R: Spatial Surplus Production Model Framework for Northern Shrimp Populations

# Spatial Surplus Production Model Framework for Northern Shrimp Populations

## Documentation for package ‘sspm’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F I M P R S T misc

## -- A --

as_discretization_method | Cast into a 'discretization_method' object
as_discretization_method-method | Cast into a 'discretization_method' object

## -- B --

borealis_simulated | Simulated biomass data

## -- C --

catch_simulated | Simulated catch data

## -- D --

discretization_method-class | sspm discretization method class

## -- E --

extract | Extract methods

## -- F --

formula_type | Accessing OR replacing 'sspm_formula' model elements
formula_type-method | Accessing OR replacing 'sspm_formula' model elements
formula_type<- | Accessing OR replacing 'sspm_formula' model elements
formula_type<--method | Accessing OR replacing 'sspm_formula' model elements
formula_vars | Accessing OR replacing 'sspm_formula' model elements
formula_vars-method | Accessing OR replacing 'sspm_formula' model elements
formula_vars<- | Accessing OR replacing 'sspm_formula' model elements
formula_vars<--method | Accessing OR replacing 'sspm_formula' model elements

## -- I --

is_fitted | Accessing OR replacing 'sspm_formula' model elements
is_fitted-method | Accessing OR replacing 'sspm_formula' model elements
is_fitted<- | Accessing OR replacing 'sspm_formula' model elements
is_fitted<--method | Accessing OR replacing 'sspm_formula' model elements
is_mapped | Accessing OR replacing 'sspm_dataset' model elements
is_mapped-method | Accessing OR replacing 'sspm_dataset' model elements
is_mapped<- | Accessing OR replacing 'sspm_dataset' model elements
is_mapped<--method | Accessing OR replacing 'sspm_dataset' model elements
is_split | Accessing OR replacing 'sspm' model elements
is_split-method | Accessing OR replacing 'sspm' model elements
is_split<- | Accessing OR replacing 'sspm' model elements
is_split<--method | Accessing OR replacing 'sspm' model elements

## -- M --

method_func | Accessing OR replacing 'discretization_method' model elements
method_func-method | Accessing OR replacing 'discretization_method' model elements
method_func<- | Accessing OR replacing 'discretization_method' model elements
method_func<--method | Accessing OR replacing 'discretization_method' model elements

## -- P --

plot | Plot 'sspm' objects
plot-method | Plot 'sspm' objects
plot.sspm | Plot 'sspm' objects
predator_simulated | Simulated predator data
predict | Predict with a SPM model
predict-method | Predict with a SPM model
predict.sspm | Predict with a SPM model
predict_intervals | GAM confidence and prediction intervals

## -- R --

raw_formula | Accessing OR replacing 'sspm_formula' model elements
raw_formula-method | Accessing OR replacing 'sspm_formula' model elements
raw_formula<- | Accessing OR replacing 'sspm_formula' model elements
raw_formula<--method | Accessing OR replacing 'sspm_formula' model elements

