3_suitability_andersen g3_suitability_andersenfleet g3_suitability_constant g3_suitability_exponential g3_suitability_exponentiall50 g3_suitability_gamma g3_suitability_richards g3_suitability_straightline |
| Gadget3 time-based data | g3_timeareadata |
| Gadget3 time-based formulas | g3_timevariable |
