Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <http://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut],
Richard Schuster [aut, cre],
Nina Morrell [aut],
Matthew Strimas-Mackey [aut],
Matthew E Watts [aut],
Peter Arcese [aut],
Joseph Bennett [aut],
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 4.1.1 dated 2019-06-06 and 4.1.3 dated 2019-09-06
prioritizr-4.1.1/prioritizr/R/add_max_phylo_objective.R |only prioritizr-4.1.1/prioritizr/man/add_max_phylo_objective.Rd |only prioritizr-4.1.1/prioritizr/man/figures/README-unnamed-chunk-11-1.png |only prioritizr-4.1.1/prioritizr/man/figures/README-unnamed-chunk-12-1.png |only prioritizr-4.1.1/prioritizr/man/figures/README-unnamed-chunk-13-1.png |only prioritizr-4.1.1/prioritizr/man/figures/README-unnamed-chunk-14-1.png |only prioritizr-4.1.1/prioritizr/tests/testthat/test_add_max_phylo_objective.R |only prioritizr-4.1.3/prioritizr/DESCRIPTION | 26 prioritizr-4.1.3/prioritizr/MD5 | 653 +- prioritizr-4.1.3/prioritizr/NAMESPACE | 359 - prioritizr-4.1.3/prioritizr/R/ArrayParameter-proto.R | 288 prioritizr-4.1.3/prioritizr/R/Collection-proto.R | 334 - prioritizr-4.1.3/prioritizr/R/ConservationModifier-proto.R | 362 - prioritizr-4.1.3/prioritizr/R/ConservationProblem-proto.R | 1206 ++-- prioritizr-4.1.3/prioritizr/R/Constraint-proto.R | 48 prioritizr-4.1.3/prioritizr/R/Decision-proto.R | 50 prioritizr-4.1.3/prioritizr/R/Id.R | 114 prioritizr-4.1.3/prioritizr/R/MiscParameter-proto.R | 208 prioritizr-4.1.3/prioritizr/R/Objective-proto.R | 44 prioritizr-4.1.3/prioritizr/R/OptimizationProblem-methods.R | 622 +- prioritizr-4.1.3/prioritizr/R/OptimizationProblem-proto.R | 402 - prioritizr-4.1.3/prioritizr/R/Parameter-proto.R | 152 prioritizr-4.1.3/prioritizr/R/Parameters-proto.R | 330 - prioritizr-4.1.3/prioritizr/R/Penalty-proto.R | 50 prioritizr-4.1.3/prioritizr/R/Portfolio-proto.R | 188 prioritizr-4.1.3/prioritizr/R/RcppExports.R | 354 - prioritizr-4.1.3/prioritizr/R/ScalarParameter-proto.R | 258 prioritizr-4.1.3/prioritizr/R/Solver-proto.R | 241 prioritizr-4.1.3/prioritizr/R/Target-proto.R | 48 prioritizr-4.1.3/prioritizr/R/add_absolute_targets.R | 432 - prioritizr-4.1.3/prioritizr/R/add_binary_decisions.R | 160 prioritizr-4.1.3/prioritizr/R/add_boundary_penalties.R | 658 +- prioritizr-4.1.3/prioritizr/R/add_connectivity_penalties.R | 1074 +-- prioritizr-4.1.3/prioritizr/R/add_contiguity_constraints.R | 610 +- prioritizr-4.1.3/prioritizr/R/add_cuts_portfolio.R | 254 prioritizr-4.1.3/prioritizr/R/add_default_decisions.R | 34 prioritizr-4.1.3/prioritizr/R/add_default_objective.R | 18 prioritizr-4.1.3/prioritizr/R/add_default_portfolio.R | 32 prioritizr-4.1.3/prioritizr/R/add_default_solver.R | 78 prioritizr-4.1.3/prioritizr/R/add_default_targets.R | 18 prioritizr-4.1.3/prioritizr/R/add_feature_contiguity_constraints.R | 748 +- prioritizr-4.1.3/prioritizr/R/add_feature_weights.R | 563 - prioritizr-4.1.3/prioritizr/R/add_gurobi_solver.R | 382 - prioritizr-4.1.3/prioritizr/R/add_locked_in_constraints.R | 678 +- prioritizr-4.1.3/prioritizr/R/add_locked_out_constraints.R | 574 - prioritizr-4.1.3/prioritizr/R/add_loglinear_targets.R | 306 - prioritizr-4.1.3/prioritizr/R/add_lpsymphony_solver.R | 280 prioritizr-4.1.3/prioritizr/R/add_mandatory_allocation_constraints.R | 204 prioritizr-4.1.3/prioritizr/R/add_manual_bounded_constraints.R |only prioritizr-4.1.3/prioritizr/R/add_manual_locked_constraints.R | 492 - prioritizr-4.1.3/prioritizr/R/add_manual_targets.R | 634 +- prioritizr-4.1.3/prioritizr/R/add_max_cover_objective.R | 368 - prioritizr-4.1.3/prioritizr/R/add_max_features_objective.R | 314 - prioritizr-4.1.3/prioritizr/R/add_max_phylo_div_objective.R |only prioritizr-4.1.3/prioritizr/R/add_max_phylo_end_objective.R |only prioritizr-4.1.3/prioritizr/R/add_max_utility_objective.R | 294 - prioritizr-4.1.3/prioritizr/R/add_min_set_objective.R | 216 prioritizr-4.1.3/prioritizr/R/add_min_shortfall_objective.R | 290 prioritizr-4.1.3/prioritizr/R/add_neighbor_contraints.R | 698 +- prioritizr-4.1.3/prioritizr/R/add_pool_portfolio.R | 314 - prioritizr-4.1.3/prioritizr/R/add_proportion_decisions.R | 144 prioritizr-4.1.3/prioritizr/R/add_relative_targets.R | 332 - prioritizr-4.1.3/prioritizr/R/add_rsymphony_solver.R | 296 - prioritizr-4.1.3/prioritizr/R/add_semicontinuous_decisions.R | 168 prioritizr-4.1.3/prioritizr/R/add_shuffle_portfolio.R | 308 - prioritizr-4.1.3/prioritizr/R/binary_stack.R | 101 prioritizr-4.1.3/prioritizr/R/boundary_matrix.R | 352 - prioritizr-4.1.3/prioritizr/R/branch_matrix.R | 113 prioritizr-4.1.3/prioritizr/R/category_layer.R | 103 prioritizr-4.1.3/prioritizr/R/category_vector.R | 122 prioritizr-4.1.3/prioritizr/R/compile.R | 258 prioritizr-4.1.3/prioritizr/R/connected_matrix.R | 361 - prioritizr-4.1.3/prioritizr/R/connectivity_matrix.R | 320 - prioritizr-4.1.3/prioritizr/R/constraints.R | 188 prioritizr-4.1.3/prioritizr/R/data.R | 391 - prioritizr-4.1.3/prioritizr/R/decisions.R | 160 prioritizr-4.1.3/prioritizr/R/deprecated.R | 72 prioritizr-4.1.3/prioritizr/R/fast_extract.R | 332 - prioritizr-4.1.3/prioritizr/R/feature_abundances.R | 324 - prioritizr-4.1.3/prioritizr/R/feature_names.R | 134 prioritizr-4.1.3/prioritizr/R/feature_representation.R | 907 +-- prioritizr-4.1.3/prioritizr/R/internal.R | 636 +- prioritizr-4.1.3/prioritizr/R/intersecting_units.R | 348 - prioritizr-4.1.3/prioritizr/R/irreplaceability.R |only prioritizr-4.1.3/prioritizr/R/loglinear_interpolation.R | 116 prioritizr-4.1.3/prioritizr/R/magrittr-operators.R | 152 prioritizr-4.1.3/prioritizr/R/marxan_boundary_data_to_matrix.R | 313 - prioritizr-4.1.3/prioritizr/R/marxan_problem.R | 722 +- prioritizr-4.1.3/prioritizr/R/misc.R | 84 prioritizr-4.1.3/prioritizr/R/new_optimization_problem.R | 42 prioritizr-4.1.3/prioritizr/R/number_of_features.R | 152 prioritizr-4.1.3/prioritizr/R/number_of_planning_units.R | 116 prioritizr-4.1.3/prioritizr/R/number_of_total_units.R | 128 prioritizr-4.1.3/prioritizr/R/number_of_zones.R | 154 prioritizr-4.1.3/prioritizr/R/objectives.R | 184 prioritizr-4.1.3/prioritizr/R/package.R | 168 prioritizr-4.1.3/prioritizr/R/parallel.R | 368 - prioritizr-4.1.3/prioritizr/R/parameters.R | 996 +-- prioritizr-4.1.3/prioritizr/R/penalties.R | 140 prioritizr-4.1.3/prioritizr/R/portfolios.R | 144 prioritizr-4.1.3/prioritizr/R/pproto.R | 150 prioritizr-4.1.3/prioritizr/R/predefined_optimization_problem.R | 198 prioritizr-4.1.3/prioritizr/R/presolve_check.R | 576 - prioritizr-4.1.3/prioritizr/R/print.R | 216 prioritizr-4.1.3/prioritizr/R/problem.R | 1658 ++--- prioritizr-4.1.3/prioritizr/R/rarity_weighted_richness.R |only prioritizr-4.1.3/prioritizr/R/replacement_cost.R |only prioritizr-4.1.3/prioritizr/R/rij_matrix.R | 262 prioritizr-4.1.3/prioritizr/R/run_calculations.R | 164 prioritizr-4.1.3/prioritizr/R/show.R | 144 prioritizr-4.1.3/prioritizr/R/simulate.R | 263 prioritizr-4.1.3/prioritizr/R/solve.R | 679 +- prioritizr-4.1.3/prioritizr/R/solvers.R | 212 prioritizr-4.1.3/prioritizr/R/targets.R | 150 prioritizr-4.1.3/prioritizr/R/tbl_df.R | 148 prioritizr-4.1.3/prioritizr/R/waiver.R | 62 prioritizr-4.1.3/prioritizr/R/zone_names.R | 140 prioritizr-4.1.3/prioritizr/R/zones.R | 382 - prioritizr-4.1.3/prioritizr/R/zzz.R | 37 prioritizr-4.1.3/prioritizr/README.md | 795 +- prioritizr-4.1.3/prioritizr/build/vignette.rds |binary prioritizr-4.1.3/prioritizr/data/sim_phylogeny.rda |binary prioritizr-4.1.3/prioritizr/inst/doc/gurobi_installation.Rmd | 382 - prioritizr-4.1.3/prioritizr/inst/doc/gurobi_installation.html | 820 +- prioritizr-4.1.3/prioritizr/inst/doc/prioritizr.Rmd | 1491 ++--- prioritizr-4.1.3/prioritizr/inst/doc/prioritizr.html | 2909 +++++----- prioritizr-4.1.3/prioritizr/inst/doc/publication_record.Rmd | 63 prioritizr-4.1.3/prioritizr/inst/doc/publication_record.html | 351 - prioritizr-4.1.3/prioritizr/inst/doc/saltspring.Rmd | 430 - prioritizr-4.1.3/prioritizr/inst/doc/saltspring.html | 862 +- prioritizr-4.1.3/prioritizr/inst/doc/tasmania.Rmd | 454 - prioritizr-4.1.3/prioritizr/inst/doc/tasmania.html | 1138 ++- prioritizr-4.1.3/prioritizr/inst/doc/zones.Rmd | 646 +- prioritizr-4.1.3/prioritizr/inst/doc/zones.html | 1904 +++--- prioritizr-4.1.3/prioritizr/inst/extdata/input.dat | 110 prioritizr-4.1.3/prioritizr/inst/extdata/simulate_data.R | 338 - prioritizr-4.1.3/prioritizr/man/ArrayParameter-class.Rd | 200 prioritizr-4.1.3/prioritizr/man/Collection-class.Rd | 194 prioritizr-4.1.3/prioritizr/man/ConservationModifier-class.Rd | 256 prioritizr-4.1.3/prioritizr/man/ConservationProblem-class.Rd | 594 +- prioritizr-4.1.3/prioritizr/man/Constraint-class.Rd | 32 prioritizr-4.1.3/prioritizr/man/Decision-class.Rd | 34 prioritizr-4.1.3/prioritizr/man/MiscParameter-class.Rd | 166 prioritizr-4.1.3/prioritizr/man/Objective-class.Rd | 26 prioritizr-4.1.3/prioritizr/man/OptimizationProblem-class.Rd | 248 prioritizr-4.1.3/prioritizr/man/OptimizationProblem-methods.Rd | 288 prioritizr-4.1.3/prioritizr/man/Parameter-class.Rd | 118 prioritizr-4.1.3/prioritizr/man/Parameters-class.Rd | 180 prioritizr-4.1.3/prioritizr/man/Penalty-class.Rd | 34 prioritizr-4.1.3/prioritizr/man/Portfolio-class.Rd | 132 prioritizr-4.1.3/prioritizr/man/ScalarParameter-class.Rd | 182 prioritizr-4.1.3/prioritizr/man/Solver-class.Rd | 166 prioritizr-4.1.3/prioritizr/man/Target-class.Rd | 32 prioritizr-4.1.3/prioritizr/man/add_absolute_targets.Rd | 308 - prioritizr-4.1.3/prioritizr/man/add_binary_decisions.Rd | 140 prioritizr-4.1.3/prioritizr/man/add_boundary_penalties.Rd | 486 - prioritizr-4.1.3/prioritizr/man/add_connectivity_penalties.Rd | 828 +- prioritizr-4.1.3/prioritizr/man/add_contiguity_constraints.Rd | 412 - prioritizr-4.1.3/prioritizr/man/add_cuts_portfolio.Rd | 170 prioritizr-4.1.3/prioritizr/man/add_default_decisions.Rd | 38 prioritizr-4.1.3/prioritizr/man/add_default_solver.Rd | 50 prioritizr-4.1.3/prioritizr/man/add_feature_contiguity_constraints.Rd | 453 - prioritizr-4.1.3/prioritizr/man/add_feature_weights.Rd | 425 - prioritizr-4.1.3/prioritizr/man/add_gurobi_solver.Rd | 188 prioritizr-4.1.3/prioritizr/man/add_locked_in_constraints.Rd | 446 - prioritizr-4.1.3/prioritizr/man/add_locked_out_constraints.Rd | 393 - prioritizr-4.1.3/prioritizr/man/add_loglinear_targets.Rd | 222 prioritizr-4.1.3/prioritizr/man/add_lsymphony_solver.Rd | 166 prioritizr-4.1.3/prioritizr/man/add_mandatory_allocation_constraints.Rd | 148 prioritizr-4.1.3/prioritizr/man/add_manual_bounded_constraints.Rd |only prioritizr-4.1.3/prioritizr/man/add_manual_locked_constraints.Rd | 276 prioritizr-4.1.3/prioritizr/man/add_manual_targets.Rd | 406 - prioritizr-4.1.3/prioritizr/man/add_max_cover_objective.Rd | 314 - prioritizr-4.1.3/prioritizr/man/add_max_features_objective.Rd | 254 prioritizr-4.1.3/prioritizr/man/add_max_phylo_div_objective.Rd |only prioritizr-4.1.3/prioritizr/man/add_max_phylo_end_objective.Rd |only prioritizr-4.1.3/prioritizr/man/add_max_utility_objective.Rd | 240 prioritizr-4.1.3/prioritizr/man/add_min_set_objective.Rd | 194 prioritizr-4.1.3/prioritizr/man/add_min_shortfall_objective.Rd | 244 prioritizr-4.1.3/prioritizr/man/add_neighbor_constraints.Rd | 384 - prioritizr-4.1.3/prioritizr/man/add_pool_portfolio.Rd | 228 prioritizr-4.1.3/prioritizr/man/add_proportion_decisions.Rd | 144 prioritizr-4.1.3/prioritizr/man/add_relative_targets.Rd | 302 - prioritizr-4.1.3/prioritizr/man/add_rsymphony_solver.Rd | 154 prioritizr-4.1.3/prioritizr/man/add_semicontinuous_decisions.Rd | 160 prioritizr-4.1.3/prioritizr/man/add_shuffle_portfolio.Rd | 164 prioritizr-4.1.3/prioritizr/man/array_parameters.Rd | 254 prioritizr-4.1.3/prioritizr/man/as.Rd | 58 prioritizr-4.1.3/prioritizr/man/as.list.Rd | 38 prioritizr-4.1.3/prioritizr/man/binary_stack.Rd | 83 prioritizr-4.1.3/prioritizr/man/boundary_matrix.Rd | 196 prioritizr-4.1.3/prioritizr/man/branch_matrix.Rd | 91 prioritizr-4.1.3/prioritizr/man/category_layer.Rd | 89 prioritizr-4.1.3/prioritizr/man/category_vector.Rd | 94 prioritizr-4.1.3/prioritizr/man/compile.Rd | 118 prioritizr-4.1.3/prioritizr/man/connected_matrix.Rd | 227 prioritizr-4.1.3/prioritizr/man/connectivity_matrix.Rd | 194 prioritizr-4.1.3/prioritizr/man/constraints.Rd | 192 prioritizr-4.1.3/prioritizr/man/decisions.Rd | 164 prioritizr-4.1.3/prioritizr/man/distribute_load.Rd | 142 prioritizr-4.1.3/prioritizr/man/fast_extract.Rd | 158 prioritizr-4.1.3/prioritizr/man/feature_abundances.Rd | 290 prioritizr-4.1.3/prioritizr/man/feature_names.Rd | 78 prioritizr-4.1.3/prioritizr/man/feature_representation.Rd | 473 - prioritizr-4.1.3/prioritizr/man/figures/README-boundary_penalties-1.png |only prioritizr-4.1.3/prioritizr/man/figures/README-contiguity_constraints-1.png |only prioritizr-4.1.3/prioritizr/man/figures/README-locked_in_constraints-1.png |only prioritizr-4.1.3/prioritizr/man/figures/README-minimal_solution-1.png |only prioritizr-4.1.3/prioritizr/man/figures/README-replacement_cost-1.png |only prioritizr-4.1.3/prioritizr/man/figures/README-unnamed-chunk-9-1.png |binary prioritizr-4.1.3/prioritizr/man/figures/logo.png |only prioritizr-4.1.3/prioritizr/man/intersecting_units.Rd | 158 prioritizr-4.1.3/prioritizr/man/irreplaceability.Rd |only prioritizr-4.1.3/prioritizr/man/is.Rd | 42 prioritizr-4.1.3/prioritizr/man/is.parallel.Rd | 72 prioritizr-4.1.3/prioritizr/man/loglinear_interpolation.Rd | 96 