tlo.methods.alri module ======================= .. automodule:: tlo.methods.alri .. autoclass:: Alri Bases: :class:`tlo.core.Module` **PARAMETERS:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - base_inc_rate_ALRI_by_RSV - LIST - baseline incidence rate of Alri caused by RSV in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_Rhinovirus - LIST - baseline incidence of Alri caused by Rhinovirus in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_HMPV - LIST - baseline incidence of Alri caused by HMPV in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_Parainfluenza - LIST - baseline incidence of Alri caused by Parainfluenza 1-4 in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_Strep_pneumoniae_PCV13 - LIST - baseline incidence of Alri caused by Streptoccocus pneumoniae PCV13 serotype in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_Strep_pneumoniae_non_PCV13 - LIST - baseline incidence of Alri caused by Streptoccocus pneumoniae non PCV13 serotype in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_Hib - LIST - baseline incidence of Alri caused by Haemophilus influenzae type b in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_H.influenzae_non_type_b - LIST - baseline incidence of Alri caused by Haemophilus influenzae non-type b in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_Enterobacteriaceae - LIST - baseline incidence of Alri caused by Enterobacteriaceae in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_other_Strepto_Enterococci - LIST - baseline incidence of Alri caused by other streptococci and Enterococci including Streptococcus pyogenes and Enterococcus faecium in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_Staph_aureus - LIST - baseline incidence of Alri caused by Staphylococcus aureus in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_Influenza - LIST - baseline incidence of Alri caused by Influenza type A, B, and C in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_P.jirovecii - LIST - baseline incidence of Alri caused by P. jirovecii in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_other_viral_pathogens - LIST - baseline incidence of Alri caused by other viral pathogens in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_other_bacterial_pathogens - LIST - baseline incidence of Alri caused by other viral pathogens in age groups 0-11, 12-23, 24-59 months, per child per year * - base_inc_rate_ALRI_by_other_pathogens_NoS - LIST - baseline incidence of Alri caused by other pathogens not otherwise specified in age groups 0-11, 12-23, 24-59 months, per child per year * - proportion_pneumonia_in_RSV_ALRI - LIST - proportion of RSV-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_Rhinovirus_ALRI - LIST - proportion of Rhinovirus-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_HMPV_ALRI - LIST - proportion of HMPV-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_Parainfluenza_ALRI - LIST - proportion of Parainfluenza-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_Strep_pneumoniae_PCV13_ALRI - LIST - proportion of S. pneumoniae PCV13-type-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_Strep_pneumoniae_non_PCV13_ALRI - LIST - proportion of S. pneumoniae non PCV13-type-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_Hib_ALRI - LIST - proportion of Hib ALRI-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_H.influenzae_non_type_b_ALRI - LIST - proportion of H.influenzae non type-b-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_Staph_aureus_ALRI - LIST - proportion of S. aureus-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_Enterobacteriaceae_ALRI - LIST - proportion of Enterobacteriaceae-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_other_Strepto_Enterococci_ALRI - LIST - proportion of other Streptococci- and Enterococci-attributed ALRI manifesting as pneumoniaby age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_Influenza_ALRI - LIST - proportion of Influenza-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_P.jirovecii_ALRI - LIST - proportion of P. jirovecii-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_other_viral_pathogens_ALRI - LIST - proportion of other viral pathogens-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_other_bacterial_pathogens_ALRI - LIST - proportion of other bacterial pathogens-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - proportion_pneumonia_in_other_pathogens_NoS_ALRI - LIST - proportion of other pathogens NoS-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) * - rr_ALRI_HIV/AIDS - REAL - relative rate of acquiring Alri for children with HIV+/AIDS * - rr_ALRI_incomplete_measles_immunisation - REAL - relative rate of acquiring Alri for children with incomplete measles immunisation * - rr_ALRI_low_birth_weight - REAL - relative rate of acquiring Alri for infants with low birth weight * - rr_ALRI_non_exclusive_breastfeeding - REAL - relative rate of acquiring Alri for not exclusive breastfeeding upto 6 months * - rr_ALRI_indoor_air_pollution - REAL - relative rate of acquiring Alri for indoor air pollution * - prob_viral_pneumonia_bacterial_coinfection - REAL - probability of primary viral pneumonia having a bacterial co-infection * - proportion_bacterial_coinfection_pathogen - LIST - list of proportions of each bacterial pathogens in a viral/bacterial co-infection pneumonia,the current values used are the pathogen attributable fractions (AFs) from PERCH for all ages. The AFs were scaled to bacterial pathogens only causes - value assumed to be the proportions of bacterial pathogens causing co-/secondary infection * - max_alri_duration_in_days_without_treatment - REAL - maximum duration in days of untreated ALRI episode, assuming an average of 7 days * - overall_progression_to_severe_ALRI - REAL - probability of progression to severe ALRI * - prob_pulmonary_complications_in_pneumonia - REAL - probability of pulmonary complications in (CXR+) pneumonia * - prob_pleural_effusion_in_pulmonary_complicated_pneumonia - REAL - probability of pleural effusion in pneumonia with pulmonary complications * - prob_empyema_in_pulmonary_complicated_pneumonia - REAL - probability of empyema in pneumonia with pulmonary complications * - prob_lung_abscess_in_pulmonary_complicated_pneumonia - REAL - probability of lung abscess in pneumonia with pulmonary complications * - prob_pneumothorax_in_pulmonary_complicated_pneumonia - REAL - probability of pneumothorax in pneumonia with pulmonary complications * - prob_hypoxaemia_in_pneumonia - REAL - probability of hypoxaemia in pneumonia cases * - prob_hypoxaemia_in_other_alri - REAL - probability of hypoxaemia in bronchiolitis and other alri cases * - prob_bacteraemia_in_pneumonia - REAL - probability of bacteraemia in pneumonia * - prob_progression_to_sepsis_with_bacteraemia - REAL - probability of progression to sepsis from bactereamia * - proportion_hypoxaemia_with_SpO2<90% - REAL - proportion of hypoxaemic children with SpO2 <90% * - scaler_on_risk_of_death - REAL - Multiplicative scaler on the overall risk of death, for the purpose of calibration. * - base_odds_death_ALRI_age<2mo - REAL - baseline odds of death from ALRI for young infants aged 0 month and severe pneumonia (base group) * - or_death_ALRI_age<2mo_very_severe_pneumonia - REAL - odds ratio of death from ALRI for young infants with very severe pneumonia * - or_death_ALRI_age<2mo_P.jirovecii - REAL - odds ratio of death from ALRI for young infants with P. jirovecii infection * - or_death_ALRI_age<2mo_by_month_increase_in_age - REAL - odds ratio of death from ALRI for young infants by 1 month increase in age (1 month olds) * - base_odds_death_ALRI_age2_59mo - REAL - baseline odds of death from ALRI for children aged 2 months, male, no SAM, and non-severe pneumonia classification (base group) * - or_death_ALRI_age2_59mo_female - REAL - odds ratio of death from ALRI for children who are female * - or_death_ALRI_age2_59mo_very_severe_pneumonia - REAL - odds ratio of death from ALRI for children with very severe pneumonia * - or_death_ALRI_age2_59mo_P.jirovecii - REAL - odds ratio of death from ALRI for children with P. jirovecii infection * - or_death_ALRI_age2_59mo_by_month_increase_in_age - REAL - odds ratio of death from ALRI by 1 month increase in age for 2 to 59 months olds * - or_death_ALRI_age2_59mo_SAM - REAL - odds ratio of death from ALRI for children with severe acute malnutrition * - or_death_ALRI_SpO2<90% - REAL - odds ratio of death from ALRI for children with oxygen saturation < 90%, base group: SpO2 <=93% * - or_death_ALRI_SpO2_90_92% - REAL - odds ratio of death from ALRI for children with oxygen saturation between 09 to 92%, base group: SpO2 <=93% * - or_death_ALRI_sepsis - REAL - odds ratio of death from ALRI for children with complication of sepsis (compared to if