Index

A

add_dynamics_to_config() (in module mnp.utils) add_output_to_subselection() (in module mnp.evaluation.subselection_output) add_to_table_data() (mnp.evaluation.subselection_output.DetailedTable method) aggregate() (mnp.preparation.aggregate_land_type_map.LandTypeMap method)

aggregate_land_type_map() (in module mnp.preparation.aggregate_land_type_map) aggregate_multiprocess() (mnp.preparation.aggregate_land_type_map.LandTypeMap method) aggregate_row() (in module mnp.preparation.aggregate_land_type_map) any2any() (mnp.preparation.species_database.SpeciesDataBase method) AssignedSpeciesMap (class in mnp.evaluation.subselection_output)

B

BiggestBottleneckMap (class in mnp.evaluation.subselection_output) bold_red (mnp.utils.CustomFormatter attribute)

bottleneck_analysis() (in module mnp.MNP) build_template() (mnp.species_models.polygon_habitat_maps.PolygonHabitatMap method)

C

calculate() (mnp.species_models.environmental_factor.EnvironmentalFactor method) (mnp.species_models.habitat_suitability.HSI method) (mnp.species_models.species_evaluation.SpeciesEvaluation method) clear_temp() (in module mnp.utils) Clustering (class in mnp.species_models.clustering) ClusteringProcedure (class in mnp.species_models.clustering) ClusterLocal (class in mnp.species_models.clustering) complying_species (mnp.config.MNPParameters attribute) config (mnp.config.MNPParameters attribute) config_info_to_temp() (in module mnp.utils) config_section_to_cover() (in module mnp.utils) content (mnp.evaluation.subselection_output.AssignedSpeciesMap attribute) (mnp.evaluation.subselection_output.HotSpotsMap attribute) (mnp.evaluation.subselection_output.KeyPopulationsCountMap attribute) copy_input_file() (in module mnp.utils) create() (mnp.evaluation.subselection_output.AssignedSpeciesMap method) (mnp.evaluation.subselection_output.BiggestBottleneckMap method) (mnp.evaluation.subselection_output.DetailedTable method) (mnp.evaluation.subselection_output.EnvironmentalBottleneckMap method) (mnp.evaluation.subselection_output.EnvironmentalFactorHotspotMap method) (mnp.evaluation.subselection_output.HotSpotsMap method) (mnp.evaluation.subselection_output.KeyPopulationsCountMap method) (mnp.evaluation.subselection_output.LandTypeMap method) (mnp.evaluation.subselection_output.QGisLayers method) (mnp.evaluation.subselection_output.RegionalContributionTable method) (mnp.evaluation.subselection_output.SubselectionMap method) (mnp.evaluation.subselection_output.SubselectionOutput method) (mnp.evaluation.subselection_output.SummaryTable method) (mnp.evaluation.subselection_output.Table method)

create_directories() (in module mnp.utils) create_output() (in module mnp.evaluation.subselection_evaluation) csv_is_readable() (in module mnp.preparation.input_verification_functions) CustomFormatter (class in mnp.utils) cyan (mnp.utils.CustomFormatter attribute)

D

DetailedTable (class in mnp.evaluation.subselection_output)

directory_contains() (in module mnp.preparation.input_verification_functions)

E

environmental_factor_hotspot_statistic (mnp.config.MNPParameters attribute) environmental_response_tables (mnp.config.MNPParameters attribute) EnvironmentalBottleneckMap (class in mnp.evaluation.subselection_output) EnvironmentalFactor (class in mnp.species_models.environmental_factor) EnvironmentalFactorHotspotMap (class in mnp.evaluation.subselection_output)

EnvironmentalFactorTemplate (class in mnp.evaluation.qgis_templates) error() (mnp.species_models.species_geo_map.SpeciesGeomapLogger method) ErrorMessage (class in mnp.preparation.io_pathways) evaluate_metapopulations() (mnp.species_models.species_evaluation.SpeciesEvaluation method) evaluate_models() (in module mnp.MNP) evaluation_results() (mnp.species_models.species_model.SpeciesModel method)

F

file_exists() (mnp.species_models.species_geo_map.SpeciesGeoMap method) filter_incomplete_cells() (in module mnp.preparation.filter_incomplete_cells) find_replace() (mnp.evaluation.qgis_templates.QgisLayerTemplate method) folders (mnp.config.MNPParameters attribute)

force_species_model_recalculation (mnp.config.MNPParameters attribute) format() (mnp.utils.CustomFormatter method) FORMATS (mnp.utils.CustomFormatter attribute) from_configparser() (mnp.config.MNPParameters class method) funcname (mnp.utils.CustomFormatter attribute)

