Index

A

add_beta_parameters() (hiv_workflow.lib.analysis.beta_distribution.BetaDistribution method) add_ingest_form_to_assets() (in module hiv_workflow.lib.utils.runtime) add_percentile_values() (hiv_workflow.lib.analysis.base_distribution.BaseDistribution method) (hiv_workflow.lib.analysis.beta_distribution.BetaDistribution method) (hiv_workflow.lib.analysis.gaussian_distribution.GaussianDistribution method) (hiv_workflow.lib.analysis.population_obs.PopulationObs method) add_post_channel_config_as_asset() (in module hiv_workflow.lib.utils.runtime) adjust_years() (hiv_workflow.lib.analysis.population_obs.PopulationObs method) AgeBin (class in hiv_workflow.lib.analysis.age_bin)

AgeBin.InvalidAgeBinFormat AgeBin.NotMergeable AGGREGATED_NODE (hiv_workflow.lib.analysis.population_obs.PopulationObs attribute) AGGREGATED_NODE_MAP (hiv_workflow.lib.analysis.hiv_analyzer.HIVAnalyzer attribute) AGGREGATED_PROVINCE (hiv_workflow.lib.analysis.population_obs.PopulationObs attribute) ALL (hiv_workflow.lib.analysis.age_bin.AgeBin attribute) ALLOWED_TYPES (hiv_workflow.lib.analysis.channel.Channel attribute) AnalyzerSheetException apply() (hiv_workflow.lib.analysis.condition.Condition method) available_algorithms() (in module hiv_workflow.lib.utils.runtime)

B

BaseDistribution (class in hiv_workflow.lib.analysis.base_distribution) BaseDistribution.UnknownDistributionException

BetaDistribution (class in hiv_workflow.lib.analysis.beta_distribution) BetaDistribution.InvalidCountChannelException BetaDistribution.InvalidEffectiveCountException

C

can_upsample_bins() (hiv_workflow.lib.analysis.age_bin.AgeBin class method) Channel (class in hiv_workflow.lib.analysis.channel) Channel.InvalidChannelType channels() (hiv_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper property) compare() (hiv_workflow.lib.analysis.base_distribution.BaseDistribution method) (hiv_workflow.lib.analysis.beta_distribution.BetaDistribution method) (hiv_workflow.lib.analysis.gaussian_distribution.GaussianDistribution method) (hiv_workflow.lib.analysis.hiv_analyzer.HIVAnalyzer method) compute_num_cores() (in module hiv_workflow.lib.utils.runtime)

compute_pop_scaling_factor() (hiv_workflow.lib.analysis.hiv_analyzer.HIVAnalyzer method) Condition (class in hiv_workflow.lib.analysis.condition) constrain_sample() (in module hiv_workflow.lib.utils.runtime) constrain_sample_wrapper() (in module hiv_workflow.lib.utils.wrappers) construct_beta_channel() (hiv_workflow.lib.analysis.beta_distribution.BetaDistribution static method) construct_gaussian_channel() (hiv_workflow.lib.analysis.gaussian_distribution.GaussianDistribution static method) construct_post_process_filename() (hiv_workflow.lib.analysis.hiv_analyzer.HIVAnalyzer class method) contains() (hiv_workflow.lib.analysis.age_bin.AgeBin method) COUNT_CHANNEL (hiv_workflow.lib.analysis.beta_distribution.BetaDistribution attribute) CSV (hiv_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper attribute)

D

DataFrameWrapper (class in hiv_workflow.lib.analysis.data_frame_wrapper) DataFrameWrapper.InconsistentStratification DataFrameWrapper.MissingRequiredData DataFrameWrapper.UnsupportedFileType DEFAULT_DELIMITER (hiv_workflow.lib.analysis.age_bin.AgeBin attribute)

DEFAULT_OUTPUT_DIR (hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite attribute) DefinedName (class in hiv_workflow.lib.utils.io.excel) detect_duplicate_items_in() (in module hiv_workflow.lib.utils.runtime) directory_for_experiment_and_file() (hiv_workflow.lib.analysis.download_analyzer_by_experiment.DownloadAnalyzerByExperiment method) DownloadAnalyzerByExperiment (class in hiv_workflow.lib.analysis.download_analyzer_by_experiment) DownloadAnalyzerByExperimentReceipt (class in hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt)

E

equals() (hiv_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper method)

F

filter() (hiv_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper method) find_missing_tuples() (hiv_workflow.lib.analysis.population_obs.PopulationObs method) fix_age_bins() (hiv_workflow.lib.analysis.population_obs.PopulationObs method)

from_directory() (hiv_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper class method) from_string() (hiv_workflow.lib.analysis.age_bin.AgeBin class method) (hiv_workflow.lib.analysis.base_distribution.BaseDistribution class method) from_uncertainty_channel() (hiv_workflow.lib.analysis.base_distribution.BaseDistribution class method)

