ConservationProblem-class: Conservation problem class
In prioritizr/prioritizr: Systematic Conservation Prioritization in R
ConservationProblem-class R Documentation
Conservation problem class
Description
This class is used to represent conservation planning problems.
It stores the data (e.g., planning units, and features) and
mathematical formulation (e.g., the objective, constraints,
and other design criteria) needed to generate prioritizations.
Most users should use problem() to generate new conservation problem
objects, and the functions distributed with the package to interact
with them (e.g., number_of_features(), number_of_planning_units()).
Only experts should use the fields and methods for this class directly.
Public fields
datalist containing data (e.g., planning units, costs).
defaultslist indicating if other fields contain defaults.
objectiveObjective object specifying the objective
function for the problem formulation.
decisionssDecision object specifying the decision types
for the problem formulation.
targetsTarget object specifying the representation
targets for the problem formulation.
constraintslist containing Constraint objects that
specify constraints for the problem formulation.
penaltieslist containing Penalty objects that specify
penalties for the problem formulation.
portfolioPortfolio object specifying the approach for
generating multiple solutions.
solverSolver object specifying the solver for
generating solutions.
Methods
Public methods
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ConservationProblem$planning_unit_indices_with_finite_costs()
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ConservationProblem$set_planning_unit_indices_with_finite_costs()
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ConservationProblem$set_feature_abundances_in_planning_units()
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ConservationProblem$feature_positive_abundances_in_planning_units()
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ConservationProblem$set_feature_positive_abundances_in_planning_units()
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Method new()
Create a new conservation problem object.
Usage
ConservationProblem$new(data = list())
Arguments
datalist containing data
Returns
A new ConservationProblem object.
Method summary()
Print extended information about the object.
Usage
ConservationProblem$summary()
Returns
Invisible TRUE.
Method print()
Print concise information about the object.
Usage
ConservationProblem$print()
Returns
Invisible TRUE.
Method show()
Display concise information about the object.
Usage
ConservationProblem$show()
Returns
Invisible TRUE.
Method repr()
Generate a character representation of the object.
Usage
ConservationProblem$repr()
Returns
A character value.
Method get_data()
Get values stored in the data field.
Usage
ConservationProblem$get_data(x)
Arguments
xcharacter name of data.
Returns
An object. If the data field does not contain an object
associated with the argument to x, then a new_waiver() object is
returned.
Method set_data()
Set values stored in the data field. Note that this method will
overwrite existing data.
Usage
ConservationProblem$set_data(x, value)
Arguments
xcharacter name of data.
valueObject to store.
Returns
Invisible TRUE.
Method number_of_planning_units()
Obtain the number of planning units. The planning units correspond to
elements in the cost data
(e.g., indices, rows, geometries, pixels) that have finite
values in at least one zone. In other words, planning unit are
elements in the cost data that do not have missing (NA) values in
every zone.
Usage
ConservationProblem$number_of_planning_units()
Returns
An integer value.
Method planning_unit_indices()
Obtain the planning unit indices.
Usage
ConservationProblem$planning_unit_indices()
Returns
An integer vector.
Method set_planning_unit_indices()
Perform calculations to cache the planning unit indices.
Usage
ConservationProblem$set_planning_unit_indices()
Returns
Invisible TRUE.
Method planning_unit_indices_with_finite_costs()
Obtain the planning unit indices that are associated with
finite cost values.
Usage
ConservationProblem$planning_unit_indices_with_finite_costs()
Returns
A list of integer vectors. Each list element corresponds to
a different zone.
Method set_planning_unit_indices_with_finite_costs()
Perform calculations to cache the planning unit indices that are
associated with finite cost values.
Usage
ConservationProblem$set_planning_unit_indices_with_finite_costs()
Returns
Invisible TRUE.
Method number_of_total_units()
Obtain the number of total units. The total units include all elements
in the cost data
(e.g., indices, rows, geometries, pixels), including those with
missing (NA) values.