prioritizr-4.1.3/prioritizr/man/marxan_boundary_data_to_matrix.Rd | 113 prioritizr-4.1.3/prioritizr/man/marxan_problem.Rd | 378 - prioritizr-4.1.3/prioritizr/man/matrix_parameters.Rd | 128 prioritizr-4.1.3/prioritizr/man/misc_parameter.Rd | 122 prioritizr-4.1.3/prioritizr/man/new_id.Rd | 70 prioritizr-4.1.3/prioritizr/man/new_optimization_problem.Rd | 48 prioritizr-4.1.3/prioritizr/man/new_waiver.Rd | 64 prioritizr-4.1.3/prioritizr/man/number_of_features.Rd | 86 prioritizr-4.1.3/prioritizr/man/number_of_planning_units.Rd | 74 prioritizr-4.1.3/prioritizr/man/number_of_total_units.Rd | 98 prioritizr-4.1.3/prioritizr/man/number_of_zones.Rd | 90 prioritizr-4.1.3/prioritizr/man/objectives.Rd | 186 prioritizr-4.1.3/prioritizr/man/parallel.Rd | 98 prioritizr-4.1.3/prioritizr/man/parameters.Rd | 66 prioritizr-4.1.3/prioritizr/man/penalties.Rd | 144 prioritizr-4.1.3/prioritizr/man/pipe.Rd | 62 prioritizr-4.1.3/prioritizr/man/portfolios.Rd | 148 prioritizr-4.1.3/prioritizr/man/pproto.Rd | 88 prioritizr-4.1.3/prioritizr/man/predefined_optimization_problem.Rd | 142 prioritizr-4.1.3/prioritizr/man/presolve_check.Rd | 368 - 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prioritizr-4.1.3/prioritizr/tests/testthat/test_add_boundary_penalties.R | 784 +- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_connectivity_penalties.R | 592 +- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_contiguity_constraints.R | 492 - prioritizr-4.1.3/prioritizr/tests/testthat/test_add_cuts_portfolio.R | 414 - prioritizr-4.1.3/prioritizr/tests/testthat/test_add_feature_contiguity_constraints.R | 878 +-- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_feature_weights.R | 726 +- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_locked_in_constraints.R | 1116 +-- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_locked_out_constraints.R | 1108 +-- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_loglinear_targets.R | 196 prioritizr-4.1.3/prioritizr/tests/testthat/test_add_mandatory_allocation_constraints.R | 370 - prioritizr-4.1.3/prioritizr/tests/testthat/test_add_manual_bounded_constraints.R |only prioritizr-4.1.3/prioritizr/tests/testthat/test_add_manual_locked_constraints.R | 340 - prioritizr-4.1.3/prioritizr/tests/testthat/test_add_manual_targets.R | 360 - prioritizr-4.1.3/prioritizr/tests/testthat/test_add_max_cover_objective.R | 1048 +-- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_max_features_objective.R | 1210 ++-- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_max_phylo_div_objective.R |only prioritizr-4.1.3/prioritizr/tests/testthat/test_add_max_phylo_end_objective.R |only prioritizr-4.1.3/prioritizr/tests/testthat/test_add_max_utility_objective.R | 1068 +-- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_min_set_objective.R | 626 +- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_min_shortfalls_objective.R | 1196 ++-- prioritizr-4.1.3/prioritizr/tests/testthat/test_add_neighbor_constraints.R | 488 - prioritizr-4.1.3/prioritizr/tests/testthat/test_add_pool_portfolio.R | 548 - prioritizr-4.1.3/prioritizr/tests/testthat/test_add_relative_targets.R | 408 - prioritizr-4.1.3/prioritizr/tests/testthat/test_add_shuffle_portfolio.R | 536 - prioritizr-4.1.3/prioritizr/tests/testthat/test_binary_stack.R | 66 prioritizr-4.1.3/prioritizr/tests/testthat/test_boundary_matrix.R | 360 - prioritizr-4.1.3/prioritizr/tests/testthat/test_branch_matrix.R | 68 prioritizr-4.1.3/prioritizr/tests/testthat/test_category_layer.R | 78 prioritizr-4.1.3/prioritizr/tests/testthat/test_category_vector.R | 58 prioritizr-4.1.3/prioritizr/tests/testthat/test_compile.R | 206 prioritizr-4.1.3/prioritizr/tests/testthat/test_connected_matrix.R | 200 prioritizr-4.1.3/prioritizr/tests/testthat/test_connectivity_matrix.R | 218 prioritizr-4.1.3/prioritizr/tests/testthat/test_decisions.R | 446 - prioritizr-4.1.3/prioritizr/tests/testthat/test_feature_abundances.R | 370 - prioritizr-4.1.3/prioritizr/tests/testthat/test_feature_representation.R | 720 +- prioritizr-4.1.3/prioritizr/tests/testthat/test_internal.R | 82 prioritizr-4.1.3/prioritizr/tests/testthat/test_intersecting_units.R | 102 prioritizr-4.1.3/prioritizr/tests/testthat/test_marxan_problem.R | 506 - prioritizr-4.1.3/prioritizr/tests/testthat/test_parallel.R | 80 prioritizr-4.1.3/prioritizr/tests/testthat/test_parameters.R | 864 +- prioritizr-4.1.3/prioritizr/tests/testthat/test_pproto.R | 200 prioritizr-4.1.3/prioritizr/tests/testthat/test_presolve_check.R | 262 prioritizr-4.1.3/prioritizr/tests/testthat/test_problem.R | 1824 +++--- prioritizr-4.1.3/prioritizr/tests/testthat/test_problem_negative.R | 1378 ++-- prioritizr-4.1.3/prioritizr/tests/testthat/test_rarity_weighted_richness.R |only prioritizr-4.1.3/prioritizr/tests/testthat/test_replacement_cost.R |only prioritizr-4.1.3/prioritizr/tests/testthat/test_rij_matrix.R | 230 prioritizr-4.1.3/prioritizr/tests/testthat/test_simulate.R | 80 prioritizr-4.1.3/prioritizr/tests/testthat/test_solve.R | 614 +- prioritizr-4.1.3/prioritizr/tests/testthat/test_solvers.R | 433 + prioritizr-4.1.3/prioritizr/tests/testthat/test_sp_to_polyset.R | 40 prioritizr-4.1.3/prioritizr/tests/testthat/test_zones.R | 78 prioritizr-4.1.3/prioritizr/vignettes/gurobi_installation.Rmd | 382 - prioritizr-4.1.3/prioritizr/vignettes/prioritizr.Rmd | 1491 ++--- prioritizr-4.1.3/prioritizr/vignettes/publication_record.Rmd | 63 prioritizr-4.1.3/prioritizr/vignettes/reference-style.csl | 402 - prioritizr-4.1.3/prioritizr/vignettes/references.bib | 666 +- prioritizr-4.1.3/prioritizr/vignettes/saltspring.Rmd | 430 - prioritizr-4.1.3/prioritizr/vignettes/tasmania.Rmd | 454 - prioritizr-4.1.3/prioritizr/vignettes/zones.Rmd | 646 +- 343 files changed, 49130 insertions(+), 46808 deletions(-)
Title: Easy-to-Use Tools for Common Forms of Random Assignment and
Sampling
Description: Generates random assignments for common experimental designs and
random samples for common sampling designs.
Author: Alexander Coppock [aut, cre],
Jasper Cooper [ctb],
Neal Fultz [ctb] (C version of restricted partitions)
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between randomizr versions 0.18.0 dated 2019-04-23 and 0.20.0 dated 2019-09-06
DESCRIPTION | 8 MD5 | 16 - R/helper_functions.R | 27 - build/vignette.rds |binary inst/doc/randomizr_vignette.html | 538 +++++++++++++++++----------------- src/onload.c | 2 src/vsample.c | 4 tests/testthat/test-block_ra.R | 15 tests/testthat/test-tricky-examples.R | 12 9 files changed, 328 insertions(+), 294 deletions(-)
Title: Google Search Console R Client
Description: Provides an interface with the Google Search Console,
formally called Google Webmaster Tools.