G

GaussianDistribution (class in hiv_workflow.lib.analysis.gaussian_distribution) GaussianDistribution.InvalidUncertaintyException generate_campaign_builder_wrapper() (in module hiv_workflow.lib.utils.wrappers) generate_config_builder_wrapper() (in module hiv_workflow.lib.utils.wrappers) generate_demographics_builder_wrapper() (in module hiv_workflow.lib.utils.wrappers) generate_map_sample_to_model_input_wrapper() (in module hiv_workflow.lib.utils.wrappers) generate_python_processing_wrapper() (in module hiv_workflow.lib.utils.wrappers) get_age_bins() (hiv_workflow.lib.analysis.population_obs.PopulationObs method)

get_analyzers() (hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite method) get_available_parameters() (in module hiv_workflow.lib.utils.builders.general) get_genders() (hiv_workflow.lib.analysis.population_obs.PopulationObs method) get_ingest_information() (in module hiv_workflow.lib.utils.project_data) get_provinces() (hiv_workflow.lib.analysis.population_obs.PopulationObs method) get_setup_functions() (hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite method) get_sheet_from_workbook() (in module hiv_workflow.lib.utils.project_data) get_years() (hiv_workflow.lib.analysis.population_obs.PopulationObs method)

H

hiv_workflow module hiv_workflow.lib module hiv_workflow.lib.analysis module hiv_workflow.lib.analysis.age_bin module hiv_workflow.lib.analysis.base_distribution module hiv_workflow.lib.analysis.beta_distribution module hiv_workflow.lib.analysis.channel module hiv_workflow.lib.analysis.condition module hiv_workflow.lib.analysis.data_frame_wrapper module hiv_workflow.lib.analysis.download_analyzer_by_experiment module hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt module hiv_workflow.lib.analysis.gaussian_distribution module hiv_workflow.lib.analysis.hiv_analyzer module hiv_workflow.lib.analysis.hiv_calib_site module hiv_workflow.lib.analysis.population_obs module hiv_workflow.lib.calibration module hiv_workflow.lib.calibration.algorithms module hiv_workflow.lib.calibration.algorithms.optim_tool module hiv_workflow.lib.utils module

hiv_workflow.lib.utils.analysis module hiv_workflow.lib.utils.builders module hiv_workflow.lib.utils.builders.demographics module hiv_workflow.lib.utils.builders.general module hiv_workflow.lib.utils.io module hiv_workflow.lib.utils.io.excel module hiv_workflow.lib.utils.project_data module hiv_workflow.lib.utils.runtime module hiv_workflow.lib.utils.wrappers module hiv_workflow.scripts module hiv_workflow.scripts.available_parameters module hiv_workflow.scripts.calibrate module hiv_workflow.scripts.download module hiv_workflow.scripts.dtk_post_process module hiv_workflow.scripts.resample module hiv_workflow.scripts.run module HIVAnalyzer (class in hiv_workflow.lib.analysis.hiv_analyzer) HIVAnalyzer.InvalidSiteException HIVAnalyzer.MissingDataException HIVAnalyzer.ProvincialityException HIVCalibSite (class in hiv_workflow.lib.analysis.hiv_calib_site)

I

IncompleteAnalyzerSpecification IncompleteDataSpecification IncompleteParameterSpecification initialize() (in module hiv_workflow.lib.calibration.algorithms.optim_tool) initialize_EMODTask() (in module hiv_workflow.lib.utils.runtime)

InvalidAgeBinException InvalidAnalyzerWeight InvalidDataframeColumnException InvalidDateException InvalidFunctionArgumentError

L

load_algorithm() (in module hiv_workflow.lib.utils.runtime) load_from_workbook() (hiv_workflow.lib.utils.io.excel.DefinedName class method)

load_model() (in module hiv_workflow.lib.utils.runtime) LOG_FLOAT_TINY (hiv_workflow.lib.analysis.base_distribution.BaseDistribution attribute) log_float_tiny (hiv_workflow.lib.analysis.hiv_analyzer.HIVAnalyzer attribute)