Usage
ConservationProblem$number_of_total_units()
Returns
An integer value.
Method planning_unit_costs()
Obtain the planning unit costs.
Usage
ConservationProblem$planning_unit_costs()
Returns
A numeric matrix.
Method set_planning_unit_costs()
Perform calculations to cache the planning unit costs.
Usage
ConservationProblem$set_planning_unit_costs()
Returns
Invisible TRUE.
Method number_of_features()
Obtain the number of features.
Usage
ConservationProblem$number_of_features()
Returns
An integer value.
Method feature_names()
Obtain the names of the features.
Usage
ConservationProblem$feature_names()
Returns
A character vector.
Method feature_abundances_in_planning_units()
Obtain the abundance of the features in the planning units.
Usage
ConservationProblem$feature_abundances_in_planning_units()
Returns
A numeric matrix. Each column corresponds to a different zone
and each row corresponds to a different feature.
Method set_feature_abundances_in_planning_units()
Perform calculations to cache the abundance of the features in the
planning units.
Usage
ConservationProblem$set_feature_abundances_in_planning_units()
Returns
Invisible TRUE.
Method feature_positive_abundances_in_planning_units()
Obtain the positive abundance of the features in the planning units.
Note that this method, unlike feature_abundances_in_planning_units,
Usage
ConservationProblem$feature_positive_abundances_in_planning_units()
Returns
A numeric matrix. Each column corresponds to a different zone
and each row corresponds to a different feature.
Method set_feature_positive_abundances_in_planning_units()
Perform calculations to cache the positive abundance of the features in
the planning units.
Usage
ConservationProblem$set_feature_positive_abundances_in_planning_units()
Returns
Invisible TRUE.
Method feature_abundances_in_total_units()
Obtain the abundance of the features in the total units.
Usage
ConservationProblem$feature_abundances_in_total_units()
Returns
A numeric matrix. Each column corresponds to a different zone
and each row corresponds to a different feature.
Method feature_targets()
Obtain the representation targets for the features.
Usage
ConservationProblem$feature_targets()
Returns
tibble::tibble() data frame.
Method number_of_zones()
Obtain the number of zones.
Usage
ConservationProblem$number_of_zones()
Returns
An integer value.
Method zone_names()
Obtain the zone names.
Usage
ConservationProblem$zone_names()
Returns
A character vector.
Method add_portfolio()
Create a new object with a portfolio added to the problem formulation.
Usage
ConservationProblem$add_portfolio(x)
Arguments
xPortfolio object.
Returns
An updated ConservationProblem object.
Method add_solver()
Create a new object with a solver added to the problem formulation.
Usage
ConservationProblem$add_solver(x)
Arguments
xSolver object.
Returns
An updated ConservationProblem object.
Method add_targets()
Create a new object with targets added to the problem formulation.
Usage
ConservationProblem$add_targets(x)
Arguments
xTarget object.
Returns
An updated ConservationProblem object.
Method add_objective()
Create a new object with an objective added to the problem formulation.
Usage
ConservationProblem$add_objective(x)
Arguments
xObjective object.
Returns
An updated ConservationProblem object.
Method add_decisions()
Create a new object with decisions added to the problem formulation.
Usage
ConservationProblem$add_decisions(x)
Arguments
xDecision object.
Returns
An updated ConservationProblem object.
Method add_constraint()
Create a new object with a constraint added to the problem formulation.
Usage
ConservationProblem$add_constraint(x)
Arguments
xConstraint object.
Returns
An updated ConservationProblem object.
Method add_penalty()
Create a new object with a penalty added to the problem formulation.
Usage
ConservationProblem$add_penalty(x)
Arguments
xPenalty object.
Returns
An updated ConservationProblem object.
Method clone()
The objects of this class are cloneable with this method.
Usage
ConservationProblem$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
Other classes:
ConservationModifier-class,
Constraint-class,
Decision-class,
Objective-class,
OptimizationProblem-class,
Penalty-class,
Portfolio-class,
Solver-class,
Target-class
prioritizr/prioritizr documentation built on March 4, 2024, 3:54 p.m.