G

geo_profile_from_hsi() (in module mnp.utils) geospatial_profile (mnp.config.MNPParameters attribute) get_complying_species() (mnp.config.MNPParameters method) get_land_type_color() (in module mnp.evaluation.qgis_templates) get_logger() (in module mnp.utils)

get_populations_array() (mnp.species_models.species_model.SpeciesModel method) get_valid_species() (in module mnp.preparation.select_valid_species) get_valid_species_selections() (in module mnp.preparation.select_valid_species) (mnp.config.MNPParameters method) grey (mnp.utils.CustomFormatter attribute) group_traits (mnp.config.MNPParameters attribute)

H

HotSpotsMap (class in mnp.evaluation.subselection_output) HSI (class in mnp.species_models.habitat_suitability)

hsi_threshold (mnp.config.MNPParameters attribute) HSIProcedure (class in mnp.species_models.habitat_suitability) HSITemplate (class in mnp.evaluation.qgis_templates)

I

identify() (mnp.preparation.io_pathways.InputPathway method) identify_land_types_per_species() (in module mnp.evaluation.subselection_output) info() (mnp.species_models.species_geo_map.SpeciesGeomapLogger method) InputPathway (class in mnp.preparation.io_pathways)

is_directory() (in module mnp.preparation.input_verification_functions) is_geospatial_raster() (in module mnp.preparation.input_verification_functions) is_species() (mnp.preparation.species_database.SpeciesDataBase method) is_valid_csv() (in module mnp.preparation.input_verification_functions)

K

key_population_area (mnp.species_models.species_evaluation.SpeciesEvaluationParameters attribute)

KeyPopulationsCountMap (class in mnp.evaluation.subselection_output)

L

land_type_suitabilities (mnp.config.MNPParameters attribute) LandTypeMap (class in mnp.evaluation.subselection_output) (class in mnp.preparation.aggregate_land_type_map) LandTypeMapTemplate (class in mnp.evaluation.qgis_templates) levelname (mnp.utils.CustomFormatter attribute)

List (class in mnp.utils) list_sources_destinations() (in module mnp.utils) log_file_to_cover() (in module mnp.utils) log_messages() (mnp.preparation.io_pathways.InputPathway method) (mnp.species_models.species_model.SpeciesModel method) log_start_completed() (in module mnp.utils)

M

make_bottleneck_map() (in module mnp.evaluation.subselection_output) make_geospatial_profile() (mnp.preparation.aggregate_land_type_map.LandTypeMap method) melt_boolean_dataframe() (in module mnp.preparation.select_valid_species) message (mnp.utils.CustomFormatter attribute) mnp module mnp() (in module mnp.MNP) mnp.config module mnp.evaluation module mnp.evaluation.qgis_templates module mnp.evaluation.subselection_evaluation module mnp.evaluation.subselection_output module mnp.MNP module mnp.preparation module mnp.preparation.aggregate_land_type_map module mnp.preparation.filter_incomplete_cells module mnp.preparation.input_verification_functions module mnp.preparation.io_pathways module mnp.preparation.read_rasters_from_cover module mnp.preparation.select_valid_species module mnp.preparation.species_database module mnp.preparation.verify_spatial_data_coverage module mnp.species_models module mnp.species_models.clustering module mnp.species_models.environmental_factor module

mnp.species_models.habitat_suitability module mnp.species_models.polygon_habitat_maps module mnp.species_models.species_evaluation module mnp.species_models.species_geo_map module mnp.species_models.species_model module mnp.species_models.species_specific_maps module mnp.utils module MNPParameters (class in mnp.config) module mnp mnp.config mnp.evaluation mnp.evaluation.qgis_templates mnp.evaluation.subselection_evaluation mnp.evaluation.subselection_output mnp.MNP mnp.preparation mnp.preparation.aggregate_land_type_map mnp.preparation.filter_incomplete_cells mnp.preparation.input_verification_functions mnp.preparation.io_pathways mnp.preparation.read_rasters_from_cover mnp.preparation.select_valid_species mnp.preparation.species_database mnp.preparation.verify_spatial_data_coverage mnp.species_models mnp.species_models.clustering mnp.species_models.environmental_factor mnp.species_models.habitat_suitability mnp.species_models.polygon_habitat_maps mnp.species_models.species_evaluation mnp.species_models.species_geo_map mnp.species_models.species_model mnp.species_models.species_specific_maps mnp.utils

