Man pages for langfob/bdpg
Package For Building and Testing Biodiversity Problem Generators
| act_on_loaded_existing_tzar_run | Execute a single action based on tzar repetition values in... |
| add_missing_PU_rows_to_PU_Count_dataframe | Add missing PUs to PU_Count data frame |
| always_set_new_or_forced_rand_seed | Always set a seed, either by generating a new one or reusing... |
| apply_const_error_to_spp_occupancy_data | Apply constant error to spp occ data |
| apply_error_to_spp_occupancy_data | Apply error to species occupancy data. |
| assert_edge_list_does_not_violate_assumptions | Assert edge list does not violate assumptions |
| bdpg | bdpg. |
| build_PU_spp_pair_indices_from_occ_matrix | Build PU spp pair indices from occ matrix |
| build_topdir_name | Build top directory name |
| ccBip | ccBip |
| ccLowDot | ccLowDot |
| ccTopDot | ccTopDot |
| check_for_imperfect_wrap | See whether wrapping species fully contain base species |
| choose_a_best_solution_ID_according_to_marxan | Choose a best solution ID according to marxan |
| compute_and_save_dist_and_network_metrics_for_prob | Compute and save the distribution and network metrics for the... |
| compute_and_set_obj_checksum | Convenience function for computing the object's checksum and... |
| compute_and_verify_rep_scores_wrt | Compute representation scores for candidate solution |
| compute_confusion_matrix_based_scores | Compute confusion matrix-based scores for candidate solution |
| compute_igraph_related_network_measures | Compute igraph-related network measures |
| compute_marxan_solution_scores | Compute marxan solution scores |
| compute_marxan_solution_scores_wrt_COR_or_APP_reps_and_costs | Compute rep and cost values of marxan solutions with respect... |
| compute_marxan_species_penalty_factor | Compute marxan species penalty factor |
| compute_network_measures_using_bipartite_package | Compute bipartite network measures using bipartite package |
| compute_num_spp_covered_by_solution | Compute number of species whose targets are met by a... |
| compute_obj_checksum | Compute a checksum for the object |
| compute_rep_fraction | Compute species representation fractions achieved |
| compute_solution_cost | Compute cost of given solution vector of PUs to include |
| create_adj_matrix_with_spp_rows_vs_PU_cols | Create adjacency matrix with species rows vs planning unit... |
| create_allowable_size_Xu_problem_from_scratch | Generate a Xu problem from scratch but insure it's less than... |
| create_and_init_APP_bdprob | Create and initialize apparent bdproblem from a correct... |
| create_APP_prob_info_by_adding_error_to_spp_occ_data | Add error to the species occupancy data and save to... |
| create_dirs_for_APP_prob | Create directories for this apparent problem. |
| create_eligible_PU_set | Create set of planning units eligible for adding species into |
| create_nodes_data_structure | Create nodes data structure |
| create_PU_spp_pair_indices | Convert edge list to PU/spp table |
| create_PU_spp_pair_names | Create PU spp pair indices |
| create_RSprob_dir_and_subdirs | Create directories for an RS problem |
| create_RSrun | Create an RSrun |
| create_RSrun_dir_and_subdirs | Create directories for an RS run |
| create_wrapping_PU_spp_table | Create wrapping PU/species table |
| create_Xu_graph | Create Xu graph |
| create_Xu_problem_from_scratch | Generate a Xu problem from scratch |
| create_Xu_problem_from_scratch_given_4_Xu_metaparams | Generate a Xu problem from scratch |
| create_Xu_problem_from_scratch_given_params | Generate a Xu problem from scratch given parameters |
| create_Xu_problem_from_scratch_not_using_4_Xu_metaparams | create_Xu_problem_from_scratch_not_using_4_Xu_metaparams |
| derive_Xu_control_parameters | Derive full Xu control params from 4 base params |
| do_APP_simple_richness_analysis_and_output | Run reserve selector on APP problem and write output from all... |
| do_COR_simple_richness_analysis_and_output | Run simple_richness on COR problem and write output from all... |
| do_Greedy_analysis_and_output | Run greedy reserve selector on bd problem and write output... |
| do_gurobi_analysis_and_output | Run reserve selector on bd problem and write output from all... |
| do_marxan_analysis_and_output | Run marxan on bd problem and write output from all analysis |
| do_rs_analysis_and_output | Run reserve selector(s) on bdproblem and write output from... |