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| ConservationProblem-class | R Documentation |
Conservation problem class
Description
This class is used to represent conservation planning problems.
It stores the data (e.g., planning units, and features) and
mathematical formulation (e.g., the objective, constraints,
and other design criteria) needed to generate prioritizations.
Most users should use problem() to generate new conservation problem
objects, and the functions distributed with the package to interact
with them (e.g., number_of_features(), number_of_planning_units()).
Only experts should use the fields and methods for this class directly.
Public fields
datalistcontaining data (e.g., planning units, costs).defaultslistindicating if other fields contain defaults.objectiveObjectiveobject specifying the objective function for the problem formulation.decisionss
Decisionobject specifying the decision types for the problem formulation.targetsTargetobject specifying the representation targets for the problem formulation.constraintslistcontainingConstraintobjects that specify constraints for the problem formulation.penaltieslistcontainingPenaltyobjects that specify penalties for the problem formulation.portfolioPortfolioobject specifying the approach for generating multiple solutions.solverSolverobject specifying the solver for generating solutions.
Methods
Public methods
-
ConservationProblem$planning_unit_indices_with_finite_costs() -
ConservationProblem$set_planning_unit_indices_with_finite_costs() -
ConservationProblem$set_feature_abundances_in_planning_units() -
ConservationProblem$feature_positive_abundances_in_planning_units() -
ConservationProblem$set_feature_positive_abundances_in_planning_units()
Method new()
Create a new conservation problem object.
Usage
ConservationProblem$new(data = list())
Arguments
datalistcontaining data
Returns
A new ConservationProblem object.
Method summary()
Print extended information about the object.
Usage
ConservationProblem$summary()
Returns
Invisible TRUE.
Method print()
Print concise information about the object.
Usage
ConservationProblem$print()
Returns
Invisible TRUE.
Method show()
Display concise information about the object.
Usage
ConservationProblem$show()
Returns
Invisible TRUE.
Method repr()
Generate a character representation of the object.
Usage
ConservationProblem$repr()
Returns
A character value.
Method get_data()
Get values stored in the data field.
Usage
ConservationProblem$get_data(x)
Arguments
xcharactername of data.
Returns
An object. If the data field does not contain an object
associated with the argument to x, then a new_waiver() object is
returned.
Method set_data()
Set values stored in the data field. Note that this method will
overwrite existing data.
Usage
ConservationProblem$set_data(x, value)
Arguments
xcharactername of data.valueObject to store.
Returns
Invisible TRUE.
Method number_of_planning_units()
Obtain the number of planning units. The planning units correspond to
elements in the cost data
(e.g., indices, rows, geometries, pixels) that have finite
values in at least one zone. In other words, planning unit are
elements in the cost data that do not have missing (NA) values in
every zone.
Usage
ConservationProblem$number_of_planning_units()
Returns
An integer value.
Method planning_unit_indices()
Obtain the planning unit indices.
Usage
ConservationProblem$planning_unit_indices()
Returns
An integer vector.
Method set_planning_unit_indices()
Perform calculations to cache the planning unit indices.
Usage
ConservationProblem$set_planning_unit_indices()
Returns
Invisible TRUE.
Method planning_unit_indices_with_finite_costs()
Obtain the planning unit indices that are associated with finite cost values.
Usage
ConservationProblem$planning_unit_indices_with_finite_costs()
Returns
A list of integer vectors. Each list element corresponds to
a different zone.
Method set_planning_unit_indices_with_finite_costs()
Perform calculations to cache the planning unit indices that are associated with finite cost values.
Usage
ConservationProblem$set_planning_unit_indices_with_finite_costs()
Returns
Invisible TRUE.
Method number_of_total_units()
Obtain the number of total units. The total units include all elements
in the cost data
(e.g., indices, rows, geometries, pixels), including those with
missing (NA) values.
