Systematic Conservation Prioritization in R

Documentation for package ‘prioritizr’ version 8.0.6

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prioritizr: Systematic Conservation Prioritization in R

-- 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_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_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_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_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_rank_importance	Evaluate solution importance using incremental ranks
eval_rank_importance-method	Evaluate solution importance using incremental ranks
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
rescale_matrix	Rescale a matrix
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