Function reference • sspm

Workflow steps
Casting boundaries Create a spatial boundaries object for your model
`spm_as_boundary()`	Create a sspm_boundary object
`sspm_boundary-class`	sspm boundary structure
Discretizing boundaries Discretize your spatial boundaries object into patches
`spm_discretize` `spm_discretize,sspm_boundary,missing,ANY-method` `spm_discretize,sspm_boundary,ANY,missing-method` `spm_discretize,sspm_boundary,character,ANY-method` `spm_discretize,sspm_boundary,function,ANY-method` `spm_discretize,sspm_boundary,discretization_method,ANY-method`	Discretize a `sspm` model object
`sspm_discrete_boundary-class`	sspm discrete boundary structure
`tesselate_voronoi()`	Perform voronoi tesselation
`triangulate_delaunay()`	Perform delaunay triangulation
`spm_methods()`	Get the list of available discretization methods
`as_discretization_method` `as_discretization_method,character,ANY-method` `as_discretization_method,missing,function-method`	Cast into a `discretization_method` object
`discretization_method-class`	sspm discretization method class
Casting datasets Create dataset objects for your raw variables
`spm_as_dataset()`	Create a `sspm_dataset` dataset structure
`sspm_dataset-class`	sspm dataset structure
Smoothing biomass Smooth the raw variables using gams
`spm_smooth()`	Smooth a variable in a sspm dataset
`spm_smooth_methods()`	Get the list of available smoothing methods
`smooth_time()` `smooth_space()` `smooth_space_time()` `smooth_lag()`	sspm Smoothing functions
Aggregating catch Aggregate the catch data according to discretized boundaries
`spm_aggregate_catch()`	Update biomass value from catch adta
`spm_aggregate()`	Aggregate a dataset or fit data variable based on a boundary
Assembling and modifiying SSPM objects Assemble the model object and prepare it for fitting
`sspm()`	Create a `sspm` model object
`sspm-class`	sspm model class
`spm_split()`	Split data in test and train sets
`spm_lag()`	Create lagged columns in a sspm smoothed data slot
Fitting the surplus production model Fit the model
`spm()`	Fit an SPM model
`sspm_fit-class`	sspm fit
`sspm_formula-class`	sspm formula object
`summary(<sspm_fit>)`	Summarises `sspm_fit` objects
Predict and plot Predict and plot results
`predict(<sspm_fit>)` `predict(<sspm_dataset>)`	Predict with a SPM model
`predict_intervals()`	GAM confidence and prediction intervals
`plot(<sspm_boundary>,<missing>)` `plot(<sspm_dataset>,<missing>)` `plot(<sspm_fit>,<missing>)`	Plot `sspm` objects
Datasets Datasets used in the vignette
`borealis_simulated`	Simulated biomass data
`catch_simulated`	Simulated catch data
`predator_simulated`	Simulated predator data
`sfa_boundaries`	SFA boundaries data
Accessors Accessors method for various objects
`spm_boundaries(<sspm_boundary>)` `spm_boundaries<-`(<sspm_boundary>) `spm_discret_method()` `spm_discret_method<-`() `spm_patches()` `spm_patches<-`() `spm_points()` `spm_points<-`() `spm_boundary()` `spm_boundary<-`() `spm_boundary_area()` `spm_boundary_area<-`() `spm_patches_area()` `spm_patches_area<-`()	Accessing OR replacing `sspm_boundary` model elements
`spm_data()` `spm_data<-`() `spm_name(<sspm_dataset>)` `spm_name<-`(<sspm_dataset>) `spm_unique_ID(<sspm_dataset>)` `spm_unique_ID<-`(<sspm_dataset>) `spm_coords_col()` `spm_coords_col<-`() `spm_time(<sspm_dataset>)` `spm_time<-`(<sspm_dataset>) `spm_biomass_vars()` `spm_biomass_vars<-`() `spm_density_vars()` `spm_density_vars<-`() `spm_formulas()` `spm_formulas<-`() `spm_smoothed_data(<sspm_dataset>)` `spm_smoothed_data<-`(<sspm_dataset>) `spm_smoothed_fit()` `spm_smoothed_fit<-`() `spm_smoothed_vars()` `spm_smoothed_vars<-`() `is_mapped()` `is_mapped<-`() `spm_boundaries(<sspm_dataset>)` `spm_boundaries<-`(<sspm_dataset>)	Accessing OR replacing `sspm_dataset` model elements
`spm_unique_ID(<sspm_fit>)` `spm_unique_ID<-`(<sspm_fit>) `spm_time(<sspm_fit>)` `spm_time<-`(<sspm_fit>) `spm_formulas(<sspm_fit>)` `spm_formulas<-`(<sspm_fit>) `spm_smoothed_data(<sspm_fit>)` `spm_smoothed_data<-`(<sspm_fit>) `spm_get_fit()` `spm_get_fit<-`() `spm_boundaries(<sspm_fit>)` `spm_boundaries<-`(<sspm_fit>) `spm_boundary(<sspm_fit>)` `spm_boundary<-`(<sspm_fit>)	Accessing OR replacing `sspm_fit` model elements
`spm_name()` `spm_name<-`() `spm_datasets()` `spm_datasets<-`() `spm_boundaries()` `spm_boundaries<-`() `spm_smoothed_data()` `spm_smoothed_data<-`() `spm_time()` `spm_time<-`() `is_split()` `is_split<-`() `spm_unique_ID()` `spm_unique_ID<-`()	Accessing OR replacing `sspm` model elements
`sspm_boundary-class`	sspm boundary structure
`$`(<sspm_boundary>) `$`(<sspm_discrete_boundary>) `$`(<sspm_dataset>) `$`(<sspm>)	Extract methods
`raw_formula()` `raw_formula<-`() `translated_formula()` `translated_formula<-`() `formula_vars()` `formula_vars<-`() `formula_type()` `formula_type<-`() `is_fitted()` `is_fitted<-`() `spm_response()` `spm_response<-`() `spm_lagged_vars()` `spm_lagged_vars<-`()	Accessing OR replacing `sspm_formula` model elements
`method_func()` `method_func<-`() `spm_name(<discretization_method>)` `spm_name<-`(<discretization_method>)	Accessing OR replacing `discretization_method` model elements

Reference

Workflow steps

Casting boundaries

Discretizing boundaries

Casting datasets

Smoothing biomass

Aggregating catch

Assembling and modifiying SSPM objects

Fitting the surplus production model

Predict and plot

Datasets

Accessors