Files in prioritizr

Systematic Conservation Prioritization in R

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

R/Target-class.R R/RcppExports.R R/category_vector.R R/add_manual_targets.R R/objectives.R R/add_gurobi_solver.R R/add_cplex_solver.R R/add_shuffle_portfolio.R R/add_max_utility_objective.R R/show.R R/all_columns_inherit.R R/OptimizationProblem-methods.R R/add_cbc_solver.R R/category_layer.R R/add_max_phylo_div_objective.R R/add_feature_weights.R R/branch_matrix.R R/as.R R/internal.R R/is_numeric_values.R R/any_nonNA.R R/print.R R/add_min_largest_shortfall_objective.R R/ConservationProblem-class.R R/summary.R R/add_mandatory_allocation_constraints.R R/connectivity_matrix.R R/add_rsymphony_solver.R R/all_proportion.R R/solvers.R R/Solver-class.R R/loglinear_interpolation.R R/any_nonzero.R R/marxan_connectivity_data_to_matrix.R R/eval_cost_summary.R R/proximity_matrix.R R/list_text.R R/rij_matrix.R R/add_default_solver.R R/add_max_features_objective.R R/marxan_boundary_data_to_matrix.R R/constraints.R R/portfolios.R R/eval_boundary_summary.R R/add_max_cover_objective.R R/assertions_raster.R R/add_loglinear_targets.R R/Constraint-class.R R/add_binary_decisions.R R/assertions_sf.R R/add_locked_in_constraints.R R/OptimizationProblem-class.R R/tbl_df.R R/all_binary.R R/data.R R/add_min_shortfall_objective.R R/simulate.R R/Penalty-class.R R/add_lpsymphony_solver.R R/add_boundary_penalties.R R/deprecated.R R/Decision-class.R R/number_of_total_units.R R/solve.R R/Portfolio-class.R R/add_compile_solver.R R/add_extra_portfolio.R R/assertions_vector.R R/eval_ferrier_importance.R R/ConservationModifier-class.R R/reexports.R R/add_neighbor_constraints.R R/targets.R R/number_of_features.R R/penalties.R R/feature_abundances.R R/binary_stack.R R/add_gap_portfolio.R R/add_contiguity_constraints.R R/repr.R R/add_semicontinuous_decisions.R R/problem.R R/optimization_problem.R R/is_same_crs.R R/number_of_planning_units.R R/add_relative_targets.R R/summaries.R R/decisions.R R/assertions_misc.R R/add_manual_bounded_constraints.R R/adjacency_matrix.R R/assertions_class.R R/add_asym_connectivity_penalties.R R/zones.R R/eval_connectivity_summary.R R/write_problem.R R/importance.R R/planning_unit_solution_status.R R/knit_print.R R/number_of_zones.R R/add_connectivity_penalties.R R/boundary_matrix.R R/all_finite.R R/feature_names.R R/package.R R/get_crs.R R/test-helpers.R R/compile.R R/eval_feature_representation_summary.R R/eval_rare_richness_importance.R R/is_spatial_extents_overlap.R R/eval_target_coverage_summary.R R/run_calculations.R R/eval_replacement_importance.R R/zone_names.R R/add_manual_locked_constraints.R R/fast_extract.R R/waiver.R R/add_top_portfolio.R R/presolve_check.R R/zzz.R R/marxan_problem.R R/assertions.R R/add_feature_contiguity_constraints.R R/all_positive.R R/add_linear_penalties.R R/cli.R R/external-classes.R R/problem-deprecated.R R/add_cuts_portfolio.R R/eval_n_summary.R R/Objective-class.R R/add_highs_solver.R R/all_columns_any_finite.R R/intersecting_units.R R/as_Matrix.R R/add_max_phylo_end_objective.R R/add_locked_out_constraints.R R/add_linear_constraints.R R/add_proportion_decisions.R R/add_min_set_objective.R R/st_geometry_classes.R R/add_absolute_targets.R R/eval_asym_connectivity_summary.R R/rescale_matrix.R