## -- S --

sfa_boundaries | SFA boundaries data
smooth_lag | sspm Smoothing functions
smooth_lag-method | sspm Smoothing functions
smooth_space | sspm Smoothing functions
smooth_space-method | sspm Smoothing functions
smooth_space_time | sspm Smoothing functions
smooth_space_time-method | sspm Smoothing functions
smooth_time | sspm Smoothing functions
smooth_time-method | sspm Smoothing functions
spm | Fit an SPM model
spm-method | Fit an SPM model
spm_ | Accessing OR replacing 'sspm' model elements
spm_aggregate | Aggregate a dataset or fit data variable based on a boundary
spm_aggregate-method | Aggregate a dataset or fit data variable based on a boundary
spm_aggregate_catch | Update biomass value from catch adta
spm_aggregate_catch-method | Update biomass value from catch adta
spm_as_boundary | Create a sspm_boundary object
spm_as_boundary-method | Create a sspm_boundary object
spm_as_dataset | Create a 'sspm_dataset' dataset structure
spm_as_dataset-method | Create a 'sspm_dataset' dataset structure
spm_biomass_vars | Accessing OR replacing 'sspm_dataset' model elements
spm_biomass_vars-method | Accessing OR replacing 'sspm_dataset' model elements
spm_biomass_vars<- | Accessing OR replacing 'sspm_dataset' model elements
spm_biomass_vars<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_boundaries | Accessing OR replacing 'sspm' model elements
spm_boundaries-method | Accessing OR replacing 'sspm_boundary' model elements
spm_boundaries-method | Accessing OR replacing 'sspm_dataset' model elements
spm_boundaries-method | Accessing OR replacing 'sspm_fit' model elements
spm_boundaries-method | Accessing OR replacing 'sspm' model elements
spm_boundaries<- | Accessing OR replacing 'sspm' model elements
spm_boundaries<--method | Accessing OR replacing 'sspm_boundary' model elements
spm_boundaries<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_boundaries<--method | Accessing OR replacing 'sspm_fit' model elements
spm_boundaries<--method | Accessing OR replacing 'sspm' model elements
spm_boundary | Accessing OR replacing 'sspm_boundary' model elements
spm_boundary-method | Accessing OR replacing 'sspm_boundary' model elements
spm_boundary-method | Accessing OR replacing 'sspm_fit' model elements
spm_boundary<- | Accessing OR replacing 'sspm_boundary' model elements
spm_boundary<--method | Accessing OR replacing 'sspm_boundary' model elements
spm_boundary<--method | Accessing OR replacing 'sspm_fit' model elements
spm_boundary_area | Accessing OR replacing 'sspm_boundary' model elements
spm_boundary_area-method | Accessing OR replacing 'sspm_boundary' model elements
spm_boundary_area<- | Accessing OR replacing 'sspm_boundary' model elements
spm_boundary_area<--method | Accessing OR replacing 'sspm_boundary' model elements
spm_coords_col | Accessing OR replacing 'sspm_dataset' model elements
spm_coords_col-method | Accessing OR replacing 'sspm_dataset' model elements
spm_coords_col<- | Accessing OR replacing 'sspm_dataset' model elements
spm_coords_col<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_data | Accessing OR replacing 'sspm_dataset' model elements
spm_data-method | Accessing OR replacing 'sspm_dataset' model elements
spm_data<- | Accessing OR replacing 'sspm_dataset' model elements
spm_data<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_datasets | Accessing OR replacing 'sspm' model elements
spm_datasets-method | Accessing OR replacing 'sspm' model elements
spm_datasets<- | Accessing OR replacing 'sspm' model elements
spm_datasets<--method | Accessing OR replacing 'sspm' model elements
spm_density_vars | Accessing OR replacing 'sspm_dataset' model elements
spm_density_vars-method | Accessing OR replacing 'sspm_dataset' model elements
spm_density_vars<- | Accessing OR replacing 'sspm_dataset' model elements
spm_density_vars<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_discretize | Discretize a 'sspm' model object
spm_discretize-method | Discretize a 'sspm' model object
spm_discret_method | Accessing OR replacing 'sspm_boundary' model elements
spm_discret_method-method | Accessing OR replacing 'sspm_boundary' model elements
spm_discret_method<- | Accessing OR replacing 'sspm_boundary' model elements
spm_discret_method<--method | Accessing OR replacing 'sspm_boundary' model elements
spm_formulas | Accessing OR replacing 'sspm_dataset' model elements
spm_formulas-method | Accessing OR replacing 'sspm_dataset' model elements
spm_formulas-method | Accessing OR replacing 'sspm_fit' model elements
spm_formulas<- | Accessing OR replacing 'sspm_dataset' model elements
spm_formulas<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_formulas<--method | Accessing OR replacing 'sspm_fit' model elements
spm_get_fit | Accessing OR replacing 'sspm_fit' model elements
spm_get_fit-method | Accessing OR replacing 'sspm_fit' model elements
spm_get_fit<- | Accessing OR replacing 'sspm_fit' model elements
spm_get_fit<--method | Accessing OR replacing 'sspm_fit' model elements
spm_lag | Create lagged columns in a sspm smoothed data slot
spm_lag-method | Create lagged columns in a sspm smoothed data slot
spm_lagged_vars | Accessing OR replacing 'sspm_formula' model elements
