Package: prioritizr 8.0.4.1

Richard Schuster

prioritizr: Systematic Conservation Prioritization in R

Systematic conservation prioritization using mixed integer linear programming (MILP). It provides a flexible interface for building and solving conservation planning problems. Once built, conservation planning problems can be solved using a variety of commercial and open-source exact algorithm solvers. By using exact algorithm solvers, solutions can be generated that are guaranteed to be optimal (or within a pre-specified optimality gap). Furthermore, conservation problems can be constructed to optimize the spatial allocation of different management actions or zones, meaning that conservation practitioners can identify solutions that benefit multiple stakeholders. To solve large-scale or complex conservation planning problems, users should install the Gurobi optimization software (available from <https://www.gurobi.com/>) and the 'gurobi' R package (see Gurobi Installation Guide vignette for details). Users can also install the IBM CPLEX software (<https://www.ibm.com/products/ilog-cplex-optimization-studio/cplex-optimizer>) and the 'cplexAPI' R package (available at <https://github.com/cran/cplexAPI>). Additionally, the 'rcbc' R package (available at <https://github.com/dirkschumacher/rcbc>) can be used to generate solutions using the CBC optimization software (<https://github.com/coin-or/Cbc>).

Authors:Jeffrey O Hanson [aut], Richard Schuster [aut, cre], Nina Morrell [aut], Matthew Strimas-Mackey [aut], Brandon P M Edwards [aut], Matthew E Watts [aut], Peter Arcese [aut], Joseph R Bennett [aut], Hugh P Possingham [aut]

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prioritizr.pdf |prioritizr.html
prioritizr/json (API)
NEWS

# Install 'prioritizr' in R:
install.packages('prioritizr', repos = c('https://prioritizr.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/prioritizr/prioritizr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

biodiversityconservationconservation-planneroptimizationprioritizationsolverspatial

131 exports 119 stars 4.81 score 40 dependencies 3 mentions 1.2k downloads

Last updated 25 days agofrom:329757a3a7

Exports:%>%%T>%Aadd_absolute_targetsadd_asym_connectivity_penaltiesadd_binary_decisionsadd_boundary_penaltiesadd_cbc_solveradd_connected_constraintsadd_connectivity_penaltiesadd_contiguity_constraintsadd_corridor_constraintsadd_cplex_solveradd_cuts_portfolioadd_default_portfolioadd_default_solveradd_extra_portfolioadd_feature_contiguity_constraintsadd_feature_weightsadd_gap_portfolioadd_gurobi_solveradd_highs_solveradd_linear_constraintsadd_linear_penaltiesadd_locked_in_constraintsadd_locked_out_constraintsadd_loglinear_targetsadd_lpsymphony_solveradd_mandatory_allocation_constraintsadd_manual_bounded_constraintsadd_manual_locked_constraintsadd_manual_targetsadd_max_cover_objectiveadd_max_features_objectiveadd_max_phylo_div_objectiveadd_max_phylo_end_objectiveadd_max_utility_objectiveadd_min_largest_shortfall_objectiveadd_min_set_objectiveadd_min_shortfall_objectiveadd_neighbor_constraintsadd_pool_portfolioadd_proportion_decisionsadd_relative_targetsadd_rsymphony_solveradd_semicontinuous_decisionsadd_shuffle_portfolioadd_top_portfolioadjacency_matrixbinary_stackboundary_matrixbranch_matrixcategory_layercategory_vectorcol_idscompilecompressed_formulationconnected_matrixconnectivity_matrixdistribute_loadeval_asym_connectivity_summaryeval_boundary_summaryeval_connectivity_summaryeval_cost_summaryeval_feature_representation_summaryeval_ferrier_importanceeval_n_summaryeval_rare_richness_importanceeval_replacement_importanceeval_target_coverage_summaryfast_extractfeature_abundancesfeature_namesfeature_representationferrier_scoreget_number_of_threadsget_sim_featuresget_sim_locked_in_rasterget_sim_locked_out_rasterget_sim_phylogenyget_sim_pu_linesget_sim_pu_pointsget_sim_pu_polygonsget_sim_pu_rasterget_sim_zones_featuresget_sim_zones_pu_polygonsget_sim_zones_pu_rasterintersecting_unitsis.parallelknit_print.ConservationProblemknit_print.OptimizationProblemlbloglinear_interpolationmarxan_boundary_data_to_matrixmarxan_connectivity_data_to_matrixmarxan_problemmodelsensencellncolnew_optimization_problemnew_waivernrownumber_of_featuresnumber_of_planning_unitsnumber_of_total_unitsnumber_of_zonesobjoptimization_problemplotpredefined_optimization_problempresolve_checkproblemproximity_matrixrarity_weighted_richnessreplacement_costrescale_matrixrhsrij_matrixrow_idsrun_calculationssenseset_number_of_threadssimulate_costsimulate_datasimulate_speciessolve.ConservationProblemubvtypewrite_problemzone_nameszones

