ebswp_fims

EBS Walleye Pollock FIMS

This site contains the rendered Quarto outputs for the EBS walleye pollock FIMS configuration in this repository.

Reports

FIMS implementation report

Scripts

Script	Purpose	Main output
`scripts/01_build_data.R`	Converts the 2024 pollock assessment inputs into the long `FIMSFrame`-ready data table used by the model.	`data/ebs_fims_data.rds`
`scripts/02_fit_model.R`	Builds the FIMS model inputs, fits the maximum-likelihood model, extracts estimates and reports, and saves a compact fit summary.	`outputs/fims_fit_summary.rds`
`scripts/03_fit_sparse_nuts.R`	Command-line scaffold for fitting the FIMS mode and then running `SparseNUTS` on the TMB objective.	`outputs/sparsenuts_fit.rds`
`scripts/04_run_retro_5_peel.R`	Runs 0- through 5-year retrospective peels and summarizes SSB and recruitment trajectories.	`outputs/retro_5_peel_summary.rds`
`scripts/05_fit_tvselex.R`	Attempts the `TVselex` model with a time-varying fishery double-logistic ascending inflection point and saves either a fit summary or failure diagnostics.	`outputs/tvselex_fit_summary.rds`
`scripts/sparsenuts_framework.R`	Shared helper functions for resolving paths, building FIMS inputs, fitting the mode, preparing retrospective peels, and saving `SparseNUTS` output.	Used by fitting, MCMC, and retrospective scripts
`fimsfit.R`	Local FIMS fitting wrapper and `FIMSFit` S4 class utilities used by the application scripts.	Fitted `FIMSFit` objects and accessor outputs

Helper Functions

Function	Source	Brief documentation
`cv_2_sd()`	`scripts/01_build_data.R`	Converts coefficient of variation values to lognormal standard deviations.
`make_index()`	`scripts/01_build_data.R`	Builds complete annual index rows for a fleet, filling missing years with `-999` and reasonable uncertainty values.
`make_agecomp()`	`scripts/01_build_data.R`	Converts age-composition matrices into long-form FIMS age-composition records with annual age grids.
`make_waa()`	`scripts/01_build_data.R`	Creates the complete weight-at-age input, including the terminal year required by FIMS.
`resolve_project_root()`	`scripts/sparsenuts_framework.R`	Finds the repository root from the current working directory.
`default_snuts_control()`	`scripts/sparsenuts_framework.R`	Provides default tuning controls for `SparseNUTS`.
`build_fims_inputs_from_payload()`	`scripts/sparsenuts_framework.R`	Creates `FIMSFrame`, configurations, parameter specifications, and initialized FIMS input from an in-memory payload.
`build_fims_inputs()`	`scripts/sparsenuts_framework.R`	Loads `data/ebs_fims_data.rds` and passes it to `build_fims_inputs_from_payload()`.
`fit_fims_mode_for_snuts()`	`scripts/sparsenuts_framework.R`	Fits the FIMS maximum-likelihood mode and returns both the fit and the built input objects for MCMC.
`make_retro_payload()`	`scripts/sparsenuts_framework.R`	Drops terminal years from data and weight-at-age inputs to create retrospective peel payloads.
`run_sparse_nuts_fims()`	`scripts/sparsenuts_framework.R`	Passes the fitted TMB objective to `SparseNUTS::sample_snuts()`.
`extract_fims_estimates()`	`scripts/sparsenuts_framework.R`	Joins FIMS JSON estimates with TMB parameter estimates and uncertainty output.
`save_sparse_nuts_results()`	`scripts/sparsenuts_framework.R`	Saves MCMC output together with mode diagnostics and basic model-input metadata.
`parse_arg()`	`scripts/03_fit_sparse_nuts.R`	Parses simple command-line options of the form `--name=value`.
`fit_one_peel()`	`scripts/04_run_retro_5_peel.R`	Fits one retrospective peel and extracts SSB and recruitment summaries.
`FIMSFit()`	`fimsfit.R`	Constructs the local S4 fitted-model object used to store input, optimizer output, reports, estimates, timing, and version metadata.
`fit_fims()`	`fimsfit.R`	Builds and optionally optimizes the FIMS/TMB objective, returning a `FIMSFit` object.
`get_*()` accessors	`fimsfit.R`	Access slots from a `FIMSFit` object, including input, report, objective, optimizer output, gradients, estimates, timing, version, and model output.
`is.FIMSFit()`	`fimsfit.R`	Checks whether an object inherits from the local `FIMSFit` class.

Render

To rebuild the site locally:

Rscript scripts/01_build_data.R
Rscript scripts/02_fit_model.R
quarto render

The rendered website is written to docs/ so it can be served directly by GitHub Pages.