src/optimization_problem.h

src/Makevars.win

src/rcpp_apply_linear_penalties.cpp

src/Makevars

src/rcpp_apply_connectivity_penalties.cpp

src/rcpp_branch_matrix.cpp

src/rcpp_list_to_matrix_indices.cpp

src/rcpp_apply_feature_contiguity_constraints.cpp

src/rcpp_apply_contiguity_constraints.cpp

src/functions.cpp

src/rcpp_apply_boundary_penalties.cpp

src/RcppExports.cpp

src/rcpp_add_linear_constraints.cpp

src/rcpp_forbid_solution.cpp

src/package.h

src/rcpp_apply_max_cover_objective.cpp

src/rcpp_apply_neighbor_constraints.cpp

src/rcpp_apply_min_largest_shortfall_objective.cpp

src/rcpp_apply_max_features_objective.cpp

src/rcpp_apply_min_set_objective.cpp

src/init.c

src/rcpp_ferrier_score.cpp

src/rcpp_apply_bounded_constraints.cpp

src/rcpp_connectivity.cpp

src/rcpp_boundary.cpp

src/rcpp_add_rij_data.cpp

src/rcpp_asym_connectivity.cpp

src/rcpp_ferrier_score.h

src/rcpp_apply_max_phylo_objective.cpp

src/rcpp_apply_min_shortfall_objective.cpp

src/rcpp_absolute_amount_held_by_solution.cpp

src/rcpp_apply_asym_connectivity_penalties.cpp

src/rcpp_apply_max_utility_objective.cpp

src/rcpp_apply_locked_constraints.cpp

src/optimization_problem.cpp

src/rcpp_apply_feature_weights.cpp

src/rcpp_apply_decisions.cpp

src/rcpp_add_zones_constraints.cpp

src/functions.h

inst/doc/calibrating_trade-offs_tutorial.Rmd inst/doc/package_overview.Rmd

inst/doc/publication_record.html

inst/doc/management_zones_tutorial.html

inst/doc/connectivity_tutorial.Rmd inst/doc/management_zones_tutorial.Rmd inst/doc/gurobi_installation_guide.Rmd