Dependencies:apeassertthatBHclassclassIntclicpp11DBIdigeste1071exactextractrfansiglueigraphKernSmoothlatticelifecyclemagrittrMASSMatrixnlmepillarpkgconfigproxyR6rasterRcppRcppArmadillorlangs2sfslamspterratibbleunitsutf8vctrswithrwk

Calibrating trade-offs tutorial

Rendered fromcalibrating_trade-offs_tutorial.Rmdusingknitr::rmarkdown_notangleon Jul 01 2024.

Last update: 2024-05-26
Started: 2021-12-01

Connectivity tutorial

Rendered fromconnectivity_tutorial.Rmdusingknitr::rmarkdown_notangleon Jul 01 2024.

Last update: 2024-04-26
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Getting started

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Last update: 2024-04-26
Started: 2017-03-10

Gurobi installation guide

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Last update: 2024-03-02
Started: 2021-12-01

Management zones tutorial

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Last update: 2024-04-26
Started: 2021-12-01

Package overview

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Last update: 2023-09-27
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Publication record

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Last update: 2024-04-26
Started: 2017-10-31

Solver benchmarks

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Last update: 2023-07-07
Started: 2021-12-01

Readme and manuals

Help Manual

Help pageTopics
Add absolute targetsadd_absolute_targets add_absolute_targets,ConservationProblem,character-method add_absolute_targets,ConservationProblem,matrix-method add_absolute_targets,ConservationProblem,numeric-method add_absolute_targets-method
Add asymmetric connectivity penaltiesadd_asym_connectivity_penalties add_asym_connectivity_penalties,ConservationProblem,ANY,ANY,array-method add_asym_connectivity_penalties,ConservationProblem,ANY,ANY,data.frame-method add_asym_connectivity_penalties,ConservationProblem,ANY,ANY,dgCMatrix-method add_asym_connectivity_penalties,ConservationProblem,ANY,ANY,Matrix-method add_asym_connectivity_penalties,ConservationProblem,ANY,ANY,matrix-method
Add binary decisionsadd_binary_decisions
Add boundary penaltiesadd_boundary_penalties add_boundary_penalties,ConservationProblem,ANY,ANY,ANY,ANY-method add_boundary_penalties,ConservationProblem,ANY,ANY,ANY,array-method add_boundary_penalties,ConservationProblem,ANY,ANY,ANY,data.frame-method add_boundary_penalties,ConservationProblem,ANY,ANY,ANY,matrix-method
Add a _CBC_ solveradd_cbc_solver
Add connectivity penaltiesadd_connectivity_penalties add_connectivity_penalties,ConservationProblem,ANY,ANY,array-method add_connectivity_penalties,ConservationProblem,ANY,ANY,data.frame-method add_connectivity_penalties,ConservationProblem,ANY,ANY,dgCMatrix-method add_connectivity_penalties,ConservationProblem,ANY,ANY,Matrix-method add_connectivity_penalties,ConservationProblem,ANY,ANY,matrix-method
Add contiguity constraintsadd_contiguity_constraints add_contiguity_constraints,ConservationProblem,ANY,ANY-method add_contiguity_constraints,ConservationProblem,ANY,data.frame-method add_contiguity_constraints,ConservationProblem,ANY,matrix-method
Add a _CPLEX_ solveradd_cplex_solver
Add Bender's cuts portfolioadd_cuts_portfolio
Add a default portfolioadd_default_portfolio
Add default solveradd_default_solver
Add an extra portfolioadd_extra_portfolio
Add feature contiguity constraintsadd_feature_contiguity_constraints add_feature_contiguity_constraints,ConservationProblem,ANY,ANY-method add_feature_contiguity_constraints,ConservationProblem,ANY,data.frame-method add_feature_contiguity_constraints,ConservationProblem,ANY,Matrix-method add_feature_contiguity_constraints,ConservationProblem,ANY,matrix-method
