Spatial Surplus Production Model Framework for Northern Shrimp Populations

Documentation for package ‘sspm’ version 1.0.3

Help Pages

-- 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