Usage
ConservationProblem$number_of_total_units()
Returns
An integer value.
Method planning_unit_costs()
Obtain the planning unit costs.
Usage
ConservationProblem$planning_unit_costs()
Returns
A numeric matrix.
Method set_planning_unit_costs()
Perform calculations to cache the planning unit costs.
Usage
ConservationProblem$set_planning_unit_costs()
Returns
Invisible TRUE.
Method number_of_features()
Obtain the number of features.
Usage
ConservationProblem$number_of_features()
Returns
An integer value.
Method feature_names()
Obtain the names of the features.
Usage
ConservationProblem$feature_names()
Returns
A character vector.
Method feature_abundances_in_planning_units()
Obtain the abundance of the features in the planning units.
Usage
ConservationProblem$feature_abundances_in_planning_units()
Returns
A numeric matrix. Each column corresponds to a different zone
and each row corresponds to a different feature.
Method set_feature_abundances_in_planning_units()
Perform calculations to cache the abundance of the features in the planning units.
Usage
ConservationProblem$set_feature_abundances_in_planning_units()
Returns
Invisible TRUE.
Method feature_positive_abundances_in_planning_units()
Obtain the positive abundance of the features in the planning units.
Note that this method, unlike feature_abundances_in_planning_units,
Usage
ConservationProblem$feature_positive_abundances_in_planning_units()
Returns
A numeric matrix. Each column corresponds to a different zone
and each row corresponds to a different feature.
Method set_feature_positive_abundances_in_planning_units()
Perform calculations to cache the positive abundance of the features in the planning units.
Usage
ConservationProblem$set_feature_positive_abundances_in_planning_units()
Returns
Invisible TRUE.
Method feature_abundances_in_total_units()
Obtain the abundance of the features in the total units.
Usage
ConservationProblem$feature_abundances_in_total_units()
Returns
A numeric matrix. Each column corresponds to a different zone
and each row corresponds to a different feature.
Method feature_targets()
Obtain the representation targets for the features.
Usage
ConservationProblem$feature_targets()
Returns
tibble::tibble() data frame.
Method number_of_zones()
Obtain the number of zones.
Usage
ConservationProblem$number_of_zones()
Returns
An integer value.
Method zone_names()
Obtain the zone names.
Usage
ConservationProblem$zone_names()
Returns
A character vector.
Method add_portfolio()
Create a new object with a portfolio added to the problem formulation.
Usage
ConservationProblem$add_portfolio(x)
Arguments
xPortfolio object.
Returns
An updated ConservationProblem object.
Method add_solver()
Create a new object with a solver added to the problem formulation.
Usage
ConservationProblem$add_solver(x)
Arguments
xSolver object.
Returns
An updated ConservationProblem object.
Method add_targets()
Create a new object with targets added to the problem formulation.
Usage
ConservationProblem$add_targets(x)
Arguments
xTarget object.
Returns
An updated ConservationProblem object.
Method add_objective()
Create a new object with an objective added to the problem formulation.
Usage
ConservationProblem$add_objective(x)
Arguments
xObjective object.
Returns
An updated ConservationProblem object.
Method add_decisions()
Create a new object with decisions added to the problem formulation.
Usage
ConservationProblem$add_decisions(x)
Arguments
xDecision object.
Returns
An updated ConservationProblem object.
Method add_constraint()
Create a new object with a constraint added to the problem formulation.
Usage
ConservationProblem$add_constraint(x)
Arguments
xConstraint object.
Returns
An updated ConservationProblem object.
Method add_penalty()
Create a new object with a penalty added to the problem formulation.
Usage
ConservationProblem$add_penalty(x)
Arguments
xPenalty object.
Returns
An updated ConservationProblem object.
Method clone()
The objects of this class are cloneable with this method.
Usage
ConservationProblem$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
Other classes:
ConservationModifier-class,
Constraint-class,
Decision-class,
Objective-class,
OptimizationProblem-class,
Penalty-class,
Portfolio-class,
Solver-class,
Target-class
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