Add feature weightsadd_feature_weights add_feature_weights,ConservationProblem,matrix-method add_feature_weights,ConservationProblem,numeric-method
Add a gap portfolioadd_gap_portfolio
Add a _Gurobi_ solveradd_gurobi_solver
Add a _HiGHS_ solveradd_highs_solver
Add linear constraintsadd_linear_constraints add_linear_constraints,ConservationProblem,ANY,ANY,character-method add_linear_constraints,ConservationProblem,ANY,ANY,dgCMatrix-method add_linear_constraints,ConservationProblem,ANY,ANY,Matrix-method add_linear_constraints,ConservationProblem,ANY,ANY,matrix-method add_linear_constraints,ConservationProblem,ANY,ANY,numeric-method add_linear_constraints,ConservationProblem,ANY,ANY,Raster-method add_linear_constraints,ConservationProblem,ANY,ANY,SpatRaster-method
Add linear penaltiesadd_linear_penalties add_linear_penalties,ConservationProblem,ANY,character-method add_linear_penalties,ConservationProblem,ANY,dgCMatrix-method add_linear_penalties,ConservationProblem,ANY,Matrix-method add_linear_penalties,ConservationProblem,ANY,matrix-method add_linear_penalties,ConservationProblem,ANY,numeric-method add_linear_penalties,ConservationProblem,ANY,Raster-method add_linear_penalties,ConservationProblem,ANY,SpatRaster-method
Add locked in constraintsadd_locked_in_constraints add_locked_in_constraints,ConservationProblem,character-method add_locked_in_constraints,ConservationProblem,logical-method add_locked_in_constraints,ConservationProblem,matrix-method add_locked_in_constraints,ConservationProblem,numeric-method add_locked_in_constraints,ConservationProblem,Raster-method add_locked_in_constraints,ConservationProblem,sf-method add_locked_in_constraints,ConservationProblem,Spatial-method add_locked_in_constraints,ConservationProblem,SpatRaster-method
Add locked out constraintsadd_locked_out_constraints add_locked_out_constraints,ConservationProblem,character-method add_locked_out_constraints,ConservationProblem,logical-method add_locked_out_constraints,ConservationProblem,matrix-method add_locked_out_constraints,ConservationProblem,numeric-method add_locked_out_constraints,ConservationProblem,Raster-method add_locked_out_constraints,ConservationProblem,sf-method add_locked_out_constraints,ConservationProblem,Spatial-method add_locked_out_constraints,ConservationProblem,SpatRaster-method
Add targets using log-linear scalingadd_loglinear_targets
Add a _SYMPHONY_ solver with _lpsymphony_add_lpsymphony_solver add_lsymphony_solver
Add mandatory allocation constraintsadd_mandatory_allocation_constraints
Add manually specified bound constraintsadd_manual_bounded_constraints add_manual_bounded_constraints,ConservationProblem,data.frame-method add_manual_bounded_constraints,ConservationProblem,tbl_df-method
Add manually specified locked constraintsadd_manual_locked_constraints add_manual_locked_constraints,ConservationProblem,data.frame-method add_manual_locked_constraints,ConservationProblem,tbl_df-method
Add manual targetsadd_manual_targets add_manual_targets,ConservationProblem,data.frame-method add_manual_targets,ConservationProblem,tbl_df-method add_manual_targets-method
Add maximum coverage objectiveadd_max_cover_objective
Add maximum feature representation objectiveadd_max_features_objective
Add maximum phylogenetic diversity objectiveadd_max_phylo_div_objective add_max_phylo_objective
Add maximum phylogenetic endemism objectiveadd_max_phylo_end_objective
