Index

_

__call__() (laser.cholera.metapop.Analyzer method) (laser.cholera.metapop.analyzer.Analyzer method) (laser.cholera.metapop.DerivedValues method) (laser.cholera.metapop.derivedvalues.DerivedValues method) (laser.cholera.metapop.HumanToHuman method) (laser.cholera.metapop.humantohuman.HumanToHuman method)

__str__() (laser.cholera.metapop.params.PropertySetEx method)

A

Analyzer (class in laser.cholera.metapop) (class in laser.cholera.metapop.analyzer)

as_ndarray() (in module laser.cholera.metapop.params)

C

calc_log_likelihood() (in module laser.cholera.likelihood) calc_log_likelihood_beta() (in module laser.cholera.calc_log_likelihood_distributions) (in module laser.cholera.likelihood) calc_log_likelihood_binomial() (in module laser.cholera.calc_log_likelihood_distributions) (in module laser.cholera.likelihood) calc_log_likelihood_gamma() (in module laser.cholera.calc_log_likelihood_distributions) (in module laser.cholera.likelihood) calc_log_likelihood_negbin() (in module laser.cholera.calc_log_likelihood_distributions) (in module laser.cholera.likelihood) calc_log_likelihood_normal() (in module laser.cholera.calc_log_likelihood_distributions) (in module laser.cholera.likelihood) calc_log_likelihood_poisson() (in module laser.cholera.calc_log_likelihood_distributions) (in module laser.cholera.likelihood) calc_log_likelihood_validation() (in module laser.cholera.likelihood) calc_model_likelihood() (in module laser.cholera.calc_model_likelihood) calc_multi_peak_magnitude_ll() (in module laser.cholera.calc_model_likelihood) calc_multi_peak_timing_ll() (in module laser.cholera.calc_model_likelihood) calculate_coupling() (in module laser.cholera.metapop.derivedvalues) calculate_coupling_for_model() (in module laser.cholera.metapop.derivedvalues) calculate_spatial_hazard() (in module laser.cholera.metapop.derivedvalues) calculate_spatial_hazard_for_model() (in module laser.cholera.metapop.derivedvalues) Census (class in laser.cholera.metapop) (class in laser.cholera.metapop.census) check() (laser.cholera.metapop.Analyzer method) (laser.cholera.metapop.analyzer.Analyzer method) (laser.cholera.metapop.Census method) (laser.cholera.metapop.census.Census method) (laser.cholera.metapop.DerivedValues method) (laser.cholera.metapop.derivedvalues.DerivedValues method) (laser.cholera.metapop.Environmental method) (laser.cholera.metapop.environmental.Environmental method) (laser.cholera.metapop.EnvToHuman method) (laser.cholera.metapop.envtohuman.EnvToHuman method) (laser.cholera.metapop.Exposed method) (laser.cholera.metapop.exposed.Exposed method) (laser.cholera.metapop.HumanToHuman method) (laser.cholera.metapop.humantohuman.HumanToHuman method) (laser.cholera.metapop.Infectious method) (laser.cholera.metapop.infectious.Infectious method) (laser.cholera.metapop.Parameters method) (laser.cholera.metapop.params.Parameters method) (laser.cholera.metapop.Recorder method) (laser.cholera.metapop.recorder.Recorder method) (laser.cholera.metapop.Recovered method) (laser.cholera.metapop.recovered.Recovered method) (laser.cholera.metapop.Susceptible method) (laser.cholera.metapop.susceptible.Susceptible method) (laser.cholera.metapop.Vaccinated method) (laser.cholera.metapop.vaccinated.Vaccinated method) (laser.cholera.test.Eradication method)

Component (class in laser.cholera.metapop.susceptible) components (laser.cholera.metapop.model.Model property) compute() (in module laser.cholera) (in module laser.cholera.core) compute_wis_parametric_row() (in module laser.cholera.calc_model_likelihood)

D

default() (laser.cholera.metapop.params.PseEncoder method) DerivedValues (class in laser.cholera.metapop) (class in laser.cholera.metapop.derivedvalues)

dict_to_propertysetex() (in module laser.cholera.metapop.params)

E

Environmental (class in laser.cholera.metapop) (class in laser.cholera.metapop.environmental) EnvToHuman (class in laser.cholera.metapop) (class in laser.cholera.metapop.envtohuman)

Eradication (class in laser.cholera.test) Exposed (class in laser.cholera.metapop) (class in laser.cholera.metapop.exposed)

G

get_daily_seasonality() (in module laser.cholera.metapop.utils) get_model_likelihood() (in module laser.cholera.likelihood)

get_parameters() (in module laser.cholera.metapop) (in module laser.cholera.metapop.params) get_pi_from_lat_long() (in module laser.cholera.metapop.utils)

H

handle_nan() (in module laser.cholera.metapop.params)

HumanToHuman (class in laser.cholera.metapop) (class in laser.cholera.metapop.humantohuman)

I

Infectious (class in laser.cholera.metapop) (class in laser.cholera.metapop.infectious)