| do_sanity_checks | Do sanity checks on parameters for wrapping a biodiversity... |
| EF | Evaluation Function to be passed to optim() |
| find_best_marxan_solutions | Find best marxan solutions |
| find_lognormal_to_wrap_around_Xu | Find lognormal to wrap around Xu problem |
| fix_0_length_list_elements | Return NA for any given value whose length is 0 |
| gen_11_variants_mixing_FP_FN_and_cost_error | Generate 11 basic variants of a problem |
| gen_20_basic_variants_including_cost_error | Generate 20 basic variants of a problem |
| gen_4_basic_variants | Create 1 of each of the 4 types of problems and run reserve... |
| gen_4_simple_random_variants_mixing_FP_FN_and_cost_error | Generate 4 simple random variants of a problem |
| gen_6_basic_variants | Generate 6 basic variants of a problem |
| gen_bdprob | Generate a base or wrapped biodiversity problem |
| gen_multi_bdprob | Generate a new bd problem by modifying or combining existing... |
| gen_new_seed_from_cur_time | Generate a new random seed based on the current time |
| gen_rounded_abundances | Generate rounded abundances |
| gen_single_bdprob_APP | Generate a single biodiversity problem with error added to it |
| gen_single_bdprob_COR | Generate a single correct biodiversity problem from scratch... |
| gen_single_bdprob_COR_from_scratch_or_Xu_bench_file | Generate a single biodiversity problem |
| gen_single_bdprob_WRAP | Generate a single wrapped biodiversity problem from a given... |
| gen_wrapped_bdprob_COR | Generate a correct wrapped Xu biodiversity problem from a... |
| get_base_cor_bdprob_for_given_app_bdprob | Get the COR bdprob whose UUID is the base UUID for the given... |
| get_bdprob_from_rds_file | Load a bdprob from an R rds output file, possibly specified... |
| get_current_os | Get name and version number of current operating system as a... |
| get_forced_seed_value_if_necessary | Get forced seed value if necessary |
| get_integerize_function | Get function to use when converting numeric values to... |
| get_marxan_solution_choice_string | Get marxan solution choice string |
| get_RSprob_path_networks | Get path to networks directory of RS problem |
| get_RSprob_path_plots | Get path to plots directory of RS problem |
| get_RSprob_path_topdir | Build top directory path for RS problem |
| get_UUID_from_file_path | Get the probable UUID of an object from its file name |
| init_for_bdpg | Initialize for biodiversity problem generation |
| init_object_graph_data | Compute graph metrics for an RSprob if requested and set the... |
| link_nodes_between_groups | Link nodes between groups |
| link_nodes_within_groups | Link nodes within groups |
| list_as_data_frame_with_0_length_vals_replaced_by_NA | Convert list to data frame with 0 length values replaced by... |
| list_with_0_length_vals_replaced_by_NA | Convert list to a new list with 0 length values replaced by... |
| load_existing_tzar_run_from_glass | Load an existing tzar run from glass |
| load_marxan_best_df_from_file_and_sort_and_add_missing_PUs | Load marxan best data frame from file, sort, add missing PUs |
| load_marxan_mvbest_df_from_file_and_sort_by_CF | Load marxan mvbest df from file and sort by CF |
| load_marxan_solutionsmatrix_and_add_missing_PUs | Load marxan solutions matrix from file, sort, add missing PUs |
| load_marxan_ssoln_df_from_file_and_sort_by_PU | Load marxan's summed solutions vector from its marxan output... |
| look_up_object_by_UUID | Search the set of files for a file name containing the UUID... |
| make_sure_no_spp_eradicated_by_setting_FNs | Make sure no species is eradicated by setting false negative... |
| make_sure_that_cor_bdprob_is_base_of_app_bdprob | Make sure that the correct bdprob is the base for the given... |
| match_FP_and_FN_counts_to_smaller_of_the_two | Match FP and FN counts to smaller of the two |
| options_are_legal_for_single_bdprob_WRAP | Check whether options for wrapping have legal values |
| plot_degree_and_abundance_dists_for_node_graph | Plot degree and abundance distributions for node graph |
| plot_final_degree_dist_for_node_graph | Plot final degree distribution for node graph |
| plot_incremental_marxan_summed_solution_representations | Plot incremental marxan summed solution representations |
| plot_incremental_marxan_summed_solution_reps_for_COR_and_APP | Plot how marxan is actually doing vs. how marxan thinks it's... |
| plot_marxan_best_solution_scores_COR_and_APP | Plot marxan best solution scores COR and APP |
