prioritizr / prioritizr

Compare 70cc07f ... +2 ... 0197bdd

98.34% 100.00% -<.01%

Overview Diff Coverage Changes Files Commits
Coverage Reach
R/problem.R R/planning_unit_solution_status.R R/eval_replacement_importance.R R/marxan_problem.R R/presolve_check.R R/eval_ferrier_importance.R R/add_cbc_solver.R R/add_linear_constraints.R R/parameters.R R/eval_rare_richness_importance.R R/add_neighbor_constraints.R R/add_linear_penalties.R R/add_feature_contiguity_constraints.R R/solve.R R/add_lpsymphony_solver.R R/add_rsymphony_solver.R R/marxan_connectivity_data_to_matrix.R R/add_locked_in_constraints.R R/add_manual_targets.R R/add_boundary_penalties.R R/add_locked_out_constraints.R R/add_connectivity_penalties.R R/add_manual_locked_constraints.R R/internal.R R/add_asym_connectivity_penalties.R R/eval_asym_connectivity_summary.R R/eval_connectivity_summary.R R/add_manual_bounded_constraints.R R/compile.R R/boundary_matrix.R R/add_contiguity_constraints.R R/zones.R R/eval_target_coverage_summary.R R/add_shuffle_portfolio.R R/intersecting_units.R R/add_max_phylo_end_objective.R R/add_feature_weights.R R/eval_feature_representation_summary.R R/fast_extract.R R/simulate.R R/add_max_phylo_div_objective.R R/add_loglinear_targets.R R/connectivity_matrix.R R/add_absolute_targets.R R/proximity_matrix.R R/add_relative_targets.R R/adjacency_matrix.R R/eval_boundary_summary.R R/rij_matrix.R R/write_problem.R R/predefined_optimization_problem.R R/add_min_largest_shortfall_objective.R R/add_cuts_portfolio.R R/add_max_utility_objective.R R/add_min_shortfall_objective.R R/add_max_features_objective.R R/OptimizationProblem-methods.R R/add_max_cover_objective.R R/pproto.R R/category_vector.R R/loglinear_interpolation.R R/add_mandatory_allocation_constraints.R R/add_semicontinuous_decisions.R R/feature_abundances.R R/distribute_load.R R/eval_cost_summary.R R/eval_n_summary.R R/binary_stack.R R/add_min_set_objective.R R/run_calculations.R R/add_binary_decisions.R R/add_proportion_decisions.R R/category_layer.R R/Id.R R/branch_matrix.R R/misc.R R/number_of_zones.R R/number_of_features.R R/feature_names.R R/zone_names.R R/number_of_planning_units.R R/tbl_df.R R/number_of_total_units.R R/add_default_objective.R R/targets.R R/add_default_decisions.R R/waiver.R R/new_optimization_problem.R R/add_default_portfolio.R R/marxan_boundary_data_to_matrix.R src/rcpp_apply_feature_contiguity_constraints.cpp src/rcpp_boundary_data.cpp src/rcpp_apply_contiguity_constraints.cpp src/optimization_problem.cpp src/rcpp_apply_boundary_penalties.cpp src/rcpp_apply_max_phylo_objective.cpp src/rcpp_apply_asym_connectivity_penalties.cpp src/rcpp_apply_min_largest_shortfall_objective.cpp src/rcpp_apply_connectivity_penalties.cpp src/rcpp_ferrier_score.cpp src/rcpp_apply_max_cover_objective.cpp src/rcpp_apply_max_utility_objective.cpp src/rcpp_add_rij_data.cpp src/rcpp_apply_max_features_objective.cpp src/rcpp_apply_min_shortfall_objective.cpp src/rcpp_boundary_data.h src/rcpp_apply_neighbor_constraints.cpp src/rcpp_sp_to_polyset.cpp src/rcpp_boundary.cpp src/rcpp_summarize_exactextractr.cpp src/rcpp_branch_matrix.cpp src/optimization_problem.h src/rcpp_absolute_amount_held_by_solution.cpp src/rcpp_apply_min_set_objective.cpp src/functions.cpp src/rcpp_list_to_matrix_indices.cpp src/rcpp_apply_linear_penalties.cpp src/rcpp_forbid_solution.cpp src/rcpp_connectivity.cpp src/rcpp_asym_connectivity.cpp src/rcpp_add_zones_constraints.cpp src/rcpp_apply_decisions.cpp src/rcpp_add_linear_constraints.cpp src/rcpp_apply_feature_weights.cpp src/rcpp_apply_bounded_constraints.cpp src/rcpp_apply_locked_constraints.cpp src/functions.h src/init.c

No flags found

Use flags to group coverage reports by test type, project and/or folders.
Then setup custom commit statuses and notifications for each flag.

e.g., #unittest #integration

#production #enterprise

#frontend #backend

Learn more about Codecov Flags here.

Showing 1 of 9 files from the diff.

@@ -288,24 +288,25 @@
Loading
288 288 
  assertthat::assert_that(
289 289 
    inherits(x, "ConservationProblem"),
290 290 
    is.matrix(solution))
291 + 
  # convert NAs in solution to zeros
292 + 
  solution[is.na(solution)] <- 0
291 293 
  # calculate amount of each feature in each planning unit
292 294 
  total <- x$feature_abundances_in_total_units()
293 295 
  held <- vapply(
294 296 
    seq_len(x$number_of_zones()),
295 297 
    FUN.VALUE = numeric(nrow(x$data$rij_matrix[[1]])),
296 298 
    function(i) {
297 - 
      Matrix::rowSums(
298 - 
        x$data$rij_matrix[[i]] *
299 + 
      as.numeric(
300 + 
        x$data$rij_matrix[[i]] %*%
299 301 
        Matrix::Matrix(
300 302 
          solution[, i],
301 - 
          ncol = nrow(solution),
302 - 
          nrow = nrow(x$data$rij_matrix[[1]]),
303 - 
          byrow = TRUE,
304 - 
          sparse = FALSE
305 - 
        ),
306 - 
        na.rm = TRUE
303 + 
          ncol = 1,
304 + 
          nrow = nrow(solution),
305 + 
          sparse = TRUE
306 + 
        )
307 307 
      )
308 - 
  })
308 + 
    }
309 + 
  )
309 310 
  # prepare output
310 311 
  if (x$number_of_zones() == 1) {
311 312 
    out <- tibble::tibble(

Everything is accounted for!

No changes detected that need to be reviewed.
What changes does Codecov check for?
Lines, not adjusted in diff, that have changed coverage data.
Files that introduced coverage data that had none before.
Files that have missing coverage data that once were tracked.

4 Commits

Jeff Hanson
98.34% ø -<.01%
fix urls
jeffreyhanson
#253 0197bdd
CI Passed
Jeffrey Hanson
Contextual
fix again
jeffreyhanson
1227b52
Jeffrey Hanson
Contextual
try again
jeffreyhanson
3ca84be
Hiding 2 contexual commits
-1
-1
Jeff Hanson
98.34% 100.00% +<.01%
fix #252
jeffreyhanson
#253 70cc07f
CI Passed
Files Coverage
R -<.01% 98.39%
src 98.22%
Project Totals (128 files) 98.34%
Loading