Systematic Conservation Prioritization in R

Documentation for package ‘prioritizr’ version 9.0.1

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prioritizr: Systematic Conservation Prioritization in R

-- A --

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_auto_targets	Add targets automatically
add_auto_targets-method	Add targets automatically
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_cost_constraints	Add cost constraints
add_cost_penalties	Add cost penalties
add_cplex_solver	Add a _CPLEX_ solver
add_cuts_portfolio	Add Bender's cuts portfolio
add_default_portfolio	Add a default 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_group_targets	Add targets based on feature groups
add_gurobi_solver	Add a _Gurobi_ solver
add_hier_approach	Add a hierarchical approach
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	Deprecation notice
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_n_targets_met_objective	Add maximum number of targets met 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	Deprecation notice
add_max_utility_objective	Deprecation notice
add_max_wtd_sum_objective	Add maximum weighted sum objective
add_min_largest_shortfall_objective	Add minimum largest shortfall objective
add_min_penalties_objective	Add minimum penalties 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_neighbor_penalties	Add neighbor penalties
add_neighbor_penalties-method	Add neighbor penalties
add_pool_portfolio	Deprecation notice
add_proportion_decisions	Add proportion decisions
add_ref_point_approach	Add a reference point approach
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_single_portfolio	Add a single portfolio
add_top_portfolio	Add a top portfolio
add_wtd_sum_approach	Add a weighted sum approach
adjacency_matrix	Adjacency matrix
adjacency_matrix.default	Adjacency matrix
adjacency_matrix.sf	Adjacency matrix
adjacency_matrix.SpatRaster	Adjacency matrix
approaches	Add an approach
approach_rel_tol_matrix	Create relative tolerance values for a multi-objective approach
approach_weights_matrix	Create weight values for a multi-objective approach
as.list-method	Manipulate tibbles
as_km2	Standardize unit to km^2
as_per_km2	Standardize unit to density per km^2

-- B --

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

-- C --

calibrate_cohon_penalty	Calibrate penalties with Cohon's method
category_layer	Category layer
category_vector	Category vector
category_vector.data.frame	Category vector
category_vector.matrix	Category vector
category_vector.sf	Category vector
compile	Compile a problem
compile.ConservationProblem	Compile a problem
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_cost_summary.ConservationProblem	Evaluate cost of solution
eval_cost_summary.MultiConservationProblem	Evaluate cost of solution
eval_feature_representation_summary	Evaluate feature representation by solution
eval_feature_representation_summary.ConservationProblem	Evaluate feature representation by solution
eval_feature_representation_summary.MultiConservationProblem	Evaluate feature representation by solution
eval_ferrier_importance	Evaluate solution importance using Ferrier scores
eval_n_summary	Evaluate number of planning units selected by solution
eval_objective_summary	Evaluate objective value of solution
eval_objective_summary.ConservationProblem	Evaluate objective value of solution
eval_objective_summary.MultiConservationProblem	Evaluate objective value of solution
eval_rank_importance	Evaluate solution importance using incremental ranks
eval_rare_richness_importance	Evaluate solution importance using rarity weighted richness scores
eval_replacement_importance	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
eval_target_coverage_summary.ConservationProblem	Evaluate target coverage by solution
eval_target_coverage_summary.MultiConservationProblem	Evaluate target coverage by solution

-- F --

fast_extract	Fast extract
feature_abundances	Feature abundances
feature_abundances.ConservationProblem	Feature abundances
feature_names	Feature names
feature_names.ConservationProblem	Feature names
feature_names.MultiConservationProblem	Feature names
feature_names.ZonesCharacter	Feature names
feature_names.ZonesSpatRaster	Feature names
feature_representation	Deprecation notice
ferrier_score	Deprecation notice

-- G --

get_number_of_threads	Deprecation notice
get_sim_complex_features	Get simulated conservation planning data
get_sim_complex_historical_features	Get simulated conservation planning data
get_sim_complex_locked_in_raster	Get simulated conservation planning data
get_sim_complex_locked_out_raster	Get simulated conservation planning data
get_sim_complex_pu_raster	Get simulated conservation planning data
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.MultiConservationProblem	Print an object for knitr package.
knit_print.OptimizationProblem	Print an object for knitr package.