L

laser module laser.cholera module laser.cholera.calc_log_likelihood_distributions module laser.cholera.calc_model_likelihood module laser.cholera.cli module laser.cholera.core module laser.cholera.iso_codes module laser.cholera.likelihood module laser.cholera.metapop module laser.cholera.metapop.analyzer module laser.cholera.metapop.census module laser.cholera.metapop.derivedvalues module laser.cholera.metapop.environmental module laser.cholera.metapop.envtohuman module laser.cholera.metapop.exposed module

laser.cholera.metapop.humantohuman module laser.cholera.metapop.infectious module laser.cholera.metapop.logsetup module laser.cholera.metapop.model module laser.cholera.metapop.params module laser.cholera.metapop.recorder module laser.cholera.metapop.recovered module laser.cholera.metapop.scenario module laser.cholera.metapop.susceptible module laser.cholera.metapop.utils module laser.cholera.metapop.vaccinated module laser.cholera.test module laser.cholera.utils module ll_cumulative_progressive_nb() (in module laser.cholera.calc_model_likelihood) load_compressed_json_parameters() (in module laser.cholera.metapop.params) load_json_parameters() (in module laser.cholera.metapop.params)

M

map_suitability_to_decay() (in module laser.cholera.metapop.environmental) mask_weights() (in module laser.cholera.calc_model_likelihood) Model (class in laser.cholera.metapop.model) module laser laser.cholera laser.cholera.calc_log_likelihood_distributions laser.cholera.calc_model_likelihood laser.cholera.cli laser.cholera.core laser.cholera.iso_codes laser.cholera.likelihood laser.cholera.metapop laser.cholera.metapop.analyzer laser.cholera.metapop.census laser.cholera.metapop.derivedvalues laser.cholera.metapop.environmental laser.cholera.metapop.envtohuman laser.cholera.metapop.exposed laser.cholera.metapop.humantohuman laser.cholera.metapop.infectious laser.cholera.metapop.logsetup laser.cholera.metapop.model laser.cholera.metapop.params laser.cholera.metapop.recorder laser.cholera.metapop.recovered laser.cholera.metapop.scenario laser.cholera.metapop.susceptible laser.cholera.metapop.utils laser.cholera.metapop.vaccinated laser.cholera.test laser.cholera.utils

N

nb_size_from_obs_weighted() (in module laser.cholera.calc_model_likelihood)

O

override_helper() (in module laser.cholera.metapop.utils)

P

Parameters (class in laser.cholera.metapop) (class in laser.cholera.metapop.params) plot() (laser.cholera.metapop.Analyzer method) (laser.cholera.metapop.analyzer.Analyzer method) (laser.cholera.metapop.Census method) (laser.cholera.metapop.census.Census method) (laser.cholera.metapop.DerivedValues method) (laser.cholera.metapop.derivedvalues.DerivedValues method) (laser.cholera.metapop.Environmental method) (laser.cholera.metapop.environmental.Environmental method) (laser.cholera.metapop.EnvToHuman method) (laser.cholera.metapop.envtohuman.EnvToHuman method) (laser.cholera.metapop.Exposed method) (laser.cholera.metapop.exposed.Exposed method) (laser.cholera.metapop.HumanToHuman method) (laser.cholera.metapop.humantohuman.HumanToHuman method) (laser.cholera.metapop.Infectious method) (laser.cholera.metapop.infectious.Infectious method) (laser.cholera.metapop.model.Model method) (laser.cholera.metapop.Parameters method) (laser.cholera.metapop.params.Parameters method) (laser.cholera.metapop.Recovered method) (laser.cholera.metapop.recovered.Recovered method) (laser.cholera.metapop.Susceptible method) (laser.cholera.metapop.susceptible.Susceptible method) (laser.cholera.metapop.Vaccinated method) (laser.cholera.metapop.vaccinated.Vaccinated method) (laser.cholera.test.Eradication method)

PropertySetEx (class in laser.cholera.metapop.params) PseEncoder (class in laser.cholera.metapop.params)

R

Recorder (class in laser.cholera.metapop) (class in laser.cholera.metapop.recorder) Recovered (class in laser.cholera.metapop) (class in laser.cholera.metapop.recovered)

RInterface (class in laser.cholera.metapop.model) run() (laser.cholera.metapop.model.Model method) run_model() (in module laser.cholera.metapop.model)

S

save_compressed_hdf5_parameters() (in module laser.cholera.metapop.recorder) save_hdf5() (in module laser.cholera.metapop.recorder) save_hdf5_parameters() (in module laser.cholera.metapop.recorder)

setup_logging() (in module laser.cholera.metapop.logsetup) sim_duration() (in module laser.cholera.utils) Susceptible (class in laser.cholera.metapop) (class in laser.cholera.metapop.susceptible)

V

Vaccinated (class in laser.cholera.metapop) (class in laser.cholera.metapop.vaccinated)

validate_parameters() (in module laser.cholera.metapop.params) visualize() (laser.cholera.metapop.model.Model method)