Add maximum utility objectiveadd_max_utility_objective
Add minimum largest shortfall objectiveadd_min_largest_shortfall_objective
Add minimum set objectiveadd_min_set_objective
Add minimum shortfall objectiveadd_min_shortfall_objective
Add neighbor constraintsadd_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
Add proportion decisionsadd_proportion_decisions
Add relative targetsadd_relative_targets add_relative_targets,ConservationProblem,character-method add_relative_targets,ConservationProblem,matrix-method add_relative_targets,ConservationProblem,numeric-method add_relative_targets-method
Add a _SYMPHONY_ solver with _Rsymphony_add_rsymphony_solver
Add semi-continuous decisionsadd_semicontinuous_decisions
Add a shuffle portfolioadd_shuffle_portfolio
Add a top portfolioadd_top_portfolio
Adjacency matrixadjacency_matrix adjacency_matrix.default adjacency_matrix.Raster adjacency_matrix.sf adjacency_matrix.SpatialLines adjacency_matrix.SpatialPoints adjacency_matrix.SpatialPolygons adjacency_matrix.SpatRaster
Binary stackbinary_stack binary_stack.Raster binary_stack.SpatRaster
Boundary matrixboundary_matrix boundary_matrix.default boundary_matrix.Raster boundary_matrix.sf boundary_matrix.SpatialLines boundary_matrix.SpatialPoints boundary_matrix.SpatialPolygons boundary_matrix.SpatRaster
Branch matrixbranch_matrix branch_matrix.default branch_matrix.phylo
Category layercategory_layer category_layer.default category_layer.Raster
Category vectorcategory_vector category_vector.data.frame category_vector.matrix category_vector.sf category_vector.Spatial
Compile a problemcompile compile.ConservationProblem
Connectivity matrixconnectivity_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
Conservation problem modifier classConservationModifier ConservationModifier-class
Conservation problem classConservationProblem ConservationProblem-class
Constraint classConstraint Constraint-class
Conservation problem constraintsconstraints
Decision classDecision Decision-class
Add decision typesdecisions
Evaluate asymmetric connectivity of solutioneval_asym_connectivity_summary eval_asym_connectivity_summary,ConservationProblem,ANY,ANY,array-method eval_asym_connectivity_summary,ConservationProblem,ANY,ANY,data.frame-method eval_asym_connectivity_summary,ConservationProblem,ANY,ANY,dgCMatrix-method eval_asym_connectivity_summary,ConservationProblem,ANY,ANY,Matrix-method eval_asym_connectivity_summary,ConservationProblem,ANY,ANY,matrix-method
Evaluate boundary length of solutioneval_boundary_summary
Evaluate connectivity of solutioneval_connectivity_summary eval_connectivity_summary,ConservationProblem,ANY,ANY,array-method eval_connectivity_summary,ConservationProblem,ANY,ANY,data.frame-method eval_connectivity_summary,ConservationProblem,ANY,ANY,dgCMatrix-method eval_connectivity_summary,ConservationProblem,ANY,ANY,Matrix-method eval_connectivity_summary,ConservationProblem,ANY,ANY,matrix-method
Evaluate cost of solutioneval_cost_summary
Evaluate feature representation by solutioneval_feature_representation_summary
Evaluate solution importance using Ferrier scoreseval_ferrier_importance eval_ferrier_importance,ConservationProblem,data.frame-method eval_ferrier_importance,ConservationProblem,matrix-method eval_ferrier_importance,ConservationProblem,numeric-method eval_ferrier_importance,ConservationProblem,Raster-method eval_ferrier_importance,ConservationProblem,sf-method eval_ferrier_importance,ConservationProblem,Spatial-method eval_ferrier_importance,ConservationProblem,SpatRaster-method