| plot_rank_abundance_dist_for_node_graph | Plot rank abundance distribution for node graph |
| read_marxan_output_files | Read various marxan outputs into this program. |
| read_Xu_problem_from_Xu_file | Read a Xu benchmark problem formatted according to the format... |
| redundancy | Latapy et al redundancy measure |
| remove_base_spp_abundances_from_wrapping_distribution | Remove base problem's species from the wrapping problems set... |
| repro_do_Greedy_analysis_and_output | Reproduce greedy reserve selection run |
| repro_RSrun | Create an RSrun |
| run_gurobi | Run gurobi linear programming optimizer |
| run_marxan | Run marxan |
| safe_sample | Safe version of R sample function |
| save_obj_with_checksum | Save object with checksum |
| save_rsprob | Save bd problem to disk |
| save_rsprob_results_data | Save problem description results for a Xu_bd_problem |
| search_for_approximating_lognormal | Search for approximating lognormal |
| see_if_marxan_best_was_actually_best | Verify whether the solution marxan chose as best was actually... |
| see_if_there_are_any_duplicate_links | See if there are any duplicate links |
| set_const_FP_and_FN_rates | Set constant FP and FN rates |
| set_marxan_controls_and_run_marxan | Set marxan controls and run marxan |
| set_new_or_forced_rand_seed_if_necessary | Set a new or forced random seed if caller specifies that |
| set_seed_if_necessary_helper | Helper function for setting a seed when necessary |
| set_up_for_and_run_gurobi | Set up for and run gurobi |
| set_up_for_and_run_gurobi_APP | Set up for and run gurobi for APP problem |
| set_up_for_and_run_gurobi_COR | Set up for and run gurobi for COR problem |
| set_up_for_and_run_marxan | Set up for and run marxan |
| set_up_for_and_run_marxan_APP | Set up for and run marxan for APP problem |
| set_up_for_and_run_marxan_COR | Set up for and run marxan for COR problem |
| set_up_for_and_run_simple_richness | Set up for and run simple_richness |
| set_up_for_and_run_simple_richness_APP | Set up for and run simple_richness for APP problem |
| set_up_for_and_run_simple_richness_COR | Set up for and run simple_richness for COR problem |
| single_action_using_tzar_reps | Execute a single action based on tzar repetition values in... |
| sort_within_rows | Sort a 2 column matrix within rows |
| std_param_defns | Standardized parameter definitions for reuse across all... |
| stop_bdpg | Wrapper for stop function to allow extra controls over... |
| strip_trailing_slash | Strip Trailing Slash Off Of Path If There Is One |
| summarize_and_plot_graph_and_distribution_structure_information | Compute final PU and species counts and plot degree and... |
| summarize_pu_and_spp_dist_data_from_marxan_puvspr_input_file | Summarize PU and spp dist data from marxan puvspr input file |
| summarize_pu_and_spp_dist_data_from_pu_spp_amt_df | Compute distributions for planning units and species from... |
| touch | Imitate unix touch function to create an empty file. |
| trim_abundances | Drop spp from abund dist if on too many or too few patches |
| validate_wrap | Validate the wrapping of a bdproblem |
| value_or_1_if_null | Get parameter value that should be integer and return 1 if... |
| value_or_FALSE_if_null | Get parameter value that should be boolean and return FALSE... |
| vb | Validate input as boolean and replace with default on empty... |
| verify_that_generated_solution_really_is_a_solution | Verify that solution does cover all species |
| vn | Validate input as numeric and replace with default on empty... |
| wrap_abundance_dist_around_Xu_problem | Wrap abundance distribution around Xu problem |
| wrap_abundances_around_eligible_set | Wrap abundances around eligible set |
| write_all_marxan_input_files | Write all marxan input files |
| write_all_marxan_input_files_from_vectors | Write all marxan input files except bound.dat and input.dat... |
| write_marxan_pu.dat_input_file | Write marxan planning units input file (pu.dat) using... |
| write_marxan_pu.dat_input_file_from_vectors | Write marxan pu.dat from vectors |
| write_marxan_puvspr.dat_input_file | Write marxan puvspr input file |
| write_marxan_spec.dat_input_file | Write species input file (spec.dat) using constant values for... |
| write_marxan_spec.dat_input_file_from_vectors | Write marxan spec.dat from vectors |
| write_network_to_marxan_files | Write network to marxan input file |
| write_results_to_files | Write results to files |