--- title: "ebswp_fims" --- # EBS Walleye Pollock FIMS This site contains the rendered Quarto outputs for the EBS walleye pollock FIMS configuration in this repository. ## Reports - [FIMS implementation report](qmd/fims-implementation.qmd) ## Scripts | Script | Purpose | Main output | |---|---|---| | `scripts/01_build_data.R` | Converts the 2024 pollock assessment inputs into the long `FIMSFrame`-ready data table used by the model. | `data/ebs_fims_data.rds` | | `scripts/02_fit_model.R` | Builds the FIMS model inputs, fits the maximum-likelihood model, extracts estimates and reports, and saves a compact fit summary. | `outputs/fims_fit_summary.rds` | | `scripts/03_fit_sparse_nuts.R` | Command-line scaffold for fitting the FIMS mode and then running `SparseNUTS` on the TMB objective. | `outputs/sparsenuts_fit.rds` | | `scripts/04_run_retro_5_peel.R` | Runs 0- through 5-year retrospective peels and summarizes SSB and recruitment trajectories. | `outputs/retro_5_peel_summary.rds` | | `scripts/05_fit_tvselex.R` | Attempts the `TVselex` model with a time-varying fishery double-logistic ascending inflection point and saves either a fit summary or failure diagnostics. | `outputs/tvselex_fit_summary.rds` | | `scripts/sparsenuts_framework.R` | Shared helper functions for resolving paths, building FIMS inputs, fitting the mode, preparing retrospective peels, and saving `SparseNUTS` output. | Used by fitting, MCMC, and retrospective scripts | | `fimsfit.R` | Local FIMS fitting wrapper and `FIMSFit` S4 class utilities used by the application scripts. | Fitted `FIMSFit` objects and accessor outputs | ## Helper Functions | Function | Source | Brief documentation | |---|---|---| | `cv_2_sd()` | `scripts/01_build_data.R` | Converts coefficient of variation values to lognormal standard deviations. | | `make_index()` | `scripts/01_build_data.R` | Builds complete annual index rows for a fleet, filling missing years with `-999` and reasonable uncertainty values. | | `make_agecomp()` | `scripts/01_build_data.R` | Converts age-composition matrices into long-form FIMS age-composition records with annual age grids. | | `make_waa()` | `scripts/01_build_data.R` | Creates the complete weight-at-age input, including the terminal year required by FIMS. | | `resolve_project_root()` | `scripts/sparsenuts_framework.R` | Finds the repository root from the current working directory. | | `default_snuts_control()` | `scripts/sparsenuts_framework.R` | Provides default tuning controls for `SparseNUTS`. | | `build_fims_inputs_from_payload()` | `scripts/sparsenuts_framework.R` | Creates `FIMSFrame`, configurations, parameter specifications, and initialized FIMS input from an in-memory payload. | | `build_fims_inputs()` | `scripts/sparsenuts_framework.R` | Loads `data/ebs_fims_data.rds` and passes it to `build_fims_inputs_from_payload()`. | | `fit_fims_mode_for_snuts()` | `scripts/sparsenuts_framework.R` | Fits the FIMS maximum-likelihood mode and returns both the fit and the built input objects for MCMC. | | `make_retro_payload()` | `scripts/sparsenuts_framework.R` | Drops terminal years from data and weight-at-age inputs to create retrospective peel payloads. | | `run_sparse_nuts_fims()` | `scripts/sparsenuts_framework.R` | Passes the fitted TMB objective to `SparseNUTS::sample_snuts()`. | | `extract_fims_estimates()` | `scripts/sparsenuts_framework.R` | Joins FIMS JSON estimates with TMB parameter estimates and uncertainty output. | | `save_sparse_nuts_results()` | `scripts/sparsenuts_framework.R` | Saves MCMC output together with mode diagnostics and basic model-input metadata. | | `parse_arg()` | `scripts/03_fit_sparse_nuts.R` | Parses simple command-line options of the form `--name=value`. | | `fit_one_peel()` | `scripts/04_run_retro_5_peel.R` | Fits one retrospective peel and extracts SSB and recruitment summaries. | | `FIMSFit()` | `fimsfit.R` | Constructs the local S4 fitted-model object used to store input, optimizer output, reports, estimates, timing, and version metadata. | | `fit_fims()` | `fimsfit.R` | Builds and optionally optimizes the FIMS/TMB objective, returning a `FIMSFit` object. | | `get_*()` accessors | `fimsfit.R` | Access slots from a `FIMSFit` object, including input, report, objective, optimizer output, gradients, estimates, timing, version, and model output. | | `is.FIMSFit()` | `fimsfit.R` | Checks whether an object inherits from the local `FIMSFit` class. | ## Render To rebuild the site locally: ```sh Rscript scripts/01_build_data.R Rscript scripts/02_fit_model.R quarto render ``` The rendered website is written to `docs/` so it can be served directly by GitHub Pages.