Function reference

Model overviews

The make_html() function generates a single html file out of gadgetutils::g3_fit() output that contains key model diagnostics. The gadget_plots() function saves a set of diagnostics plots into a folder.

make_html(): Save diagnostic graphs to a single html document

gadget_plots(): Wrapper for plot.gadget.fit that saves all diagnostic graphs to a directory

Plotting functions

The package produces plots in four categories:

plot_*() functions plot gadget model output generated using gadgetutils::g3_fit(). These functions have a generic shorthand, the plot(), with param argument specifying the type of plot.
dplot_*() functions plot gadget model input data generated using mfdb, gadgetutils::g3_data() or gadgetutils::add_g3_attributes() functions.
the g3d_plot() function plots data directly from a gadget model object.
g3plot_* functions plot gadget suitability (selectivity) functions.

The `plot_*` for `g3_fit` output

These functions make the plots typically used in asssessment and model diagnostics. Some of the functions have return_data argument, which can be used to quickly grab associated data for further analyses, custom plots and tables.

General

plot(<gadget.fit>): Plot gadget.fit object

plot_annual(): Plot annual ICES type of graphic returning central model data

plot_adist(): Plot model age distributions for stocks by year

plot_ageclass(): Plot an age class from the model

plot_agecomp(): Plot of age composition from the model

plot_agelength(): Plot of fitted growth for each age-length component

plot_growth(): Plot of average growth for each stock

Stock status

plot_biomass(): Plot stock biomasses

plot_ssb(): Plot spawning stock biomass

plot_rec(): Plot recruitment

plot_sr(): Plot stock-recruitment relationship

plot_si(): Plot survey indices

Catches and fleets

plot_catch(): Plot catches

plot_f(): Plot fishing mortality

plot_hr(): Plot harvest rate

plot_suitability(): Plot suitability

Distributions

plot_catchdist(): Plot catch distributions

plot_ldist(): Plot model length distributions for stocks by year

plot_stockcomp(): Plot model stock composition

plot_stockdist(): Plot stock distribution

Parameters and fit

plot_likelihood(): Plot likelihood summary

plot_param(): Plot parameter values relative to their boundaries

plot_resid(): Plot residuals for catch distributions

plot_weight(): Plot parameter weights

Model diagnostics

These functions require a list of gadget.fit objects generated using the gadgetutils::g3_jitter(), gadgetutils::g3_leaveout(), and gadgetutils::g3_retro() functions.

plot_jitter(): Plot central model output from a jitter analysis

plot_leaveout(): Plot central model output from a leave-out analysis

plot_retro(): Plot model biomass from a retrospective analysis

The `dplot_*` for gadget input data

These functions plot gadget input data attempting to highlight attributes, which guide the model fitting, but are often difficult to notice otherwise.

dplot_adist(): Plot age distribution data for a gadget3 model

dplot_aldist(): Plot age-length distribution data for a gadget3 model

dplot_ldist(): Plot length distribution data for a gadget3 model

dplot_sexr(): Plot sex ratio data for a gadget3 model

dplot_stockdist(): Plot stock distribution data for a gadget3 model

dplot_catch(): Plot catch data for a gadget3 model

The `g3d_plot` for gadget model objects

The g3d_plot() function plots all observational data passed into a TMB or R gadget model.

g3d_plot(): Plot of data passed into a gadget model

The `g3plot_*` for suitability functions

These plot gadget suitability functions, which can be difficult to comprehend without visualizing. The model parameters can be extracted from a gadget.fit object or typed in manually.

g3plot_andersen(): Plot Andersen suitability using model parameters

g3plot_exponentiall50(): Plot exponentiall50 suitability using model parameters

Example data

Datasets to demonstrate plot functions.

fit: An example gadget.fit object.

aldist_example: Age-length input data to gadget

ldist_example: Length input data to gadget

sexratio_example: Sex input data to gadget

stockdist_example: Maturity input data to gadget

TrawlNor_catches Internat_catches OtherNor_catches Internat_catches OtherRus_catches TrawlRus_catches TrawlNor_catches: Catch input data to gadget