# Systematic Conservation Prioritization in R

## Documentation for package ‘prioritizr’ version 8.0.2

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

## Help Pages

A B C D E F G I K L M N O P R S T U V W Z

## -- A --

A | Optimization problem methods
A-method | Optimization problem methods
add_absolute_targets | Add absolute targets
add_absolute_targets-method | Add absolute targets
add_asym_connectivity_penalties | Add asymmetric connectivity penalties
add_asym_connectivity_penalties-method | Add asymmetric connectivity penalties
add_binary_decisions | Add binary decisions
add_boundary_penalties | Add boundary penalties
add_boundary_penalties-method | Add boundary penalties
add_cbc_solver | Add a _CBC_ solver
add_connected_constraints | Deprecation notice
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_corridor_constraints | Deprecation notice
add_cplex_solver | Add a _CPLEX_ solver
add_cuts_portfolio | Add Bender's cuts portfolio
add_default_solver | Add 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_highs_solver | Add a _HiGHS_ solver
add_linear_constraints | Add linear constraints
add_linear_constraints-method | Add linear constraints
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_manual_bounded_constraints | Add manually specified bound constraints
add_manual_bounded_constraints-method | Add manually specified bound 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_largest_shortfall_objective | Add minimum largest shortfall 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_pool_portfolio | Deprecation notice
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
adjacency_matrix.SpatRaster | Adjacency matrix
as.list-method | Manipulate tibbles

## -- B --

binary_stack | Binary stack
binary_stack.Raster | Binary stack
binary_stack.SpatRaster | 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
boundary_matrix.SpatRaster | Boundary matrix
branch_matrix | Branch matrix
branch_matrix.default | Branch matrix
branch_matrix.phylo | Branch matrix

## -- C --

category_layer | Category layer
category_layer.default | Category layer
category_layer.Raster | 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
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
connected_matrix | Deprecation notice
connectivity_matrix | Connectivity matrix
connectivity_matrix-method | Connectivity matrix
ConservationModifier | Conservation problem modifier class
ConservationModifier-class | Conservation problem modifier class
ConservationProblem | Conservation problem class
ConservationProblem-class | Conservation problem class
Constraint | Constraint class
Constraint-class | Constraint class
constraints | Conservation problem constraints

## -- D --

Decision | Decision class
Decision-class | Decision class
decisions | Add decision types
distribute_load | Deprecation notice

## -- E --

eval_asym_connectivity_summary | Evaluate asymmetric connectivity of solution
eval_asym_connectivity_summary-method | Evaluate asymmetric connectivity of solution
eval_boundary_summary | Evaluate boundary length of solution
eval_connectivity_summary | Evaluate connectivity of solution
eval_connectivity_summary-method | Evaluate connectivity of solution
eval_cost_summary | Evaluate cost of solution
eval_feature_representation_summary | Evaluate feature representation by solution
eval_ferrier_importance | Evaluate solution importance using Ferrier scores
eval_ferrier_importance-method | Evaluate solution importance using Ferrier scores
eval_n_summary | Evaluate number of planning units selected by solution
eval_rare_richness_importance | Evaluate solution importance using rarity weighted richness scores
eval_rare_richness_importance-method | Evaluate solution importance using rarity weighted richness scores
eval_replacement_importance | Evaluate solution importance using replacement cost scores
eval_replacement_importance-method | Evaluate solution importance using replacement cost scores
eval_target_coverage_summary | Evaluate target coverage by solution
eval_target_coverage_summary-method | Evaluate target coverage by solution

## -- 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.ConservationProblem | Feature names
feature_names.ZonesCharacter | Feature names
feature_names.ZonesRaster | Feature names
feature_names.ZonesSpatRaster | Feature names
feature_representation | Deprecation notice
ferrier_score | Deprecation notice

## -- G --

get_number_of_threads | Deprecation notice
get_sim_features | Get simulated conservation planning data
get_sim_locked_in_raster | Get simulated conservation planning data
get_sim_locked_out_raster | Get simulated conservation planning data
get_sim_phylogeny | Get simulated conservation planning data
get_sim_pu_lines | Get simulated conservation planning data
get_sim_pu_points | Get simulated conservation planning data
get_sim_pu_polygons | Get simulated conservation planning data
get_sim_pu_raster | Get simulated conservation planning data
get_sim_zones_features | Get simulated conservation planning data
get_sim_zones_pu_polygons | Get simulated conservation planning data
get_sim_zones_pu_raster | Get simulated conservation planning data

## -- I --

importance | Evaluate solution importance
intersecting_units | Find intersecting units
intersecting_units-method | Find intersecting units
irreplaceability | Evaluate solution importance
is.parallel | Deprecation notice

## -- K --

knit_print | Print an object for knitr package.
knit_print.ConservationProblem | Print an object for knitr package.
knit_print.OptimizationProblem | Print an object for knitr package.