spm_lagged_vars-method | Accessing OR replacing 'sspm_formula' model elements
spm_lagged_vars<- | Accessing OR replacing 'sspm_formula' model elements
spm_lagged_vars<--method | Accessing OR replacing 'sspm_formula' model elements
spm_methods | Get the list of available discretization methods
spm_name | Accessing OR replacing 'sspm' model elements
spm_name-method | Accessing OR replacing 'discretization_method' model elements
spm_name-method | Accessing OR replacing 'sspm_dataset' model elements
spm_name<- | Accessing OR replacing 'sspm' model elements
spm_name<--method | Accessing OR replacing 'discretization_method' model elements
spm_name<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_patches | Accessing OR replacing 'sspm_boundary' model elements
spm_patches-method | Accessing OR replacing 'sspm_boundary' model elements
spm_patches<- | Accessing OR replacing 'sspm_boundary' model elements
spm_patches<--method | Accessing OR replacing 'sspm_boundary' model elements
spm_patches_area | Accessing OR replacing 'sspm_boundary' model elements
spm_patches_area-method | Accessing OR replacing 'sspm_boundary' model elements
spm_patches_area<- | Accessing OR replacing 'sspm_boundary' model elements
spm_patches_area<--method | Accessing OR replacing 'sspm_boundary' model elements
spm_points | Accessing OR replacing 'sspm_boundary' model elements
spm_points-method | Accessing OR replacing 'sspm_boundary' model elements
spm_points<- | Accessing OR replacing 'sspm_boundary' model elements
spm_points<--method | Accessing OR replacing 'sspm_boundary' model elements
spm_response | Accessing OR replacing 'sspm_formula' model elements
spm_response-method | Accessing OR replacing 'sspm_formula' model elements
spm_response<- | Accessing OR replacing 'sspm_formula' model elements
spm_response<--method | Accessing OR replacing 'sspm_formula' model elements
spm_smooth | Smooth a variable in a sspm dataset
spm_smooth-method | Smooth a variable in a sspm dataset
spm_smoothed_data | Accessing OR replacing 'sspm' model elements
spm_smoothed_data-method | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_data-method | Accessing OR replacing 'sspm_fit' model elements
spm_smoothed_data-method | Accessing OR replacing 'sspm' model elements
spm_smoothed_data<- | Accessing OR replacing 'sspm' model elements
spm_smoothed_data<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_data<--method | Accessing OR replacing 'sspm_fit' model elements
spm_smoothed_data<--method | Accessing OR replacing 'sspm' model elements
spm_smoothed_fit | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_fit-method | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_fit<- | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_fit<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_vars | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_vars-method | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_vars<- | Accessing OR replacing 'sspm_dataset' model elements
spm_smoothed_vars<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_smooth_methods | Get the list of available smoothing methods
spm_split | Split data in test and train sets
spm_split-method | Split data in test and train sets
spm_time | Accessing OR replacing 'sspm' model elements
spm_time-method | Accessing OR replacing 'sspm_dataset' model elements
spm_time-method | Accessing OR replacing 'sspm_fit' model elements
spm_time-method | Accessing OR replacing 'sspm' model elements
spm_time<- | Accessing OR replacing 'sspm' model elements
spm_time<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_time<--method | Accessing OR replacing 'sspm_fit' model elements
spm_time<--method | Accessing OR replacing 'sspm' model elements
spm_unique_ID | Accessing OR replacing 'sspm' model elements
spm_unique_ID-method | Accessing OR replacing 'sspm_dataset' model elements
spm_unique_ID-method | Accessing OR replacing 'sspm_fit' model elements
spm_unique_ID-method | Accessing OR replacing 'sspm' model elements
spm_unique_ID<- | Accessing OR replacing 'sspm' model elements
spm_unique_ID<--method | Accessing OR replacing 'sspm_dataset' model elements
spm_unique_ID<--method | Accessing OR replacing 'sspm_fit' model elements
spm_unique_ID<--method | Accessing OR replacing 'sspm' model elements
sspm | Create a 'sspm' model object
sspm-class | sspm model class
sspm-method | Create a 'sspm' model object
sspm_boundary-class | sspm boundary structure
sspm_dataset-class | sspm dataset structure
sspm_discrete_boundary-class | sspm discrete boundary structure
sspm_fit-class | sspm fit
sspm_formula-class | sspm formula object
summary | Summarises 'sspm_fit' objects
summary-method | Summarises 'sspm_fit' objects
summary.sspm | Summarises 'sspm_fit' objects

## -- T --

tesselate_voronoi | Perform voronoi tesselation
translated_formula | Accessing OR replacing 'sspm_formula' model elements
translated_formula-method | Accessing OR replacing 'sspm_formula' model elements
translated_formula<- | Accessing OR replacing 'sspm_formula' model elements
translated_formula<--method | Accessing OR replacing 'sspm_formula' model elements
triangulate_delaunay | Perform delaunay triangulation

## -- misc --

$-method | Extract methods