Author: Mark Edmondson [aut, cre],
Jennifer Bryan [ctb],
Parzakonis Manos [ctb]
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between searchConsoleR versions 0.3.0 dated 2018-01-03 and 0.4.0 dated 2019-09-06
DESCRIPTION | 10 - LICENSE | 4 MD5 | 62 +++++------ NAMESPACE | 3 R/auth.R | 17 --- R/getData.R | 106 ++++++++---------- R/options.R | 6 - R/reqParse.R | 1 R/utility.R | 2 README.md | 6 - build/vignette.rds |binary inst/doc/searchConsoleR-intro.html | 197 ++++++++++++++++++++++++++++++++++- man/add_sitemap.Rd | 1 man/add_website.Rd | 1 man/crawl_errors.Rd | 1 man/delete_sitemap.Rd | 1 man/delete_website.Rd | 2 man/error_sample_url.Rd | 4 man/fix_sample_url.Rd | 4 man/list_crawl_error_samples.Rd | 4 man/list_sitemaps.Rd | 2 man/list_websites.Rd | 1 man/lookupCountryCode.Rd | 1 man/parseDimFilterGroup.Rd | 1 man/parse_crawlerror_sample.Rd | 1 man/parse_crawlerrors.Rd | 1 man/parse_errorsample_url.Rd | 1 man/parse_search_analytics.Rd | 1 man/parse_sitemaps.Rd | 1 man/scr_auth.Rd | 6 - man/search_analytics.Rd | 12 +- tests/testthat/test-searchConsoleR.R | 2 32 files changed, 327 insertions(+), 135 deletions(-)
More information about searchConsoleR at CRAN
Permanent link
Title: Online Time Series Anomaly Detectors
Description: Implements a set of online fault detectors for time-series, called: PEWMA see M. Carter
et al. (2012) <doi:10.1109/SSP.2012.6319708>, SD-EWMA and TSSD-EWMA see H. Raza et al.
(2015) <doi:10.1016/j.patcog.2014.07.028>, KNN-CAD see E. Burnaev et al. (2016)
<arXiv:1608.04585>, KNN-LDCD see V. Ishimtsev et al. (2017) <arXiv:1706.03412> and
CAD-OSE see M. Smirnov (2018) <https://github.com/smirmik/CAD>. The first three
algorithms belong to prediction-based techniques and the last three belong to
window-based techniques. In addition, the SD-EWMA and PEWMA algorithms are algorithms
designed to work in stationary environments, while the other four
are algorithms designed to work in non-stationary environments.
Author: Alaiñe Iturria [aut, cre],
Jacinto Carrasco [aut],
Francisco Herrera [aut],
Santiago Charramendieta [aut],
Karmele Intxausti [aut]
Maintainer: Alaiñe Iturria <aiturria@ikerlan.es>
Diff between otsad versions 0.1.0 dated 2019-04-01 and 0.2.0 dated 2019-09-06
DESCRIPTION | 6 - MD5 | 80 ++++++++------- NEWS.md |only R/GetDetectorScore.R | 6 + R/GetDetectorScore_getWindowLength.R | 22 +++- R/GetDetectorScore_getWindowsLimits.R | 22 +++- R/GetDetectorScore_normalizeScore.R | 11 ++ R/GetNumTrainingValues.R | 7 + R/PlotDetections.R | 20 +++ R/ReduceAnomalies.R | 58 ++++++++--- R/cp_knn_cad.R | 5 R/cp_sd_ewma.R | 1 R/cp_tssd_ewma.R | 2 R/ip_knn_cad.R | 108 ++++++++++++-------- R/ip_pewma.R | 4 R/ip_sd_ewma.R | 5 R/ip_tssd_ewma.R | 131 +++++++++++++++--------- R/ocp_sd_ewma.R | 1 R/oip_pewma.R | 4 R/oip_sd_ewma.R | 5 R/oip_tssd_ewma.R | 137 ++++++++++++++++---------- README.md | 61 +++++++++-- build/vignette.rds |binary inst/doc/otsad.R | 4 inst/doc/otsad.Rnw | 51 +++++++-- inst/doc/otsad.pdf |binary man/CpTsSdEwma.Rd | 2 man/IpTsSdEwma.Rd | 47 +++----- man/OipTsSdEwma.Rd | 48 +++------ man/ReduceAnomalies.Rd | 79 +++++++++++++- man/figures/README-plot.Anomaly-1.png |binary tests/examples/ip_tssd_ewma_example.R | 31 ++--- tests/examples/oip_tssd_ewma_example.R | 34 ++---- tests/examples/reduceAnomalies_example.R | 66 +++++++++++- tests/testthat/test_getDetectorScore.R |only tests/testthat/test_getLabels.R |only tests/testthat/test_getNullAndPerfectScores.R |only tests/testthat/test_getNumTrainingValues.R |only tests/testthat/test_getWindowLength.R |only tests/testthat/test_getWindowsLimits.R |only tests/testthat/test_ip_tssd_ewma.R | 20 --- tests/testthat/test_normalizeScore.R |only tests/testthat/test_oip_tssd_ewma.R | 21 --- tests/testthat/test_reduceAnomalies.R |only vignettes/otsad-concordance.tex |only vignettes/otsad.Rnw | 51 +++++++-- 46 files changed, 749 insertions(+), 401 deletions(-)