## -- 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 matrix format
marxan_connectivity_data_to_matrix | Convert _Marxan_ connectivity data to 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
modelsense | Optimization problem methods
modelsense-method | Optimization problem methods

## -- N --

ncell-method | Optimization problem methods
ncol-method | Optimization problem methods
ncol-method | Manipulate tibbles
new_optimization_problem | Deprecation notice
new_waiver | Waiver
nrow-method | Optimization problem methods
nrow-method | Manipulate tibbles
number_of_features | Number of features
number_of_features.ConservationProblem | Number of features
number_of_features.OptimizationProblem | Number of features
number_of_features.ZonesCharacter | Number of features
number_of_features.ZonesRaster | Number of features
number_of_features.ZonesSpatRaster | Number of features
number_of_planning_units | Number of planning units
number_of_planning_units.ConservationProblem | Number of planning units
number_of_planning_units.OptimizationProblem | Number of planning units
number_of_total_units | Number of total units
number_of_total_units.ConservationProblem | Number of total units
number_of_zones | Number of zones
number_of_zones.ConservationProblem | Number of zones
number_of_zones.OptimizationProblem | Number of zones
number_of_zones.ZonesCharacter | Number of zones
number_of_zones.ZonesRaster | Number of zones
number_of_zones.ZonesSpatRaster | Number of zones

## -- O --

obj | Optimization problem methods
obj-method | Optimization problem methods
Objective | Objective class
Objective-class | Objective class
objectives | Add an objective
OptimizationProblem | Optimization problem class
OptimizationProblem-class | Optimization problem class
OptimizationProblem-methods | Optimization problem methods
optimization_problem | Optimization problem

## -- P --

penalties | Add a penalty
Penalty | Penalty class
Penalty-class | Penalty class
Portfolio | Portfolio class
Portfolio-class | Portfolio class
portfolios | Add portfolios
predefined_optimization_problem | Deprecation notice
presolve_check | Presolve check
presolve_check.ConservationProblem | Presolve check
presolve_check.OptimizationProblem | Presolve check
prioritizr | prioritizr: Systematic Conservation Prioritization in R
prioritizr-deprecated | Deprecation notice
problem | Conservation planning problem
problem-method | Conservation planning problem
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
proximity_matrix.SpatRaster | Proximity matrix

## -- R --

rarity_weighted_richness | Deprecation notice
replacement_cost | Deprecation notice
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 --

sense | Optimization problem methods
sense-method | Optimization problem methods
set_number_of_threads | Deprecation notice
show | Show
show-method | Show
simulate_cost | Simulate cost data
simulate_cost.Raster | Simulate cost data
simulate_cost.SpatRaster | Simulate cost data
simulate_data | Simulate data
simulate_data.Raster | Simulate data
simulate_data.SpatRaster | Simulate data
simulate_species | Simulate species habitat suitability data
simulate_species.Raster | Simulate species habitat suitability data
simulate_species.SpatRaster | Simulate species habitat suitability data
sim_data | Get simulated conservation planning data
sim_features | Get simulated conservation planning data
sim_locked_in_raster | Get simulated conservation planning data
sim_locked_out_raster | Get simulated conservation planning data
sim_phylogeny | Get simulated conservation planning data
sim_pu_lines | Get simulated conservation planning data
sim_pu_points | Get simulated conservation planning data
sim_pu_polygons | Get simulated conservation planning data
sim_pu_raster | Get simulated conservation planning data
sim_zones_features | Get simulated conservation planning data
sim_zones_pu_polygons | Get simulated conservation planning data
sim_zones_pu_raster | Get simulated conservation planning data
solve | Solve
solve.ConservationProblem | Solve
Solver | Solver class
Solver-class | Solver class
solvers | Add solvers
summaries | Evaluate solutions using summary statistics

## -- T --

Target | Target class
Target-class | Target class
targets | Add representation targets
tibble-methods | Manipulate tibbles

## -- U --

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

## -- V --

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

## -- W --

write_problem | Write problem

## -- Z --

Zones | Management zones
zones | Management zones
Zones-class | Management zones
ZonesCharacter | Management zones
ZonesRaster | Management zones
ZonesSpatRaster | Management zones
zone_names | Zone names
zone_names.ConservationProblem | Zone names
zone_names.ZonesCharacter | Zone names
zone_names.ZonesRaster | Zone names
zone_names.ZonesSpatRaster | Zone names