-- L --

linear_interpolation	Linear interpolation
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
MultiConservationProblem	Multi-objective conservation problem class
MultiConservationProblem-class	Multi-objective conservation problem class
MultiObjApproach	Multi-objective approach class
MultiObjApproach-class	Multi-objective approach class
multi_compile	Compile a multi-objective optimization problem
multi_compile.list	Compile a multi-objective optimization problem
multi_compile.MultiConservationProblem	Compile a multi-objective optimization problem
multi_problem	Multi-objective conservation planning problem

-- N --

ncol-method	Manipulate tibbles
new_optimization_problem	Deprecation notice
new_waiver	Waiver
nrow-method	Manipulate tibbles
number_of_features	Number of features
number_of_features.ConservationProblem	Number of features
number_of_features.MultiConservationProblem	Number of features
number_of_features.OptimizationProblem	Number of features
number_of_features.ZonesCharacter	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.MultiConservationProblem	Number of planning units
number_of_planning_units.OptimizationProblem	Number of planning units
number_of_problems	Number of problems
number_of_problems.ConservationProblem	Number of problems
number_of_problems.MultiConservationProblem	Number of features
number_of_total_units	Number of total units
number_of_total_units.ConservationProblem	Number of total units
number_of_total_units.MultiConservationProblem	Number of total units
number_of_zones	Number of zones
number_of_zones.ConservationProblem	Number of zones
number_of_zones.MultiConservationProblem	Number of zones
number_of_zones.OptimizationProblem	Number of zones
number_of_zones.ZonesCharacter	Number of zones
number_of_zones.ZonesSpatRaster	Number of zones

-- O --

Objective	Objective class
Objective-class	Objective class
objectives	Add an objective
OptimizationProblem	Optimization problem class
OptimizationProblem-class	Optimization problem class
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.MultiConservationProblem	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
problem_names	Problem names
problem_names.MultiConservationProblem	Feature names
proximity_matrix	Proximity matrix
proximity_matrix.default	Proximity matrix
proximity_matrix.sf	Proximity matrix
proximity_matrix.SpatRaster	Proximity matrix

-- R --

rarity_weighted_richness	Deprecation notice
replacement_cost	Deprecation notice
rescale_matrix	Rescale a matrix
rij_matrix	Feature by planning unit matrix
rij_matrix.sf	Feature by planning unit matrix
rij_matrix.SpatRaster	Feature by planning unit matrix
run_calculations	Run calculations

-- S --

set_number_of_threads	Deprecation notice
show	Show
show-method	Show
simulate_cost	Simulate cost data
simulate_data	Simulate data
simulate_species	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
solve.MultiConservationProblem	Solve
Solver	Solver class
Solver-class	Solver class
solvers	Add solvers
spec_absolute_targets	Specify absolute targets
spec_area_targets	Specify targets based on area units
spec_duran_targets	Specify targets following Durán _et al._ (2020)
spec_interp_absolute_targets	Specify targets based on interpolating absolute thresholds
spec_interp_area_targets	Specify targets based on interpolating area-based thresholds
spec_jung_targets	Specify targets following Jung _et al._ (2021)
spec_max_targets	Specify targets based on maxima
spec_min_targets	Specify targets based on minima
spec_polak_targets	Specify targets following Polak _et al._ (2015)
spec_pop_size_targets	Specify targets based on population size
spec_relative_targets	Specify relative targets
spec_rl_ecosystem_targets	Specify targets based on the IUCN Red List of Ecosystems
spec_rl_species_targets	Specify targets based on the IUCN Red List of Threatened Species
spec_rodrigues_targets	Specify targets following Rodrigues _et al._ (2004)
spec_rule_targets	Specify targets following a set of rules
spec_sreekar_targets	Specify targets following Sreekar and Watson (2026)
spec_ward_targets	Specify targets following Ward _et al._ (2025)
spec_watson_targets	Specify targets following Watson _et al._ (2010)
spec_wilson_targets	Specify targets following Wilson _et al._ (2010)
summaries	Evaluate solutions using summary statistics

-- T --

Target	Target class
Target-class	Target class
TargetMethod	Target setting method class
TargetMethod-class	Target setting method class
targets	Add representation targets
tibble-methods	Manipulate tibbles

-- W --

Weight	Weight class
Weight-class	Weight class
write_problem	Write problem

-- Z --

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