not) * - or_death_ALRI_pneumothorax - REAL - odds ratio of death from ALRI for children with complication of pneumothorax (compared to if not) * - prob_cough_in_pneumonia - REAL - probability of cough in pneumonia * - prob_difficult_breathing_in_pneumonia - REAL - probability of difficulty breathing in pneumonia * - prob_fever_in_pneumonia - REAL - probability of fever in pneumonia * - prob_chest_indrawing_in_pneumonia - REAL - probability of chest indrawing in pneumonia * - prob_tachypnoea_in_pneumonia - REAL - probability of tachypnoea in pneumonia * - prob_danger_signs_in_pneumonia - REAL - probability of any danger sign in pneumonia, including: : unable to drink, convulsions, cyanosis, head nodding/bobbing, irritability, abnormally sleepy, lethargy, nasal flaring, grunting * - prob_cough_in_other_alri - REAL - probability of cough in bronchiolitis or other alri * - prob_difficult_breathing_in_other_alri - REAL - probability of difficulty breathing in bronchiolitis or other alri * - prob_fever_in_other_alri - REAL - probability of fever in bronchiolitis or other alri * - prob_tachypnoea_in_other_alri - REAL - probability of tachypnoea in bronchiolitis or other alri * - prob_chest_indrawing_in_other_alri - REAL - probability of chest wall indrawing in bronchiolitis or other alri * - prob_danger_signs_in_other_alri - REAL - probability of any danger signs in bronchiolitis or other alri * - prob_danger_signs_in_sepsis - REAL - probability of any danger signs in ALRI complicated by sepsis * - prob_danger_signs_in_SpO2<90% - REAL - probability of any danger signs in children with SpO2 <90% * - prob_danger_signs_in_SpO2_90-92% - REAL - probability of any danger signs in children with SpO2 between 90-92% * - prob_chest_indrawing_in_SpO2<90% - REAL - probability of chest indrawing in children with SpO2 <90% * - prob_chest_indrawing_in_SpO2_90-92% - REAL - probability of chest indrawing in children with SpO2 between 90-92% * - prob_cyanosis_in_other_alri - REAL - probability of cyanosis in bronchiolitis or other alri * - prob_cyanosis_in_pneumonia - REAL - probability of cyanosis in pneumonia * - prob_cyanosis_in_SpO2<90% - REAL - probability of cyanosis when SpO2 < 90% * - rr_Strep_pneum_VT_ALRI_with_PCV13_age<2y - REAL - relative rate of acquiring S. pneumoniae vaccine-type Alri for children under 2 years of age immunised wth PCV13 * - rr_Strep_pneum_VT_ALRI_with_PCV13_age2to5y - REAL - relative rate of acquiring S. pneumoniae vaccine-type Alri for children aged 2 to 5 immunised wth PCV13 * - rr_all_strains_Strep_pneum_ALRI_with_PCV13 - REAL - relative rate of acquiring S. pneumoniae all types Alri for children immunised wth PCV13 * - effectiveness_Hib_vaccine_on_Hib_strains - REAL - effectiveness of Hib vaccine against H. influenzae typ-b ALRI * - rr_Hib_ALRI_with_Hib_vaccine - REAL - relative rate of acquiring H. influenzae type-b Alri for children immunised wth Hib vaccine * - days_between_treatment_and_cure - INT - number of days between any treatment being given in an HSI and the cure occurring. * - tf_1st_line_antibiotic_for_severe_pneumonia - REAL - Risk of treatment failure for a person with danger_signs_pneumonia being treated with first lineintravenous antibiotics * - rr_tf_1st_line_antibiotics_if_cyanosis - REAL - Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has the symptom of cyanosis.having that symptom. * - rr_tf_1st_line_antibiotics_if_SpO2<90% - REAL - Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has oxygen saturation < 90%. * - rr_tf_1st_line_antibiotics_if_abnormal_CXR - REAL - Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has a disease_type of "pneumonia". * - rr_tf_1st_line_antibiotics_if_MAM - REAL - Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has un_clinical_acute_malnutrition == "MAM". * - rr_tf_1st_line_antibiotics_if_SAM - REAL - Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has un_clinical_acute_malnutrition == "SAM". * - rr_tf_1st_line_antibiotics_if_HIV/AIDS - REAL - Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has HIV and is not currently being treated. * - or_mortality_improved_oxygen_systems - REAL - Odds Ratio for the effect of oxygen provision to a person that needs oxygen who receives it, compares to a patient who does not. N.B. The inverse of this is used to reflect the increase in odds of death for a patient that needs oxygen but does not receive