inst/doc/calibrating_trade-offs_tutorial.html

inst/doc/solver_benchmarks.html

inst/doc/prioritizr.html

inst/doc/package_overview.html

inst/doc/prioritizr.Rmd

inst/doc/connectivity_tutorial.html

inst/doc/gurobi_installation_guide.html

inst/doc/solver_benchmarks.Rmd inst/doc/publication_record.Rmd

inst/testdata/polyset_lines.rds

inst/testdata/targets.rds

inst/testdata/polyset_polygons.rds

inst/testdata/rij.rds

inst/extdata/sim_zones_pu_polygons.gpkg

inst/extdata/sim_pu_lines.gpkg

inst/extdata/sim_zones_features_1.tif

inst/extdata/sim_pu_polygons.gpkg

inst/extdata/sim_features.tif

inst/extdata/sim_pu_points.gpkg

inst/extdata/sim_zones_features_3.tif

inst/extdata/sim_zones_features_2.tif

inst/extdata/sim_phylogeny.txt

inst/extdata/sim_locked_out_raster.tif

inst/extdata/sim_zones_pu_raster.tif

inst/extdata/sim_locked_in_raster.tif

inst/extdata/sim_pu_raster.tif

inst/extdata/marxan/input.dat

inst/extdata/marxan/input/puvspr.dat

inst/extdata/marxan/input/pu.dat

inst/extdata/marxan/input/bound.dat

inst/extdata/marxan/input/spec.dat

inst/knitr/print.Rmd

build/vignette.rds

build/partial.rdb

tests/testthat.R tests/testthat/test_internal.R tests/testthat/test_is_numeric_values.R tests/testthat/test_eval_rare_richness_importance.R tests/testthat/test_category_layer.R tests/testthat/test_add_min_set_objective.R tests/testthat/test_get_crs.R tests/testthat/test_boundary_matrix.R tests/testthat/test_eval_asym_connectivity_summary.R tests/testthat/test_assertions.R tests/testthat/test_add_max_phylo_end_objective.R tests/testthat/test_problem_negative.R tests/testthat/test_add_max_features_objective.R tests/testthat/test_add_max_utility_objective.R tests/testthat/test_feature_abundances.R tests/testthat/test_eval_n_summary.R tests/testthat/test_connectivity_matrix.R tests/testthat/helper_sf.R tests/testthat/test_add_manual_targets.R tests/testthat/test_eval_replacement_importance.R tests/testthat/test_add_relative_targets.R tests/testthat/test_add_gap_portfolio.R tests/testthat/test_add_cbc_solver.R tests/testthat/test_assertions_class.R tests/testthat/test_add_linear_penalties.R tests/testthat/test_eval_feature_representation_summary.R tests/testthat/helper_connectivity.R tests/testthat/test_zones.R tests/testthat/test_problem-deprecated.R tests/testthat/test_add_connectivity_penalties.R tests/testthat/test_compile.R tests/testthat/helper_ferrier_scores.R tests/testthat/test_fast_extract.R tests/testthat/test_Waiver.R tests/testthat/test_prioritizrdata.R tests/testthat/test_rij_matrix.R tests/testthat/test_intersecting_units.R tests/testthat/test_add_min_largest_shortfall_objective.R tests/testthat/test_add_mandatory_allocation_constraints.R tests/testthat/test_marxan_connectivity_data_to_matrix.R tests/testthat/test_helper_raster.R tests/testthat/test_presolve_check.R tests/testthat/test_eval_target_coverage_summary.R tests/testthat/test_ConservationModifier.R tests/testthat/test_binary_stack.R tests/testthat/test_eval_cost_summary.R tests/testthat/test_add_feature_contiguity_constraints.R tests/testthat/test_write_problem.R tests/testthat/helper_asym_connectivity.R tests/testthat/test_branch_matrix.R tests/testthat/test_adjacency_matrix.R tests/testthat/test_add_contiguity_constraints.R tests/testthat/test_add_top_portfolio.R tests/testthat/test_add_min_shortfall_objective.R tests/testthat/test_add_gurobi_solver.R tests/testthat/test_problem.R tests/testthat/test_add_cuts_portfolio.R tests/testthat/test_all_columns_any_finite.R tests/testthat/test_add_extra_portfolio.R tests/testthat/test_add_absolute_targets.R tests/testthat/test_eval_connectivity_summary.R tests/testthat/test_add_lpsymphony_solver.R tests/testthat/test_documentation.R tests/testthat/test_add_cplex_solver.R tests/testthat/helper_skip.R tests/testthat/test_add_max_phylo_div_objective.R tests/testthat/test_add_locked_in_constraints.R tests/testthat/test_add_asym_connectivity_penalties.R tests/testthat/test_assertions_vector.R tests/testthat/test_all_binary.R tests/testthat/test_repr.R tests/testthat/test_decisions.R tests/testthat/test_OptimizationProblem.R tests/testthat/test_marxan_problem.R tests/testthat/test_all_proportion.R tests/testthat/test_add_linear_constraints.R tests/testthat/test_add_neighbor_constraints.R tests/testthat/test_any_nonzero.R tests/testthat/test_add_max_cover_objective.R tests/testthat/test_add_locked_out_constraints.R tests/testthat/helper_raster.R tests/testthat/test_assertions_sf.R tests/testthat/test_add_manual_bounded_constraints.R tests/testthat/test_proximity_matrix.R tests/testthat/test_eval_boundary_summary.R tests/testthat/test_assertions_misc.R tests/testthat/test_simulate.R tests/testthat/test_add_manual_locked_constraints.R tests/testthat/test_all_positive.R tests/testthat/test_st_geometry_classes.R tests/testthat/test_assertions_raster.R tests/testthat/test_is_spatial_extents_overlap.R tests/testthat/test_category_vector.R tests/testthat/test_add_boundary_penalties.R tests/testthat/test_eval_ferrier_importance.R tests/testthat/test_cplex.R tests/testthat/test_add_loglinear_targets.R tests/testthat/test_as_Matrix.R tests/testthat/test_planning_unit_solution_status.R tests/testthat/setup.R tests/testthat/test_run_calculations.R tests/testthat/test_add_rsymphony_solver.R tests/testthat/test_add_feature_weights.R tests/testthat/test_add_shuffle_portfolio.R tests/testthat/test_add_highs_solver.R tests/testthat/test_all_finite.R tests/testthat/test_solve.R tests/testthat/test_any_nonNA.R tests/testthat/test_marxan_boundary_data_to_matrix.R tests/testthat/helper_boundary.R tests/testthat/test_all_columns_inherit.R tests/testthat/test_rescale_matrix.R tests/testthat/test_add_default_solver.R tests/testthat/_snaps/assertions.md vignettes/calibrating_trade-offs_tutorial.Rmd vignettes/package_overview.Rmd vignettes/connectivity_tutorial.Rmd vignettes/management_zones_tutorial.Rmd vignettes/gurobi_installation_guide.Rmd

