langfob/bdpg
Package For Building and Testing Biodiversity Problem Generators

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In langfob/bdpg: Package For Building and Testing Biodiversity Problem Generators

[SHOULD ADD SECTIONS TO THIS OR CREATE A NEW VIGNETTE THAT IS TASK-BASED AND GIVES YAML FILES/SECTIONS FOR COMMON TASKS GENERATING 1 PROBLEM OR GENERATING 4 VARIANTS OR DOING TONS OF RUNS, ETC.]

Introduction

The bdpg package allows many different parameters for many different actions to be input through its parameters list. This R list can be built in any way you like, however, one very common way is to build a yaml file that is read and converted to an R (e.g., by running under tzar). While the parameters list doesn't have to be loaded in this way, the yaml file format provides a nicely structured way of viewing and explaining parameters and groups of parameters. Consequently, explanations in this vignette will be phrased in terms of yaml code that could produce their settings in the parameters list.

Special notes

Switching subgroups of parameters on and off without removing from input file

Sometimes sets of parameters will be ignored entirely when a related master boolean parameter is set in a particular way. This is designed to make it easy to switch off certain things in the yaml file without having to delete all of the related flags. This is particularly desirable during debugging when you may know that a problem has nothing to do with a certain set of parameters and you want the run to be done more quickly by skipping that part of the code. For example, some of the network metrics are very time-consuming to compute. If compute_network_metrics is set to FALSE, then all parameters related to network metrics will be ignored and the metrics will not be computed.

Run identification

Example

    full_output_dir_with_slash: $$output_path$$

    runset_description: |
        Small set of runs of a Xu hard scenario with error generation both
        on and off plus running simulated annealing and richness heuristic.

    runset_name: $$runset$$
    runset_abbrev: "bdpgSingleRunForTestAndDebug"

    run_id: $$run_id$$

Useful sets

SET_NAME

Specific parameters

full_output_dir_with_slash

    full_output_dir_with_slash: $$output_path$$

runset_description

    runset_description: |
        Small set of runs of a Xu hard scenario with error generation both
        on and off plus running simulated annealing and richness heuristic.

runset_name

    runset_name: $$runset$$

runset_abbrev

    runset_abbrev: "bdpgSingleRunForTestAndDebug"

run_id

    run_id: $$run_id$$

MISC

Conversion of floats to integers

Example

    integerize_string: "round"

Useful sets

SET_NAME

Specific parameters

integerize_string

    integerize_string: "round"

Flag files

Example

    too_many_possible_links_error_flag_file_name: $$output_path$$too_many_possible_links_error_flag_file.txt

Useful sets

SET_NAME

Specific parameters

too_many_possible_links_error_flag_file_name [BELONGS WITH XU STUFF? ]

    too_many_possible_links_error_flag_file_name: $$output_path$$too_many_possible_links_error_flag_file.txt

Summary file names [ ARE THESE STILL USED? ]

Example

#    summary_filename: prob_diff_results.csv
#    summary_without_run_id_filename: prob_diff_results_with_0_run_id.csv

Useful sets

SET_NAME

Specific parameters

summary_filename

#    summary_filename: prob_diff_results.csv

summary_without_run_id_filename

#    summary_without_run_id_filename: prob_diff_results_with_0_run_id.csv

Random seed control

Overall seed control

Example

    set_rand_seed_at_creation_of_all_new_major_objects: FALSE
    bdpg_run_init_rand_seed: 1763688087

Useful sets

SET_NAME

Specific parameters

set_rand_seed_at_creation_of_all_new_major_objects

    set_rand_seed_at_creation_of_all_new_major_objects: FALSE

bdpg_run_init_rand_seed

     bdpg_run_init_rand_seed: 1763688087
 ```

--------------------------------------------------------------------------------

# Xu benchmark problems

If you're reading the Xu problem from a file in Xu's benchmark problem file format instead of generating it, you need to give the input file name and the cost of the correct solution (since it's not specified in the file).

### Example

