{ "_id": "6a2345bf530b9bc726bd546a", "Package": "prioritizr", "Type": "Package", "Version": "9.0.0.0", "Title": "Systematic Conservation Prioritization in R", "Description": "Systematic conservation prioritization using mixed integer\nlinear programming (MILP). It provides a flexible interface for\nbuilding and solving conservation planning problems. Once\nbuilt, conservation planning problems can be solved using a\nvariety of commercial and open-source exact algorithm solvers.\nBy using exact algorithm solvers, solutions can be generated\nthat are guaranteed to be optimal (or within a pre-specified\noptimality gap). Furthermore, conservation problems can be\nconstructed to optimize the spatial allocation of different\nmanagement actions or zones, meaning that conservation\npractitioners can identify solutions that benefit multiple\nstakeholders. To solve large-scale or complex conservation\nplanning problems, users should install the Gurobi optimization\nsoftware (available from ) and the\n'gurobi' R package (see Gurobi Installation Guide vignette for\ndetails). Users can also install the IBM CPLEX software\n()\nand the 'cplexAPI' R package (available at\n). Additionally, the 'rcbc' R\npackage (available at )\ncan be used to generate solutions using the CBC optimization\nsoftware (). For further\ndetails, see Hanson et al. (2025) .", "Authors@R": "c(person(c('Jeffrey', 'O'), 'Hanson',\nemail = 'jeffrey.hanson@uqconnect.edu.au', role = c('aut'),\ncomment = c(ORCID = '0000-0002-4716-6134')),\nperson(c('Richard'), 'Schuster',\nemail = 'richard.schuster@glel.carleton.ca', role = c('aut', 'cre'),\ncomment = c(ORCID = '0000-0003-3191-7869')),\nperson(c('Nina'), 'Morrell',\nemail = 'nina.morrell@ubc.ca', role = c('aut')),\nperson(c('Matthew'), 'Strimas-Mackey',\nemail = 'mstrimas@gmail.com', role = c('aut'),\ncomment = c(ORCID = '0000-0001-8929-7776')),\nperson(c('Sandra'), 'Neubert',\nemail = 's.neubert@uq.edu.au', role = c('aut'),\ncomment = c(ORCID = '0000-0002-3112-4116')),\nperson(c('Brandon', 'P', 'M'), 'Edwards',\nemail = 'brandonedwards3@cmail.carleton.ca', role = c('aut'),\ncomment = c(ORCID = '0000-0003-0865-3076')),\nperson(c('Matthew', 'E'), 'Watts',\nemail = 'm.watts@uq.edu.au', role = c('aut')),\nperson(c('Peter'), 'Arcese',\nemail = 'peter.arcese@ubc.ca', role = c('aut'),\ncomment = c(ORCID = 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Adjunct Professor, Carleton University. Conservation + dataviz + community science.", "uuid": 3445092 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "version": ">= 1.0.7", "role": "LinkingTo" }, { "package": "RcppArmadillo", "version": ">= 0.10.7.3.0", "role": "LinkingTo" }, { "package": "BH", "version": ">= 1.75.0-0", "role": "LinkingTo" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "R6", "version": ">= 2.5.1", "role": "Imports" }, { "package": "rlang", "version": ">= 1.1.0", "role": "Imports" }, { "package": "cli", "version": ">= 3.6.0", "role": "Imports" }, { "package": "sf", "version": ">= 1.0-12", "role": "Imports" }, { "package": "units", "version": ">= 0.8.7", "role": "Imports" }, { "package": "terra", "version": ">= 1.8-54", "role": "Imports" }, { "package": "raster", "version": ">= 3.6.11", "role": "Imports" }, { "package": "Matrix", 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"add_manual_bounded_constraints,ConservationProblem,data.frame-method", "add_manual_bounded_constraints,ConservationProblem,tbl_df-method" ] }, { "page": "add_manual_locked_constraints", "title": "Add manually specified locked constraints", "concept": [ "constraints" ], "topics": [ "add_manual_locked_constraints", "add_manual_locked_constraints,ConservationProblem,data.frame-method", "add_manual_locked_constraints,ConservationProblem,tbl_df-method" ] }, { "page": "add_manual_targets", "title": "Add manual targets", "concept": [ "targets" ], "topics": [ "add_manual_targets", "add_manual_targets,ConservationProblem,data.frame-method", "add_manual_targets,ConservationProblem,tbl_df-method", "add_manual_targets-method" ] }, { "page": "add_max_cover_objective", "title": "Add