# Systematic Conservation Prioritization in R

## Documentation for package ‘prioritizr’ version 5.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D F I L M N O P R S T U V Z misc

## -- A --

A | Optimization problem methods
A-method | Optimization problem methods
add_absolute_targets | Add absolute targets
add_absolute_targets-method | Add absolute targets
add_binary_decisions | Add binary decisions
add_boundary_penalties | Add boundary penalties
add_connectivity_penalties | Add connectivity penalties
add_connectivity_penalties-method | Add connectivity penalties
add_contiguity_constraints | Add contiguity constraints
add_contiguity_constraints-method | Add contiguity constraints
add_cuts_portfolio | Add Bender's cuts portfolio
add_default_decisions | Add default decisions
add_default_solver | Default solver
add_extra_portfolio | Add an extra portfolio
add_feature_contiguity_constraints | Add feature contiguity constraints
add_feature_contiguity_constraints-method | Add feature contiguity constraints
add_feature_weights | Add feature weights
add_feature_weights-method | Add feature weights
add_gap_portfolio | Add a gap portfolio
add_gurobi_solver | Add a _Gurobi_ solver
add_linear_penalties | Add linear penalties
add_linear_penalties-method | Add linear penalties
add_locked_in_constraints | Add locked in constraints
add_locked_in_constraints-method | Add locked in constraints
add_locked_out_constraints | Add locked out constraints
add_locked_out_constraints-method | Add locked out constraints
add_loglinear_targets | Add targets using log-linear scaling
add_lpsymphony_solver | Add a SYMPHONY solver with _lpsymphony_
add_lsymphony_solver | Add a SYMPHONY solver with _lpsymphony_
add_mandatory_allocation_constraints | Add mandatory allocation constraints
add_mandatory_allocation_constraints-method | Add mandatory allocation constraints
add_manual_bounded_constraints | Add manually specified bounds constraints
add_manual_bounded_constraints-method | Add manually specified bounds constraints
add_manual_locked_constraints | Add manually specified locked constraints
add_manual_locked_constraints-method | Add manually specified locked constraints
add_manual_targets | Add manual targets
add_manual_targets-method | Add manual targets
add_max_cover_objective | Add maximum coverage objective
add_max_features_objective | Add maximum feature representation objective
add_max_phylo_div_objective | Add maximum phylogenetic diversity objective
add_max_phylo_end_objective | Add maximum phylogenetic endemism objective
add_max_phylo_objective | Add maximum phylogenetic diversity objective
add_max_utility_objective | Add maximum utility objective
add_min_set_objective | Add minimum set objective
add_min_shortfall_objective | Add minimum shortfall objective
add_neighbor_constraints | Add neighbor constraints
add_neighbor_constraints-method | Add neighbor constraints
add_proportion_decisions | Add proportion decisions
add_relative_targets | Add relative targets
add_relative_targets-method | Add relative targets
add_rsymphony_solver | Add a SYMPHONY solver with _Rsymphony_
add_semicontinuous_decisions | Add semi-continuous decisions
add_shuffle_portfolio | Add a shuffle portfolio
add_top_portfolio | Add a top portfolio
adjacency_matrix | Adjacency matrix
adjacency_matrix.default | Adjacency matrix
adjacency_matrix.Raster | Adjacency matrix
adjacency_matrix.sf | Adjacency matrix
adjacency_matrix.SpatialLines | Adjacency matrix
adjacency_matrix.SpatialPoints | Adjacency matrix
adjacency_matrix.SpatialPolygons | Adjacency matrix
ArrayParameter | Array parameter prototype
ArrayParameter-class | Array parameter prototype
array_parameters | Array parameters
as | Coerce object to another object
as.Id | Coerce object to another object
as.Id.character | Coerce object to another object
as.list-method | Manipulate tibbles
as.list.OptimizationProblem | Convert 'OptimizationProblem' to list
as.list.Parameters | Coerce object to another object
as.list.Zones | Coerce object to another object