```yaml
    read_Xu_problem_from_Xu_bench_file: TRUE

    Xu_bench_infile_name:  "/Users/bill/D/Projects/ProblemDifficulty/data/Xu - problem difficulty datasets/frb30-15-msc with MSC 420/frb30-15-1.msc"
#"/Users/bill/Desktop/Papers downloaded/Problem difficulty/Problem difficulty datasets/Xu - problem difficulty datasets/frb30-15-msc with MSC 420/frb30-15-1.msc"

    given_correct_solution_cost: 420

Useful sets

SET_NAME

Specific parameters

read_Xu_problem_from_Xu_bench_file

    read_Xu_problem_from_Xu_bench_file: TRUE

Xu_bench_infile_name

    Xu_bench_infile_name:  "/Users/bill/D/Projects/ProblemDifficulty/data/Xu - problem difficulty datasets/frb30-15-msc with MSC 420/frb30-15-1.msc"

given_correct_solution_cost

    given_correct_solution_cost: 420

Reserve selection

Gurobi reserve selector

Example

    do_gurobi: TRUE

    use_given_time_as_limit: TRUE
    time_limit: 600
    use_marxan_time_as_limit: FALSE

    use_gap_limit: TRUE
    gap_limit: 0.005

Useful sets

SET_NAME

Specific parameters

do_gurobi

    do_gurobi: TRUE

use_given_time_as_limit

    use_given_time_as_limit: TRUE

use_marxan_time_as_limit

    use_marxan_time_as_limit: FALSE

use_given_time_as_limit

    use_given_time_as_limit: TRUE

use_gap_limit

    use_gap_limit: TRUE

gap_limit

    gap_limit: 0.005

Marxan simulated annealing reserve selector

Example

    run_marxan: TRUE

    marxan_runmode: 1
    marxan_heurtype: -1

        #  marxan control parameters
        #
        #  If marxan_use_default_input_parameters is TRUE, then all of these
        #  marxan_... parameters set in this file are ignored and marxan's
        #  default values are used instead.
        #  The one exception to this is the variable marxan_spf_const,
        #  which is a bit different from all the other parameters and is set
        #  in the just below the marxan_... parameters in this file.
    marxan_use_default_input_parameters: FALSE

#    marxan_input_parameters_file_name: "/Users/bill/D/Marxan/input.dat"
    marxan_input_parameters_file_name: "$$library_path(marxanLibrary)$$input.dat"

    marxan_dir: "$$library_path(marxanLibrary)$$"
#    marxan_input_dir: "$$library_path(marxanLibrary)$$input/"
#    marxan_output_dir: "$$library_path(marxanLibrary)$$output/"
    marxan_pu_file_name: "pu.dat"
    marxan_spec_file_name: "spec.dat"
    marxan_puvspr_file_name: "puvspr.dat"


    marxan_num_reps: 100
    marxan_num_iterations: "1000000"

#    marxan_num_reps: 1
#    marxan_num_iterations: "10000"

    marxan_spf_rule: "POWER_OF_10"

Useful sets

SET_NAME

Specific parameters

run_marxan

    run_marxan: TRUE

marxan_runmode

    marxan_runmode: 1

marxan_heurtype

    marxan_heurtype: -1

marxan_use_default_input_parameters

    marxan_use_default_input_parameters: FALSE

marxan_input_parameters_file_name

    marxan_input_parameters_file_name: "$$library_path(marxanLibrary)$$input.dat"

marxan_dir

    marxan_dir: "$$library_path(marxanLibrary)$$"

marxan_pu_file_name

    marxan_pu_file_name: "pu.dat"

marxan_spec_file_name

    marxan_spec_file_name: "spec.dat"

marxan_puvspr_file_name

    marxan_puvspr_file_name: "puvspr.dat"

marxan_num_reps

    marxan_num_reps: 100

marxan_num_iterations

    marxan_num_iterations: "1000000"

marxan_spf_rule

    marxan_spf_rule: "POWER_OF_10"

Xu problem generation

Problem size control

Example

        #  NOTE that the choice of random seed in the yaml file is important
        #  for this single run test because the example creates a test problem
        #  based on drawing the control parameters from a random distribution.
        #  When the seed was 111, the test crashed with the message below.
        #  When I changed it to 701, it ran to completion.
        #       Failing:  max_possible_tot_num_links ( 3291 ) > maximum allowed ( 2000 ).
        #       Save workspace image to ~/D/rdv-framework/projects/rdvPackages/biodivprobgen/.RData? [y/n/c]:
        #  However, the fail was just what it was supposed to do when those
        #  parameters came up, so the yaml file could be changed to use 111
        #  instead of 701 if you want to induce a crash to test that error
        #  trapping.
#    seed: 701

        #  2017 12 06 - BTL
        #  Instead, you could just set the total number of links or spp
        #  to some tiny amount that was sure to fail.