vignettes/references.bib

vignettes/prioritizr.Rmd

vignettes/reference-style.csl

vignettes/solver_benchmarks.Rmd vignettes/publication_record.Rmd

vignettes/figures/free-academic-license-page.png

vignettes/figures/cmd-windows-success.png

vignettes/figures/model-test.png

vignettes/figures/map.jpg

vignettes/figures/actual-license.png

man/add_min_set_objective.Rd man/add_locked_in_constraints.Rd man/add_cplex_solver.Rd man/add_max_utility_objective.Rd man/compile.Rd man/write_problem.Rd man/OptimizationProblem-class.Rd man/tibble-methods.Rd man/OptimizationProblem-methods.Rd man/add_cbc_solver.Rd man/eval_asym_connectivity_summary.Rd man/feature_names.Rd man/rij_matrix.Rd man/add_binary_decisions.Rd man/add_cuts_portfolio.Rd man/number_of_total_units.Rd man/reexports.Rd man/boundary_matrix.Rd man/eval_replacement_importance.Rd man/add_lsymphony_solver.Rd man/Constraint-class.Rd man/feature_abundances.Rd man/category_layer.Rd man/loglinear_interpolation.Rd man/add_extra_portfolio.Rd man/adjacency_matrix.Rd man/add_shuffle_portfolio.Rd man/number_of_zones.Rd man/add_semicontinuous_decisions.Rd man/add_top_portfolio.Rd man/ConservationProblem-class.Rd man/objectives.Rd man/solvers.Rd man/knit_print.Rd man/add_default_solver.Rd man/zone_names.Rd man/number_of_features.Rd man/add_manual_locked_constraints.Rd man/connectivity_matrix.Rd man/eval_feature_representation_summary.Rd man/simulate_cost.Rd man/add_relative_targets.Rd man/summaries.Rd man/solve.Rd man/run_calculations.Rd man/new_waiver.Rd man/marxan_boundary_data_to_matrix.Rd man/zones.Rd man/add_min_largest_shortfall_objective.Rd man/add_neighbor_constraints.Rd man/eval_connectivity_summary.Rd man/add_contiguity_constraints.Rd man/add_absolute_targets.Rd man/add_boundary_penalties.Rd man/add_min_shortfall_objective.Rd man/constraints.Rd man/add_linear_penalties.Rd man/eval_n_summary.Rd man/eval_target_coverage_summary.Rd man/add_manual_bounded_constraints.Rd man/rescale_matrix.Rd man/add_locked_out_constraints.Rd man/Penalty-class.Rd man/add_feature_weights.Rd man/Target-class.Rd man/add_loglinear_targets.Rd man/branch_matrix.Rd man/marxan_problem.Rd man/simulate_species.Rd man/presolve_check.Rd man/add_max_phylo_div_objective.Rd man/intersecting_units.Rd man/portfolios.Rd man/add_max_phylo_end_objective.Rd man/targets.Rd man/problem.Rd man/prioritizr-deprecated.Rd man/add_rsymphony_solver.Rd man/add_feature_contiguity_constraints.Rd man/eval_cost_summary.Rd man/category_vector.Rd man/eval_boundary_summary.Rd man/add_gap_portfolio.Rd man/prioritizr.Rd man/add_connectivity_penalties.Rd man/marxan_connectivity_data_to_matrix.Rd man/number_of_planning_units.Rd man/penalties.Rd man/importance.Rd man/Objective-class.Rd man/eval_rare_richness_importance.Rd man/show.Rd man/ConservationModifier-class.Rd man/add_proportion_decisions.Rd man/add_manual_targets.Rd man/add_max_cover_objective.Rd man/fast_extract.Rd man/add_gurobi_solver.Rd man/proximity_matrix.Rd man/add_mandatory_allocation_constraints.Rd man/eval_ferrier_importance.Rd man/simulate_data.Rd man/Decision-class.Rd man/binary_stack.Rd man/add_asym_connectivity_penalties.Rd man/add_max_features_objective.Rd man/Solver-class.Rd man/sim_data.Rd man/Portfolio-class.Rd man/add_highs_solver.Rd man/decisions.Rd man/add_linear_constraints.Rd man/optimization_problem.Rd

man/figures/README-planning_units-1.png

man/figures/README-locked_in_constraints-2.png

man/figures/logo.png

man/figures/README-minimal_solution-1.png

man/figures/README-locked_out_constraints-2.png

man/figures/README-features-1.png

man/figures/README-importance-1.png

man/figures/README-boundary_penalties-1.png

man/figures/README-locked_in_constraints-1.png

man/figures/README-locked_out_constraints-1.png

man/figures/README-/minimal_solution.svg

man/figures/README-/locked_out_constraints.svg

man/figures/README-/locked_in_constraints.svg

man/figures/README-/unnamed-chunk-6.svg

man/figures/README-/planning_units.svg

man/figures/README-/features.svg

man/figures/README-/importance.svg

man/figures/README-/unnamed-chunk-11.svg

man/figures/README-/eval_performance.svg

man/figures/README-/boundary_penalties.svg

man/figures/README-/unnamed-chunk-7.svg

prioritizr documentation built on Aug. 9, 2023, 1:06 a.m.