Title: Integrative Differential Network Analysis in Genomics
Description: Fits covariate dependent partial correlation matrices for integrative models to identify differential networks between two groups. The methods are described in Class et. al., (2018) <doi:10.1093/bioinformatics/btx750> and Ha et. al., (2015) <doi:10.1093/bioinformatics/btv406>.
Author: Caleb A. Class <caclass@mdanderson.org>, Min Jin Ha <mjha@mdanderson.org>
Maintainer: Caleb A. Class <caclass@mdanderson.org>
Diff between iDINGO versions 1.0.2 dated 2017-10-12 and 1.0.3 dated 2019-09-06
DESCRIPTION | 14 +++++++------- MD5 | 5 +++-- NEWS.md | 4 ++++ inst |only 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Change-Point Estimation for Expensive and High-Dimensional
Models
Description: This implements the methods developed in, L. Bybee and Y. Atchade. (2018). Contains a series of methods for estimating change-points given user specified black-box models. The methods include binary segmentation for multiple change-point estimation. For estimating each individual change-point the package includes simulated annealing, brute force, and, for Gaussian graphical models, an applications specific rank-one update implementation. Additionally, code for estimating Gaussian graphical models is included. The goal of this package is to allow for the efficient estimation of change-points in complicated models with high dimensional data.
Author: Leland Bybee
Maintainer: Leland Bybee <lelandb@umich.edu>
Diff between changepointsHD versions 0.3.1 dated 2019-03-16 and 0.3.2 dated 2019-09-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary tests/test_changepoints.R | 1 + 4 files changed, 8 insertions(+), 7 deletions(-)
More information about changepointsHD at CRAN
Permanent link
Title: High Precision Timing of R Expressions
Description: Tools to accurately benchmark and analyze execution times for R expressions.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between bench versions 1.0.3 dated 2019-08-28 and 1.0.4 dated 2019-09-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 9 +++++++++ R/bench_time.R | 4 +++- R/expression.R | 4 ++-- man/bench_memory.Rd | 4 +++- 6 files changed, 25 insertions(+), 12 deletions(-)
Title: Relevance-Integrated Statistical Inference Engine
Description: A framework of methods to perform customized inference at individual level
by taking contextual covariates into account. Three main functions are provided
in this package: (i) LASER(): it generates specially-designed artificial relevant
samples for a given case; (ii) g2l.proc(): computes customized fdr(z|x); and (iii)
rEB.proc(): performs empirical Bayes inference based on LASERs. The details can be
found in Mukhopadhyay, S., and Wang, K (2019, Technical Report).
Author: Subhadeep Mukhopadhyay, Kaijun Wang
Maintainer: Kaijun Wang <kaijunwang.19@gmail.com>
Diff between LPRelevance versions 1.0 dated 2019-08-05 and 2.0 dated 2019-09-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/Finite.rEB.R | 40 +++++++++++++++++++++++++++++----------- R/LASER.R | 36 ++++++++++++++++++++++++++---------- build/partial.rdb |binary man/LASER.Rd | 3 ++- man/g2l.proc.Rd | 3 ++- man/rEB.proc.Rd | 3 ++- 8 files changed, 72 insertions(+), 35 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-03 1.0.2
2018-07-25 1.0.1
2018-06-06 1.0.0
2018-06-04 0.99.9