N

name (mnp.evaluation.subselection_output.RegionalContributionTable attribute) (mnp.evaluation.subselection_output.SummaryTable attribute)

name_info() (mnp.species_models.species_model.SpeciesModel method) Nature (class in mnp.species_models.habitat_suitability)

O

occurs_in_formula() (in module mnp.preparation.input_verification_functions)

OutputPathway (class in mnp.preparation.io_pathways)

P

path_exists() (in module mnp.preparation.input_verification_functions) PolygonHabitatMap (class in mnp.species_models.polygon_habitat_maps) population_array() (mnp.species_models.species_evaluation.SpeciesEvaluation method) PopulationMapTemplate (class in mnp.evaluation.qgis_templates) possibly_viable_threshold (mnp.species_models.species_evaluation.SpeciesEvaluationParameters attribute)

PreCalculated (class in mnp.species_models.habitat_suitability) prepare_input() (in module mnp.MNP) produce_nkeys_map() (in module mnp.species_models.species_specific_maps) produce_nkeys_maps() (in module mnp.species_models.species_specific_maps) pxl_area (mnp.config.MNPParameters attribute) (mnp.species_models.species_evaluation.SpeciesEvaluationParameters attribute)

Q

QGisLayers (class in mnp.evaluation.subselection_output)

QgisLayerTemplate (class in mnp.evaluation.qgis_templates)

R

rand_web_color_hex() (in module mnp.evaluation.qgis_templates) raster_has_resolution() (in module mnp.preparation.input_verification_functions) rasters_have_identical_bounds() (in module mnp.preparation.input_verification_functions) read_aggregated_map() (in module mnp.preparation.aggregate_land_type_map) read_from_file() (mnp.species_models.species_geo_map.SpeciesGeoMap method) read_geospatial_profile() (mnp.config.MNPParameters method) read_rasters_from_cover() (in module mnp.preparation.read_rasters_from_cover) read_template_lines() (mnp.evaluation.qgis_templates.QgisLayerTemplate method) red (mnp.utils.CustomFormatter attribute) region_evaluation_results() (mnp.species_models.species_model.SpeciesModel method) region_names (mnp.config.MNPParameters attribute) RegionalContributionTable (class in mnp.evaluation.subselection_output) RegionalSpeciesEvaluation (class in mnp.species_models.species_evaluation) reset (mnp.utils.CustomFormatter attribute) response_020 (mnp.config.MNPParameters attribute)

response_080 (mnp.config.MNPParameters attribute) response_100 (mnp.config.MNPParameters attribute) results() (mnp.species_models.species_evaluation.SpeciesEvaluation method) run() (mnp.species_models.clustering.ClusteringProcedure method) (mnp.species_models.clustering.ClusterLocal method) (mnp.species_models.habitat_suitability.HSIProcedure method) (mnp.species_models.habitat_suitability.Nature method) (mnp.species_models.habitat_suitability.PreCalculated method) run_and_evaluate() (in module mnp.MNP) run_clustering() (mnp.species_models.species_model.SpeciesModel method) run_evaluation() (mnp.species_models.species_model.SpeciesModel method) run_hsi() (mnp.species_models.species_model.SpeciesModel method) run_regional_evaluation() (mnp.species_models.species_model.SpeciesModel method) run_species() (in module mnp.species_models.species_model) run_species_models() (in module mnp.species_models.species_model)

S

save() (mnp.preparation.aggregate_land_type_map.LandTypeMap method) save_config_and_log() (in module mnp.MNP) save_environmental_factor_raster() (mnp.species_models.habitat_suitability.HSI method) save_geospatial_profile() (mnp.preparation.aggregate_land_type_map.LandTypeMap method) save_qlr() (mnp.evaluation.subselection_output.LandTypeMap method) save_qml() (mnp.evaluation.subselection_output.BiggestBottleneckMap method) (mnp.evaluation.subselection_output.EnvironmentalFactorHotspotMap method) (mnp.evaluation.subselection_output.HotSpotsMap method) save_raster() (mnp.species_models.species_geo_map.SpeciesGeoMap method) save_rasters (mnp.config.MNPParameters attribute) save_spatial_mask() (in module mnp.preparation.verify_spatial_data_coverage) slugify() (in module mnp.utils) small_pop_slope (mnp.config.MNPParameters attribute) (mnp.species_models.species_evaluation.SpeciesEvaluationParameters attribute) small_pop_threshold_area (mnp.config.MNPParameters attribute) (mnp.species_models.species_evaluation.SpeciesEvaluationParameters attribute)