maximum coverage objective", "concept": [ "objectives" ], "topics": [ "add_max_cover_objective" ] }, { "page": "add_max_n_targets_met_objective", "title": "Add maximum number of targets met objective", "concept": [ "objectives" ], "topics": [ "add_max_n_targets_met_objective" ] }, { "page": "add_max_phylo_div_objective", "title": "Add maximum phylogenetic diversity objective", "concept": [ "objectives" ], "topics": [ "add_max_phylo_div_objective" ] }, { "page": "add_max_phylo_end_objective", "title": "Add maximum phylogenetic endemism objective", "concept": [ "objectives" ], "topics": [ "add_max_phylo_end_objective" ] }, { "page": "add_max_wtd_sum_objective", "title": "Add maximum weighted sum objective", "concept": [ "objectives" ], "topics": [ "add_max_wtd_sum_objective" ] }, { "page": "add_min_largest_shortfall_objective", "title": "Add minimum largest shortfall objective", "concept": [ "objectives" ], "topics": [ "add_min_largest_shortfall_objective" ] }, { "page": "add_min_penalties_objective", "title": "Add minimum penalties objective", "concept": [ "objectives" ], "topics": [ "add_min_penalties_objective" ] }, { "page": "add_min_set_objective", "title": "Add minimum set objective", "concept": [ "objectives" ], "topics": [ "add_min_set_objective" ] }, { "page": "add_min_shortfall_objective", "title": "Add minimum shortfall objective", "concept": [ "objectives" ], "topics": [ "add_min_shortfall_objective" ] }, { "page": "add_neighbor_constraints", "title": "Add neighbor constraints", "concept": [ "constraints" ], "topics": [ "add_neighbor_constraints", "add_neighbor_constraints,ConservationProblem,ANY,ANY,ANY,ANY-method", "add_neighbor_constraints,ConservationProblem,ANY,ANY,ANY,array-method", "add_neighbor_constraints,ConservationProblem,ANY,ANY,ANY,data.frame-method", "add_neighbor_constraints,ConservationProblem,ANY,ANY,ANY,matrix-method" ] }, { "page": "add_neighbor_penalties", "title": "Add neighbor penalties", "concept": [ "penalties" ], "topics": [ "add_neighbor_penalties", "add_neighbor_penalties,ConservationProblem,ANY,ANY,ANY-method", "add_neighbor_penalties,ConservationProblem,ANY,ANY,array-method", "add_neighbor_penalties,ConservationProblem,ANY,ANY,data.frame-method", "add_neighbor_penalties,ConservationProblem,ANY,ANY,Matrix-method", "add_neighbor_penalties,ConservationProblem,ANY,ANY,matrix-method" ] }, { "page": "add_proportion_decisions", "title": "Add proportion decisions", "concept": [ "decisions" ], "topics": [ "add_proportion_decisions" ] }, { "page": "add_ref_point_approach", "title": "Add a reference point approach", "concept": [ "approaches" ], "topics": [ "add_ref_point_approach" ] }, { "page": "add_relative_targets", "title": "Add relative targets", "concept": [ "targets" ], "topics": [ "add_relative_targets", "add_relative_targets,ConservationProblem,character-method", "add_relative_targets,ConservationProblem,matrix-method", "add_relative_targets,ConservationProblem,numeric-method", "add_relative_targets-method" ] }, { "page": "add_rsymphony_solver", "title": "Add a _SYMPHONY_ solver with _Rsymphony_", "concept": [ "solvers" ], "topics": [ "add_rsymphony_solver" ] }, { "page": "add_semicontinuous_decisions", "title": "Add semi-continuous decisions", "concept": [ "decisions" ], "topics": [ "add_semicontinuous_decisions" ] }, { "page": "add_shuffle_portfolio", "title": "Add a shuffle portfolio", "concept": [ "portfolios" ], "topics": [ "add_shuffle_portfolio" ] }, { "page": "add_single_portfolio", "title": "Add a single portfolio", "concept": [ "portfolios" ], "topics": [ "add_single_portfolio" ] }, { "page": "add_top_portfolio", "title": "Add a top portfolio", "concept": [ "portfolios" ], "topics": [ "add_top_portfolio" ] }, { "page": "add_wtd_sum_approach", "title": "Add a weighted sum approach", "concept": [ "approaches" ], "topics": [ "add_wtd_sum_approach" ] }, { "page": "adjacency_matrix", "title": "Adjacency matrix", "topics": [ "adjacency_matrix", "adjacency_matrix.default", "adjacency_matrix.Raster", "adjacency_matrix.sf", "adjacency_matrix.SpatialLines", "adjacency_matrix.SpatialPoints", "adjacency_matrix.SpatialPolygons", "adjacency_matrix.SpatRaster" ] }, { "page": "approach_rel_tol_matrix", "title": "Create relative tolerance values for a multi-objective approach", "topics": [ "approach_rel_tol_matrix" ] }, { "page": "approach_weights_matrix", "title": "Create weight values for a multi-objective approach", "topics": [ "approach_weights_matrix" ] }, { "page": "approaches", "title": "Add an approach", "concept": [ "overviews" ], "topics": [ "approaches" ] }, { "page": "as_km2", "title": "Standardize unit to km^2", "topics": [ "as_km2" ] }, { "page": "as_per_km2", "title": "Standardize unit to density per km^2", "topics": [ "as_per_km2" ] }, { "page": "binary_stack", "title": "Binary stack", "topics": [ "binary_stack", "binary_stack.Raster", "binary_stack.SpatRaster" ] }, { "page": "boundary_matrix", "title": "Boundary matrix", "topics": [ "boundary_matrix", "boundary_matrix.default", "boundary_matrix.Raster", "boundary_matrix.sf", "boundary_matrix.SpatialLines", "boundary_matrix.SpatialPoints", "boundary_matrix.SpatialPolygons", "boundary_matrix.SpatRaster" ] }, { "page": "branch_matrix", "title": "Branch matrix", "topics": [ "branch_matrix", "branch_matrix.default", "branch_matrix.phylo" ] }, { "page": "calibrate_cohon_penalty", "title": "Calibrate penalties with Cohon's method", "topics": [ "calibrate_cohon_penalty" ] }, { "page": "category_layer", "title": "Category layer", "topics": [ "category_layer", "category_layer.default", "category_layer.Raster" ] }, { "page": "category_vector", "title": "Category vector", "topics": [ "category_vector", "category_vector.data.frame", "category_vector.matrix", "category_vector.sf", "category_vector.Spatial" ] }, { "page": "compile", "title": "Compile a problem", "topics": [ "compile", "compile.ConservationProblem" ] }, { "page": "connectivity_matrix", "title": "Connectivity matrix", "topics": [ "connectivity_matrix", "connectivity_matrix,Raster,Raster-method", "connectivity_matrix,sf,character-method", "connectivity_matrix,sf,Raster-method", "connectivity_matrix,sf,SpatRaster-method", "connectivity_matrix,Spatial,character-method", "connectivity_matrix,Spatial,Raster-method", "connectivity_matrix,SpatRaster,SpatRaster-method" ] }, { "page": "ConservationModifier-class", "title": "Conservation problem modifier class", "concept": [ "classes" ], "topics": [ "ConservationModifier", "ConservationModifier-class" ] }, { "page": "ConservationProblem-class", "title": "Conservation problem class", "concept": [ "classes" ], "topics": [ "ConservationProblem", "ConservationProblem-class" ] }, { "page": "Constraint-class", "title": "Constraint class", "concept": [ "classes" ], "topics": [ "Constraint", "Constraint-class" ] }, { "page": "constraints", "title": "Conservation problem constraints", "concept": [ "overviews" ], "topics": [ "constraints" ] }, { "page": "Decision-class", "title": "Decision class", "concept": [ "classes" ], "topics": [ "Decision", "Decision-class" ] }, { "page": "decisions", "title": "Add decision types", "concept": [ "overviews" ], "topics": [ "decisions" ] }, { "page": "do_run_example", "title": "Do run example?", "topics": [ "do_run_example" ] }, { "page": "eval_asym_connectivity_summary", "title": "Evaluate asymmetric connectivity of solution", "concept": [ "summaries" ], "topics": [ "eval_asym_connectivity_summary", "eval_asym_connectivity_summary,GenericConservationProblem,ANY,ANY,array-method", "eval_asym_connectivity_summary,GenericConservationProblem,ANY,ANY,data.frame-method", "eval_asym_connectivity_summary,GenericConservationProblem,ANY,ANY,dgCMatrix-method", "eval_asym_connectivity_summary,GenericConservationProblem,ANY,ANY,Matrix-method", "eval_asym_connectivity_summary,GenericConservationProblem,ANY,ANY,matrix-method" ] }, { "page": "eval_boundary_summary", "title": "Evaluate boundary length of solution", "concept": [ "summaries" ], "topics": [ "eval_boundary_summary" ] }, { "page": "eval_connectivity_summary", "title": "Evaluate connectivity of solution", "concept": [ "summaries" ], "topics": [ "eval_connectivity_summary", "eval_connectivity_summary,GenericConservationProblem,ANY,ANY,array-method", "eval_connectivity_summary,GenericConservationProblem,ANY,ANY,data.frame-method", "eval_connectivity_summary,GenericConservationProblem,ANY,ANY,dgCMatrix-method", "eval_connectivity_summary,GenericConservationProblem,ANY,ANY,Matrix-method", "eval_connectivity_summary,GenericConservationProblem,ANY,ANY,matrix-method" ] }, { "page": "eval_cost_summary", "title": "Evaluate cost of solution", "concept": [ "summaries" ], "topics": [ "eval_cost_summary", "eval_cost_summary.ConservationProblem", "eval_cost_summary.MultiConservationProblem" ] }, { "page": "eval_feature_representation_summary", "title": "Evaluate feature representation by solution", "concept": [ "summaries" ], "topics": [ "eval_feature_representation_summary", "eval_feature_representation_summary.ConservationProblem", "eval_feature_representation_summary.MultiConservationProblem" ] }, { "page": "eval_ferrier_importance", "title": "Evaluate solution importance using Ferrier scores", "concept": [ "importances" ], "topics": [ "eval_ferrier_importance" ] }, { "page": "eval_n_summary", "title": "Evaluate number of planning units selected by solution", "concept": [ "summaries" ], "topics": [ "eval_n_summary" ] }, { "page": "eval_objective_summary", "title": "Evaluate objective value of solution", "concept": [ "summaries" ], "topics": [ "eval_objective_summary", "eval_objective_summary.ConservationProblem", "eval_objective_summary.MultiConservationProblem" ] }, { "page": "eval_rank_importance", "title": "Evaluate solution importance using incremental ranks", "concept": [ "importances" ], "topics": [ "eval_rank_importance" ] }, { "page": "eval_rare_richness_importance", "title": "Evaluate solution importance using rarity weighted richness scores", "concept": [ "importances" ], "topics": [ "eval_rare_richness_importance" ] }, { "page": "eval_replacement_importance", "title": "Evaluate solution importance using replacement cost scores", "concept": [ "importances" ], "topics": [ "eval_replacement_importance" ] }, { "page": "eval_target_coverage_summary", "title": "Evaluate target coverage by solution", "concept": [ "summaries" ], "topics": [ "eval_target_coverage_summary", "eval_target_coverage_summary,ConservationProblem,data.frame-method", "eval_target_coverage_summary,ConservationProblem,matrix-method", "eval_target_coverage_summary,ConservationProblem,numeric-method", "eval_target_coverage_summary,ConservationProblem,Raster-method", "eval_target_coverage_summary,ConservationProblem,sf-method", "eval_target_coverage_summary,ConservationProblem,Spatial-method", "eval_target_coverage_summary,ConservationProblem,SpatRaster-method", "eval_target_coverage_summary.ConservationProblem", "eval_target_coverage_summary.MultiConservationProblem" ] }, { "page": "fast_extract", "title": "Fast extract", "topics": [ "fast_extract", "fast_extract,Raster,sf-method", "fast_extract,Raster,sfc-method", "fast_extract,Raster,Spatial-method", "fast_extract,SpatRaster,sf-method", "fast_extract,SpatRaster,sfc-method", "fast_extract,SpatRaster,Spatial-method" ] }, { "page": "feature_abundances", "title": "Feature abundances", "topics": [ "feature_abundances", "feature_abundances.ConservationProblem" ] }, { "page": "feature_names", "title": "Feature names", "topics": [ "feature_names", "feature_names.ConservationProblem", "feature_names.MultiConservationProblem", "feature_names.ZonesCharacter", "feature_names.ZonesRaster", "feature_names.ZonesSpatRaster", "problem_names.MultiConservationProblem" ] }, { "page": "importance", "title": "Evaluate solution importance", "concept": [ "overviews" ], "topics": [ "importance", "irreplaceability" ] }, { "page": "intersecting_units", "title": "Find intersecting units", "topics": [ "intersecting_units", 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