## -- B --

binary_matrix_parameter | Matrix parameters
binary_parameter | Scalar parameters
binary_parameter_array | Array parameters
binary_stack | Binary stack
boundary_matrix | Boundary matrix
boundary_matrix.default | Boundary matrix
boundary_matrix.Raster | Boundary matrix
boundary_matrix.sf | Boundary matrix
boundary_matrix.SpatialLines | Boundary matrix
boundary_matrix.SpatialPoints | Boundary matrix
boundary_matrix.SpatialPolygons | Boundary matrix
branch_matrix | Branch matrix
branch_matrix.default | Branch matrix
branch_matrix.phylo | Branch matrix

## -- C --

category_layer | Category layer
category_vector | Category vector
category_vector.data.frame | Category vector
category_vector.matrix | Category vector
category_vector.sf | Category vector
category_vector.Spatial | Category vector
Collection | Collection prototype
Collection-class | Collection prototype
col_ids | Optimization problem methods
col_ids-method | Optimization problem methods
compile | Compile a problem
compile.ConservationProblem | Compile a problem
compressed_formulation | Optimization problem methods
compressed_formulation-method | Optimization problem methods
connectivity_matrix | Connectivity matrix
connectivity_matrix-method | Connectivity matrix
ConservationModifier | Conservation problem modifier prototype
ConservationModifier-class | Conservation problem modifier prototype
ConservationProblem | Conservation problem class
ConservationProblem-class | Conservation problem class
Constraint | Constraint prototype
Constraint-class | Constraint prototype
constraints | Conservation problem constraints

## -- D --

Decision | Decision prototype
Decision-class | Decision prototype
decisions | Specify the type of decisions
distribute_load | Distribute load

## -- F --

fast_extract | Fast extract
fast_extract-method | Fast extract
feature_abundances | Feature abundances
feature_abundances.ConservationProblem | Feature abundances
feature_names | Feature names
feature_names-method | Feature names
feature_representation | Feature representation
feature_representation-method | Feature representation
ferrier_score | Ferrier irreplaceability score
ferrier_score-method | Ferrier irreplaceability score

## -- I --

Id | Identifier
integer_parameter | Scalar parameters
integer_parameter_array | Array parameters
intersecting_units | Find intersecting units
intersecting_units-method | Find intersecting units
irreplaceability | Irreplaceability
is | Is it?
is.Id | Is it?
is.Waiver | Is it?

## -- L --

lb | Optimization problem methods
lb-method | Optimization problem methods
loglinear_interpolation | Log-linear interpolation

## -- M --

marxan_boundary_data_to_matrix | Convert _Marxan_ boundary data to a matrix format
marxan_problem | _Marxan_ conservation problem
marxan_problem.character | _Marxan_ conservation problem
marxan_problem.data.frame | _Marxan_ conservation problem
marxan_problem.default | _Marxan_ conservation problem
matrix_parameters | Matrix parameters
MiscParameter | Miscellaneous parameter prototype
MiscParameter-class | Miscellaneous parameter prototype
misc_parameter | Miscellaneous parameter
modelsense | Optimization problem methods
modelsense-method | Optimization problem methods

## -- N --

ncell | Optimization problem methods
ncell-method | Optimization problem methods
ncol | Optimization problem methods
ncol-method | Optimization problem methods
ncol-method | Manipulate tibbles
new_id | Identifier
new_optimization_problem | Optimization problem
new_waiver | Waiver
nrow | Optimization problem methods
nrow-method | Optimization problem methods
nrow-method | Manipulate tibbles
number_of_features | Number of features
number_of_features-method | Number of features
number_of_planning_units | Number of planning units
number_of_planning_units-method | Number of planning units
number_of_total_units | Number of total units
number_of_total_units-method | Number of total units
number_of_zones | Number of zones
number_of_zones-method | Number of zones
numeric_matrix_parameter | Matrix parameters
numeric_parameter | Scalar parameters
numeric_parameter_array | Array parameters