species_names (mnp.config.MNPParameters attribute) species_traits (mnp.config.MNPParameters attribute) SpeciesDataBase (class in mnp.preparation.species_database) SpeciesEvaluation (class in mnp.species_models.species_evaluation) SpeciesEvaluationParameters (class in mnp.species_models.species_evaluation) SpeciesGeoMap (class in mnp.species_models.species_geo_map) SpeciesGeomapLogger (class in mnp.species_models.species_geo_map) SpeciesModel (class in mnp.species_models.species_model) SubRegion (class in mnp.species_models.species_evaluation) subselection_tables (mnp.config.MNPParameters attribute) SubselectionEvaluation (class in mnp.evaluation.subselection_evaluation) SubselectionMap (class in mnp.evaluation.subselection_output) SubselectionOutput (class in mnp.evaluation.subselection_output) summary_table_to_file() (mnp.species_models.species_evaluation.SpeciesEvaluation method) SummaryTable (class in mnp.evaluation.subselection_output)

T

Table (class in mnp.evaluation.subselection_output) time (mnp.utils.CustomFormatter attribute) to_file() (mnp.evaluation.subselection_output.AssignedSpeciesMap method) (mnp.evaluation.subselection_output.BiggestBottleneckMap method) (mnp.evaluation.subselection_output.EnvironmentalFactorHotspotMap method) (mnp.evaluation.subselection_output.HotSpotsMap method) (mnp.evaluation.subselection_output.LandTypeMap method) (mnp.evaluation.subselection_output.QGisLayers method) (mnp.evaluation.subselection_output.SubselectionMap method) (mnp.evaluation.subselection_output.SubselectionOutput method) (mnp.evaluation.subselection_output.Table method)

trait_info() (mnp.species_models.species_evaluation.SpeciesEvaluation method) (mnp.species_models.species_model.SpeciesModel method)

U

update_results_dictionary() (mnp.species_models.species_evaluation.RegionalSpeciesEvaluation method) (mnp.species_models.species_evaluation.SpeciesEvaluation method)

update_status() (mnp.preparation.io_pathways.VerificationProcedure method) update_viability_class() (mnp.species_models.species_evaluation.SpeciesEvaluation method)

V

valid_species_subselections (mnp.config.MNPParameters attribute) VerificationProcedure (class in mnp.preparation.io_pathways) verify() (mnp.preparation.io_pathways.InputPathway method) verify_local_distance() (in module mnp.preparation.input_verification_functions) verify_parameters() (in module mnp.preparation.input_verification_functions) verify_spatial_data_coverage() (in module mnp.preparation.verify_spatial_data_coverage) verify_user_input() (in module mnp.preparation.io_pathways) VerifyEnvironmentalTable (class in mnp.preparation.io_pathways) VerifyHasEnvironmentalFactors (class in mnp.preparation.io_pathways) VerifyHSIFromDisk (class in mnp.preparation.io_pathways)

VerifyIsGeospatialRasterAndResolution (class in mnp.preparation.io_pathways) VerifyLandTypeDirectory (class in mnp.preparation.io_pathways) VerifyMetadataComment (class in mnp.preparation.io_pathways) VerifyParameters (class in mnp.preparation.io_pathways) VerifyRasterAndGeospatialProfileBounds (class in mnp.preparation.io_pathways) VerifyRasterBounds (class in mnp.preparation.io_pathways) VerifySpeciesSubselection (class in mnp.preparation.io_pathways) VerifySpeciesTraits (class in mnp.preparation.io_pathways) VerifyTable (class in mnp.preparation.io_pathways) viable_threshold (mnp.species_models.species_evaluation.SpeciesEvaluationParameters attribute)

W

warning() (mnp.species_models.species_geo_map.SpeciesGeomapLogger method) write() (mnp.species_models.polygon_habitat_maps.PolygonHabitatMap method)

write_explanatory_table() (mnp.evaluation.subselection_output.AssignedSpeciesMap method) write_to_file() (mnp.evaluation.qgis_templates.QgisLayerTemplate method)

Y

yellow (mnp.utils.CustomFormatter attribute)