    max_allowed_possible_tot_num_links: 1500
    max_allowed_num_spp: 2000


    derive_alpha_from_n__num_groups_and_opt_frac_0.5: FALSE
    use_unif_rand_alpha__: FALSE
    alpha__: 0.52

    use_unif_rand_n__num_groups: TRUE
    n__num_groups_lower_bound: 61
    n__num_groups_upper_bound: 62

#            n__num_groups_upper_bound: 80
#            use_unif_rand_n__num_groups: TRUE
#            n__num_groups_lower_bound: 8
#            n__num_groups_upper_bound: 100

    use_unif_rand_r__density: FALSE
    r__density: 0.8
#            use_unif_rand_r__density: TRUE
#            r__density_lower_bound: 0.01
#            r__density_upper_bound: 5.0

    use_unif_rand_p__prop_of_links_between_groups: TRUE
    p__prop_of_links_between_groups_lower_bound: 0.01
    p__prop_of_links_between_groups_upper_bound: 0.99

#--------------------

        #  Parameters for building a multi-problem by wrapping a lognormal
        #  distribution around a base Xu problem.

    gen_multi_bdproblem: TRUE
    wrap_lognormal_dist_around_Xu: TRUE
    allow_imperfect_wrap: TRUE    #  new variable - BTL - 2017 12 13
    desired_Xu_spp_frac_of_all_spp: 0.5
    solution_frac_of_landscape: 0.3
    desired_max_abundance_frac: 0.7
    dep_set_PUs_eligible: FALSE
    add_one_to_lognormal_abundances: FALSE
#            seed_value_for_search: 11    #  no longer set this way - BTL - 2017 12 13
    max_search_iterations: 500

    plot_rounded_abundances: TRUE

Useful sets

SET_NAME

Specific parameters

max_allowed_possible_tot_num_links

    max_allowed_possible_tot_num_links: 1500

max_allowed_num_spp

    max_allowed_num_spp: 2000

Problem types to generate

Example

    gen_4_basic_variants: TRUE
    single_action_using_tzar_reps: FALSE    #TRUE

Useful sets

SET_NAME

Specific parameters

gen_4_basic_variants

    gen_4_basic_variants: TRUE

single_action_using_tzar_reps

    single_action_using_tzar_reps: FALSE    #TRUE

Xu base parameters (alpha, p, n, r)

Example

    derive_alpha_from_n__num_groups_and_opt_frac_0.5: FALSE
    use_unif_rand_alpha__: FALSE
    alpha__: 0.52

    use_unif_rand_n__num_groups: TRUE
    n__num_groups_lower_bound: 61
    n__num_groups_upper_bound: 62

#            n__num_groups_upper_bound: 80
#            use_unif_rand_n__num_groups: TRUE
#            n__num_groups_lower_bound: 8
#            n__num_groups_upper_bound: 100

    use_unif_rand_r__density: FALSE
    r__density: 0.8
#            use_unif_rand_r__density: TRUE
#            r__density_lower_bound: 0.01
#            r__density_upper_bound: 5.0

    use_unif_rand_p__prop_of_links_between_groups: TRUE
    p__prop_of_links_between_groups_lower_bound: 0.01
    p__prop_of_links_between_groups_upper_bound: 0.99

Useful sets

SET_NAME

Specific parameters

derive_alpha_from_n__num_groups_and_opt_frac_0.5

    derive_alpha_from_n__num_groups_and_opt_frac_0.5: FALSE

use_unif_rand_alpha__

    use_unif_rand_alpha__: FALSE

n__num_groups_lower_bound

alpha__lower_bound - Definition - Type/Allowed values - Default value - Rules

#    alpha__lower_bound: 0.2

alpha__upper_bound

#    alpha__upper_bound: 0.3

alpha__

    alpha__: 0.52

use_unif_rand_n__num_groups

    use_unif_rand_n__num_groups: TRUE

n__num_groups_lower_bound

#    n__num_groups_lower_bound: 61

n__num_groups_upper_bound

    n__num_groups_upper_bound: 62

n__num_groups

    n__num_groups: 50

use_unif_rand_r__density

    use_unif_rand_r__density: FALSE

r__density

    r__density: 0.8

r__density_lower_bound

#            r__density_lower_bound: 0.01

use_unif_rand_p__prop_of_links_between_groups

    use_unif_rand_p__prop_of_links_between_groups: TRUE

p__prop_of_links_between_groups_lower_bound

    p__prop_of_links_between_groups_lower_bound: 0.01

p__prop_of_links_between_groups_upper_bound

    p__prop_of_links_between_groups_upper_bound: 0.99

p__prop_of_links_between_groups

#    p__prop_of_links_between_groups: 0.5

Xu wrapped problem parameters

Parameters for building a multi-problem by wrapping a lognormal distribution around a base Xu problem.