## -- O --

obj | Optimization problem methods
obj-method | Optimization problem methods
Objective | Objective prototype
Objective-class | Objective prototype
objectives | Problem objective
OptimizationProblem | Optimization problem class
OptimizationProblem-class | Optimization problem class
OptimizationProblem-methods | Optimization problem methods

## -- P --

Parameter | Parameter class
Parameter-class | Parameter class
Parameters | Parameters class
parameters | Parameters
Parameters-class | Parameters class
penalties | Conservation problem penalties
Penalty | Penalty prototype
Penalty-class | Penalty prototype
pipe | Pipe operator
Portfolio | Portfolio prototype
Portfolio-class | Portfolio prototype
portfolios | Solution portfolios
pproto | Create a new 'pproto' object
predefined_optimization_problem | Predefined optimization problem
presolve_check | Presolve check
presolve_check.ConservationProblem | Presolve check
presolve_check.OptimizationProblem | Presolve check
print | Print
print-method | Print
print.ArrayParameter | Print
print.ConservationModifier | Print
print.ConservationProblem | Print
print.Id | Print
print.OptimizationProblem | Print
print.ScalarParameter | Print
print.Solver | Print
print.Zones | Print
prioritizr | prioritizr: Systematic Conservation Prioritization in R
problem | Conservation planning problem
problem-method | Conservation planning problem
proportion_parameter | Scalar parameters
proportion_parameter_array | Array parameters
proximity_matrix | Proximity matrix
proximity_matrix.default | Proximity matrix
proximity_matrix.Raster | Proximity matrix
proximity_matrix.sf | Proximity matrix
proximity_matrix.SpatialLines | Proximity matrix
proximity_matrix.SpatialPoints | Proximity matrix
proximity_matrix.SpatialPolygons | Proximity matrix

## -- R --

rarity_weighted_richness | Rarity weighted richness
rarity_weighted_richness-method | Rarity weighted richness
replacement_cost | Replacement cost
replacement_cost-method | Replacement cost
rhs | Optimization problem methods
rhs-method | Optimization problem methods
rij_matrix | Feature by planning unit matrix
rij_matrix-method | Feature by planning unit matrix
row_ids | Optimization problem methods
row_ids-method | Optimization problem methods
run_calculations | Run calculations

## -- S --

ScalarParameter | Scalar parameter prototype
ScalarParameter-class | Scalar parameter prototype
scalar_parameters | Scalar parameters
sense | Optimization problem methods
sense-method | Optimization problem methods
show | Show
show-method | Show
simulate_cost | Simulate cost data
simulate_data | Simulate data
simulate_species | Simulate species habitat suitability data
sim_data | Simulated conservation planning data
sim_features | Simulated conservation planning data
sim_features_zones | Simulated conservation planning data
sim_locked_in_raster | Simulated conservation planning data
sim_locked_out_raster | Simulated conservation planning data
sim_phylogeny | Simulated conservation planning data
sim_pu_lines | Simulated conservation planning data
sim_pu_points | Simulated conservation planning data
sim_pu_polygons | Simulated conservation planning data
sim_pu_raster | Simulated conservation planning data
sim_pu_sf | Simulated conservation planning data
sim_pu_zones_polygons | Simulated conservation planning data
sim_pu_zones_sf | Simulated conservation planning data
sim_pu_zones_stack | Simulated conservation planning data
solve | Solve
solve-method | Solve
Solver | Solver prototype
Solver-class | Solver prototype
solvers | Problem solvers

## -- T --

Target | Target prototype
Target-class | Target prototype
targets | Targets
tee | Tee operator
tibble-methods | Manipulate tibbles

## -- U --

ub | Optimization problem methods
ub-method | Optimization problem methods

## -- V --

vtype | Optimization problem methods
vtype-method | Optimization problem methods

## -- Z --

Zones | Management zones
zones | Management zones
Zones-class | Management zones
ZonesCharacter | Management zones
ZonesRaster | Management zones
zone_names | Zone names
zone_names-method | Zone names

## -- misc --

%>% | Pipe operator
%T>% | Tee operator