Evaluate number of planning units selected by solutioneval_n_summary
Evaluate solution importance using rarity weighted richness scoreseval_rare_richness_importance eval_rare_richness_importance,ConservationProblem,data.frame-method eval_rare_richness_importance,ConservationProblem,matrix-method eval_rare_richness_importance,ConservationProblem,numeric-method eval_rare_richness_importance,ConservationProblem,Raster-method eval_rare_richness_importance,ConservationProblem,sf-method eval_rare_richness_importance,ConservationProblem,Spatial-method eval_rare_richness_importance,ConservationProblem,SpatRaster-method
Evaluate solution importance using replacement cost scoreseval_replacement_importance eval_replacement_importance,ConservationProblem,data.frame-method eval_replacement_importance,ConservationProblem,matrix-method eval_replacement_importance,ConservationProblem,numeric-method eval_replacement_importance,ConservationProblem,Raster-method eval_replacement_importance,ConservationProblem,sf-method eval_replacement_importance,ConservationProblem,Spatial-method eval_replacement_importance,ConservationProblem,SpatRaster-method
Evaluate target coverage by solutioneval_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
Fast extractfast_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
Feature abundancesfeature_abundances feature_abundances.ConservationProblem
Feature namesfeature_names feature_names.ConservationProblem feature_names.ZonesCharacter feature_names.ZonesRaster feature_names.ZonesSpatRaster
Evaluate solution importanceimportance irreplaceability
Find intersecting unitsintersecting_units intersecting_units,ANY,Raster-method intersecting_units,ANY,Spatial-method intersecting_units,data.frame,ANY-method intersecting_units,Raster,ANY-method intersecting_units,sf,sf-method intersecting_units,sf,SpatRaster-method intersecting_units,Spatial,ANY-method intersecting_units,SpatRaster,sf-method intersecting_units,SpatRaster,SpatRaster-method
Print an object for knitr package.knit_print knit_print.ConservationProblem knit_print.OptimizationProblem
Log-linear interpolationloglinear_interpolation
Convert _Marxan_ boundary data to matrix formatmarxan_boundary_data_to_matrix
Convert _Marxan_ connectivity data to matrix formatmarxan_connectivity_data_to_matrix
_Marxan_ conservation problemmarxan_problem marxan_problem.character marxan_problem.data.frame marxan_problem.default
Waivernew_waiver
Number of featuresnumber_of_features number_of_features.ConservationProblem number_of_features.OptimizationProblem number_of_features.ZonesCharacter number_of_features.ZonesRaster number_of_features.ZonesSpatRaster
Number of planning unitsnumber_of_planning_units number_of_planning_units.ConservationProblem number_of_planning_units.OptimizationProblem
Number of total unitsnumber_of_total_units number_of_total_units.ConservationProblem
Number of zonesnumber_of_zones number_of_zones.ConservationProblem number_of_zones.OptimizationProblem number_of_zones.ZonesCharacter number_of_zones.ZonesRaster number_of_zones.ZonesSpatRaster
Objective classObjective Objective-class
Add an objectiveobjectives
Optimization problemoptimization_problem
Optimization problem classOptimizationProblem OptimizationProblem-class
Optimization problem methodsA A,OptimizationProblem-method col_ids col_ids,OptimizationProblem-method compressed_formulation compressed_formulation,OptimizationProblem-method lb lb,OptimizationProblem-method modelsense modelsense,OptimizationProblem-method ncell,OptimizationProblem-method ncol,OptimizationProblem-method nrow,OptimizationProblem-method obj obj,OptimizationProblem-method OptimizationProblem-methods rhs rhs,OptimizationProblem-method row_ids row_ids,OptimizationProblem-method sense sense,OptimizationProblem-method ub ub,OptimizationProblem-method vtype vtype,OptimizationProblem-method