M

map() (hiv_workflow.lib.analysis.download_analyzer_by_experiment.DownloadAnalyzerByExperiment method) (hiv_workflow.lib.analysis.hiv_analyzer.HIVAnalyzer method) map_sample_to_model_input() (in module hiv_workflow.lib.utils.runtime) merge() (hiv_workflow.lib.analysis.age_bin.AgeBin method) (hiv_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper method) merge_bins() (hiv_workflow.lib.analysis.age_bin.AgeBin class method) metadata (hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite attribute) MissingRequiredWorksheet model_population_in_year() (in module hiv_workflow.lib.utils.analysis) module hiv_workflow hiv_workflow.lib hiv_workflow.lib.analysis hiv_workflow.lib.analysis.age_bin hiv_workflow.lib.analysis.base_distribution hiv_workflow.lib.analysis.beta_distribution hiv_workflow.lib.analysis.channel hiv_workflow.lib.analysis.condition hiv_workflow.lib.analysis.data_frame_wrapper hiv_workflow.lib.analysis.download_analyzer_by_experiment hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt hiv_workflow.lib.analysis.gaussian_distribution hiv_workflow.lib.analysis.hiv_analyzer hiv_workflow.lib.analysis.hiv_calib_site hiv_workflow.lib.analysis.population_obs hiv_workflow.lib.calibration hiv_workflow.lib.calibration.algorithms hiv_workflow.lib.calibration.algorithms.optim_tool hiv_workflow.lib.utils hiv_workflow.lib.utils.analysis hiv_workflow.lib.utils.builders hiv_workflow.lib.utils.builders.demographics hiv_workflow.lib.utils.builders.general hiv_workflow.lib.utils.io hiv_workflow.lib.utils.io.excel hiv_workflow.lib.utils.project_data hiv_workflow.lib.utils.runtime hiv_workflow.lib.utils.wrappers hiv_workflow.scripts hiv_workflow.scripts.available_parameters hiv_workflow.scripts.calibrate hiv_workflow.scripts.download hiv_workflow.scripts.dtk_post_process hiv_workflow.scripts.resample hiv_workflow.scripts.run

N

needs_pop_scaling() (hiv_workflow.lib.analysis.channel.Channel property)

NON_PROVINCIAL (hiv_workflow.lib.analysis.population_obs.PopulationObs attribute)

O

ObsMetadataException

P

ParameterOutOfRange parse_ingest_data_from_xlsm() (in module hiv_workflow.lib.utils.project_data) per_group() (hiv_workflow.lib.analysis.download_analyzer_by_experiment.DownloadAnalyzerByExperiment method) PopulationObs (class in hiv_workflow.lib.analysis.population_obs)

prepare() (hiv_workflow.lib.analysis.base_distribution.BaseDistribution method) (hiv_workflow.lib.analysis.beta_distribution.BetaDistribution method) (hiv_workflow.lib.analysis.gaussian_distribution.GaussianDistribution method) PROVINCIAL (hiv_workflow.lib.analysis.population_obs.PopulationObs attribute)

R

read_block() (in module hiv_workflow.lib.utils.io.excel) read_list() (in module hiv_workflow.lib.utils.io.excel)

reduce() (hiv_workflow.lib.analysis.download_analyzer_by_experiment.DownloadAnalyzerByExperiment method) (hiv_workflow.lib.analysis.hiv_analyzer.HIVAnalyzer method) run_number (hiv_workflow.lib.analysis.download_analyzer_by_experiment.DownloadAnalyzerByExperiment attribute)

S

sample_tag (hiv_workflow.lib.analysis.download_analyzer_by_experiment.DownloadAnalyzerByExperiment attribute) set_arguments() (in module hiv_workflow.lib.calibration.algorithms.optim_tool) set_coital_act_rates() (in module hiv_workflow.lib.utils.builders.demographics) set_concurrency_parameters() (in module hiv_workflow.lib.utils.builders.demographics) set_condom_usage_probabilities() (in module hiv_workflow.lib.utils.builders.demographics) set_initial_risk_distribution() (in module hiv_workflow.lib.utils.builders.demographics) set_pair_formation_rates() (in module hiv_workflow.lib.utils.builders.demographics)

set_parameters() (in module hiv_workflow.lib.utils.builders.general) set_python_processing() (in module hiv_workflow.lib.utils.runtime) set_relationship_durations() (in module hiv_workflow.lib.utils.builders.demographics) set_risk_assortivities() (in module hiv_workflow.lib.utils.builders.demographics) SIM_RESULT_CHANNEL (hiv_workflow.lib.analysis.hiv_analyzer.HIVAnalyzer attribute) SiteNodeMappingException SPLIT_REGEX (hiv_workflow.lib.analysis.age_bin.AgeBin attribute) STR_FORMAT (hiv_workflow.lib.analysis.age_bin.AgeBin attribute)

T

to_tuple() (hiv_workflow.lib.analysis.age_bin.AgeBin method)

U

UNCERTAINTY_CHANNEL (hiv_workflow.lib.analysis.beta_distribution.BetaDistribution attribute) (hiv_workflow.lib.analysis.gaussian_distribution.GaussianDistribution attribute)

UnsupportedFileFormat

V

verify_required_items() (hiv_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper method)

W

WEIGHT_CHANNEL (hiv_workflow.lib.analysis.population_obs.PopulationObs attribute)