Example

    gen_multi_bdproblem: TRUE
    wrap_lognormal_dist_around_Xu: TRUE
    allow_imperfect_wrap: TRUE    #  new variable - BTL - 2017 12 13
    desired_Xu_spp_frac_of_all_spp: 0.5
    solution_frac_of_landscape: 0.3
    desired_max_abundance_frac: 0.7
    dep_set_PUs_eligible: FALSE
    add_one_to_lognormal_abundances: FALSE
    max_search_iterations: 500
    plot_rounded_abundances: TRUE

Useful sets

SET_NAME

Specific parameters

gen_multi_bdproblem

    gen_multi_bdproblem: TRUE

wrap_lognormal_dist_around_Xu

    wrap_lognormal_dist_around_Xu: TRUE

allow_imperfect_wrap

    allow_imperfect_wrap: TRUE    #  new variable - BTL - 2017 12 13

desired_Xu_spp_frac_of_all_spp

    desired_Xu_spp_frac_of_all_spp: 0.5

solution_frac_of_landscape

    solution_frac_of_landscape: 0.3

desired_max_abundance_frac

    desired_max_abundance_frac: 0.7

dep_set_PUs_eligible

    dep_set_PUs_eligible: FALSE

add_one_to_lognormal_abundances

    add_one_to_lognormal_abundances: FALSE

max_search_iterations

    max_search_iterations: 500

plot_rounded_abundances

    plot_rounded_abundances: TRUE

Error generation

Example

    apply_error_to_spp_occupancy_data: TRUE
#            match_error_counts: TRUE
    match_error_counts: FALSE

    #--------------------

        #  Constant errors

    spp_occ_FP_error_type: "CONSTANT"
    spp_occ_FP_const_rate: 0  #0.05  #0  #0.1

    spp_occ_FN_error_type: "CONSTANT"
    spp_occ_FN_const_rate: 0.05  #0.1  #0.1

Useful sets

SET_NAME

Specific parameters

apply_error_to_spp_occupancy_data

    apply_error_to_spp_occupancy_data: TRUE

match_error_counts

    match_error_counts: FALSE

spp_occ_FP_error_type

    spp_occ_FP_error_type: "CONSTANT"

spp_occ_FP_const_rate

    spp_occ_FP_const_rate: 0  #0.05  #0  #0.1

spp_occ_FN_error_type

    spp_occ_FN_error_type: "CONSTANT"

spp_occ_FN_const_rate

    spp_occ_FN_const_rate: 0.05  #0.1  #0.1

Network measures

Example

    compute_network_metrics: FALSE    #  if FALSE, overrides all other network flags below

    compute_network_metrics_COR: TRUE
    compute_network_metrics_APP: TRUE
    compute_network_metrics_wrapped_COR: TRUE
    compute_network_metrics_wrapped_APP: TRUE

    use_igraph_metrics:    TRUE

    use_bipartite_metrics: TRUE
    #bipartite_metrics_to_use:     "ALLBUTDD"
#    bipartite_metrics_to_use:     "all_except_slow_indices"
    bipartite_metrics_to_use:     "quick_test"

Useful sets

SET_NAME

Specific parameters

compute_network_metrics

    compute_network_metrics: FALSE    #  if FALSE, overrides all other network flags below

compute_network_metrics_COR

    compute_network_metrics_COR: TRUE

compute_network_metrics_APP

    compute_network_metrics_APP: TRUE

compute_network_metrics_wrapped_COR

    compute_network_metrics_wrapped_COR: TRUE

compute_network_metrics_wrapped_APP

    compute_network_metrics_wrapped_APP: TRUE

use_igraph_metrics

    use_igraph_metrics:    TRUE

use_bipartite_metrics

    use_bipartite_metrics: TRUE

bipartite_metrics_to_use

    bipartite_metrics_to_use:     "quick_test"

TEMPLATE

PARAMETER_GROUP

PARAMETER_SUBGROUP

Example

Useful sets

SET_NAME

Specific parameters

PARAMETER_NAME

END TEMPLATE



langfob/bdpg documentation built on Dec. 8, 2022, 5:33 a.m.

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