Add a penaltypenalties
Penalty classPenalty Penalty-class
Portfolio classPortfolio Portfolio-class
Add portfoliosportfolios
Presolve checkpresolve_check presolve_check.ConservationProblem presolve_check.OptimizationProblem
prioritizr: Systematic Conservation Prioritization in Rprioritizr-package prioritizr
Deprecation noticeadd_connected_constraints add_corridor_constraints add_pool_portfolio connected_matrix distribute_load feature_representation ferrier_score get_number_of_threads is.parallel new_optimization_problem predefined_optimization_problem prioritizr-deprecated rarity_weighted_richness replacement_cost set_number_of_threads
Conservation planning problemproblem problem,data.frame,character-method problem,data.frame,data.frame-method problem,data.frame,ZonesCharacter-method problem,matrix,data.frame-method problem,numeric,data.frame-method problem,Raster,Raster-method problem,Raster,ZonesRaster-method problem,sf,character-method problem,sf,Raster-method problem,sf,SpatRaster-method problem,sf,ZonesCharacter-method problem,sf,ZonesRaster-method problem,sf,ZonesSpatRaster-method problem,Spatial,character-method problem,Spatial,Raster-method problem,Spatial,ZonesCharacter-method problem,Spatial,ZonesRaster-method problem,SpatRaster,SpatRaster-method problem,SpatRaster,ZonesRaster-method problem,SpatRaster,ZonesSpatRaster-method
Proximity matrixproximity_matrix proximity_matrix.default proximity_matrix.Raster proximity_matrix.sf proximity_matrix.SpatialLines proximity_matrix.SpatialPoints proximity_matrix.SpatialPolygons proximity_matrix.SpatRaster
Rescale a matrixrescale_matrix
Feature by planning unit matrixrij_matrix rij_matrix,Raster,Raster-method rij_matrix,sf,Raster-method rij_matrix,sf,SpatRaster-method rij_matrix,Spatial,Raster-method rij_matrix,SpatRaster,SpatRaster-method
Run calculationsrun_calculations
Showshow show,ConservationModifier-method show,ConservationProblem-method show,Id-method show,OptimizationProblem-method show,Solver-method
Get simulated conservation planning dataget_sim_features get_sim_locked_in_raster get_sim_locked_out_raster get_sim_phylogeny get_sim_pu_lines get_sim_pu_points get_sim_pu_polygons get_sim_pu_raster get_sim_zones_features get_sim_zones_pu_polygons get_sim_zones_pu_raster sim_data sim_features sim_locked_in_raster sim_locked_out_raster sim_phylogeny sim_pu_lines sim_pu_points sim_pu_polygons sim_pu_raster sim_zones_features sim_zones_pu_polygons sim_zones_pu_raster
Simulate cost datasimulate_cost simulate_cost.Raster simulate_cost.SpatRaster
Simulate datasimulate_data simulate_data.Raster simulate_data.SpatRaster
Simulate species habitat suitability datasimulate_species simulate_species.Raster simulate_species.SpatRaster
Solvesolve solve.ConservationProblem
Solver classSolver Solver-class
Add solverssolvers
Evaluate solutions using summary statisticssummaries
Target classTarget Target-class
Add representation targetstargets
Manipulate tibblesas.list,tbl_df-method ncol,tbl_df-method nrow,tbl_df-method tibble-methods
Write problemwrite_problem
Zone nameszone_names zone_names.ConservationProblem zone_names.ZonesCharacter zone_names.ZonesRaster zone_names.ZonesSpatRaster
Management zonesZones zones Zones-class ZonesCharacter ZonesRaster ZonesSpatRaster