it. * - tf_3day_amoxicillin_for_fast_breathing_with_SpO2>=90% - REAL - probability of treatment failure by day 6 or relapse by day 14 of 3-day course amoxicillin for treating fast-breathing pneumonia * - tf_3day_amoxicillin_for_chest_indrawing_with_SpO2>=90% - REAL - probability of treatment failure by day 6 or relapse by day 14 of 3-day course amoxicillin for treating chest-indrawing pneumonia without hypoxaemia (SpO2>=90%) * - tf_5day_amoxicillin_for_chest_indrawing_with_SpO2>=90% - REAL - probability of treatment failure by day 6 or relapse by day 14 of 5-day course amoxicillin for treating chest-indrawing pneumonia without hypoxaemia (SpO2>=90%) * - tf_7day_amoxicillin_for_fast_breathing_pneumonia_in_young_infants - REAL - probability of treatment failure by day 6 or relapse by day 14 of 5-day course amoxicillin for treating chest-indrawing pneumonia without hypoxaemia (SpO2>=90%) * - tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2>=90% - REAL - probability of treatment failure by day 2 for oral amoxicillin given to severe pneumonia (danger-signs) without hypoxaemia (SpO2>=93%) * - tf_oral_amoxicillin_only_for_non_severe_pneumonia_with_SpO2<90% - REAL - probability of treatment failure or relapsefor oral amoxicillin given to non-severe pneumonia (fast-breathing or chest-indrawing) with hypoxaemia (SpO2<90%) * - tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2<90% - REAL - probability of treatment failure or relapsefor oral amoxicillin given to severe pneumonia (danger-signs) with hypoxaemia (SpO2<90%) * - tf_2nd_line_antibiotic_for_severe_pneumonia - REAL - probability of treatment failure by end of IV therapy for 2nd line antibiotic either cloxacillin or ceftriaxone to treat severe pneumonia (danger-signs) * - sensitivity_of_classification_of_fast_breathing_pneumonia_facility_level0 - REAL - sensitivity of correct classification and treatment decision by the HSA trained in iCCM, using paper-based tools, for fast-breathing pneumonia * - sensitivity_of_classification_of_danger_signs_pneumonia_facility_level0 - REAL - sensitivity of correct classification and referral decision by the HSA trained in iCCM, using paper-based tools, for danger-signs pneumonia * - sensitivity_of_classification_of_non_severe_pneumonia_facility_level1 - REAL - sensitivity of correct classification and treatment decision for non-severe pneumonia at facility level 1a and 1b * - sensitivity_of_classification_of_severe_pneumonia_facility_level1 - REAL - sensitivity of correct classification and referral decision for severe pneumonia at facility level 1a and 1b * - sensitivity_of_classification_of_non_severe_pneumonia_facility_level2 - REAL - sensitivity of correct classification and treatment decision for non-severe pneumonia at facility level 2 * - sensitivity_of_classification_of_severe_pneumonia_facility_level2 - REAL - sensitivity of correct classification and treatment decision for severe pneumonia at facility level 2 * - prob_iCCM_severe_pneumonia_treated_as_fast_breathing_pneumonia - REAL - probability of misdiagnosis of iCCM severe pneumonia (with chest-indrawing or danger signs) given treatment for non-severe pneumonia (fast-breathing) at facility level O * - prob_IMCI_severe_pneumonia_treated_as_non_severe_pneumonia - REAL - probability of misdiagnosis of IMCI severe pneumonia (with danger signs) given treatment for non-severe pneumonia ( fast-breathing or chest-indrawing) at facility level 1a/1b/2 * - or_care_seeking_perceived_severe_illness - REAL - The Odds Ratio for healthcare seeking for the symptom of chest-indrawing * - pulse_oximeter_and_oxygen_is_available - CATEGORICAL - Control the availability of the pulse oximeter and oxygen. "Default" does not over-ride availability; "Yes" forces them to be available; "No" forces them to not be available. Possible values are: [Yes, No, Default, ] * - prob_for_followup_if_treatment_failure - REAL - The probability for scheduling a follow-up appointment following treatment failure **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - ri_current_infection_status - BOOL - Does the person currently have an infection with a pathogen that can cause Alri. * - ri_primary_pathogen - CATEGORICAL - If infected, what is the pathogen with which the person is currently infected. (np.nan if not infected). Possible values are: [Enterobacteriaceae, H.influenzae_non_type_b, HMPV, Hib, Influenza, P.jirovecii, Parainfluenza, RSV, Rhinovirus, Staph_aureus, Strep_pneumoniae_PCV13, Strep_pneumoniae_non_PCV13, other_Strepto_Enterococci, other_bacterial_pathogens, other_pathogens_NoS, other_viral_pathogens, ] * - ri_secondary_bacterial_pathogen - CATEGORICAL - If infected, is there a secondary bacterial pathogen (np.nan if none or not applicable). Possible values are: [Strep_pneumoniae_PCV13, Strep_pneumoniae_non_PCV13, Hib, H.influenzae_non_type_b, Staph_aureus, Enterobacteriaceae, other_Strepto_Enterococci, other_bacterial_pathogens, ] * - ri_disease_type - CATEGORICAL - If infected, what disease type is the person currently suffering from.. Possible values are: [other_alri, pneumonia, ] * - ri_SpO2_level - CATEGORICAL - Peripheral oxygen saturation level (Sp02), measure for hypoxaemia. Possible values are: [<90%, 90-92%, >=93%, ] * - ri_on_treatment - BOOL - Is this person currently receiving treatment. * - ri_start_of_current_episode - DATE - date of onset of current Alri event (pd.NaT is not infected) * - ri_scheduled_recovery_date - DATE - (scheduled) date of recovery from current Alri event (pd.NaT is not infected or episode is scheduled to end in death) * - ri_scheduled_death_date - DATE - (scheduled) date of death caused by current Alri event (pd.NaT is not infected or episode will not cause death) * - ri_end_of_current_episode - DATE - date on which the last episode of Alri is resolved, (including allowing for the possibility that a cure is scheduled following onset). This is used to determine when a new episode can begin. This stops successive episodes interfering with one another. **Class attributes:** CAUSES_OF_DEATH : {'ALRI_Enterobacteriaceae': , 'ALRI_H.influenzae_non_type_b': , 'ALRI_HMPV': , 'ALRI_Hib': , 'ALRI_Influenza': , 'ALRI_P.jirovecii': , 'ALRI_Parainfluenza': , 'ALRI_RSV': , 'ALRI_Rhinovirus': , 'ALRI_Staph_aureus': , 'ALRI_Strep_pneumoniae_PCV13': , 'ALRI_Strep_pneumoniae_non_PCV13': , 'ALRI_other_Strepto_Enterococci': , 'ALRI_other_bacterial_pathogens': , 'ALRI_other_pathogens_NoS': , 'ALRI_other_viral_pathogens': } CAUSES_OF_DISABILITY : {'ALRI_Enterobacteriaceae': , 'ALRI_H.influenzae_non_type_b': , 'ALRI_HMPV': , 'ALRI_Hib': , 'ALRI_Influenza': , 'ALRI_P.jirovecii': , 'ALRI_Parainfluenza': , 'ALRI_RSV': , 'ALRI_Rhinovirus': , 'ALRI_Staph_aureus': , 'ALRI_Strep_pneumoniae_PCV13': , 'ALRI_Strep_pneumoniae_non_PCV13': , 'ALRI_other_Strepto_Enterococci': , 'ALRI_other_bacterial_pathogens': , 'ALRI_other_pathogens_NoS': , 'ALRI_other_viral_pathogens': } INIT_DEPENDENCIES : {'NewbornOutcomes', 'Wasting', 'Lifestyle', 'Epi', 'Hiv', 'Demography', 'SymptomManager'} METADATA : {, , , } OPTIONAL_INIT_DEPENDENCIES : {'HealthBurden'} all_pathogens : ['Enterobacteriaceae', 'H.influenzae_non_type_b', 'HMPV', 'Hib', 'Influenza', 'P.jirovecii', 'Parainfluenza', 'RSV', 'Rhinovirus', 'Staph_aureus', 'Strep_pneumoniae_PCV13', 'Strep_pneumoniae_non_PCV13', 'other_Strepto_Enterococci', 'other_bacterial_pathogens', 'other_pathogens_NoS', 'other_viral_pathogens'] all_symptoms : ['chest_indrawing', 'cough', 'cyanosis', 'danger_signs', 'difficult_breathing', 'fever', 'tachypnoea'] antibiotics : ['1st_line_IV_antibiotics', 'Amoxicillin_tablet_or_suspension_3days', 'Amoxicillin_tablet_or_suspension_5days', 'Amoxicillin_tablet_or_suspension_7days'] classifications : ['chest_indrawing_pneumonia', 'cough_or_cold', 'danger_signs_pneumonia', 'fast_breathing_pneumonia'] complications : ['empyema', 'hypoxaemia', 'lung_abscess', 'pleural_effusion', 'pneumothorax', 'sepsis'] disease_types : ['other_alri', 'pneumonia'] pathogens : {'viral': ['RSV', 'Rhinovirus', 'HMPV', 'Parainfluenza', 'Influenza', 'other_viral_pathogens'], 'bacterial': ['Strep_pneumoniae_PCV13', 'Strep_pneumoniae_non_PCV13', 'Hib', 'H.influenzae_non_type_b', 'Staph_aureus', 'Enterobacteriaceae', 'other_Strepto_Enterococci', 'other_bacterial_pathogens'], 'fungal/other': ['P.jirovecii', 'other_pathogens_NoS']} **Functions (defined or overridden in class Alri):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: check_params_read_in_ok .. automethod:: define_symptoms .. automethod:: pre_initialise_population .. automethod:: initialise_population .. automethod:: initialise_simulation .. automethod:: on_birth .. automethod:: report_daly_values .. automethod:: over_ride_availability_of_certain_consumables .. automethod:: look_up_consumables .. automethod:: end_episode .. automethod:: cancel_death_and_schedule_cure .. automethod:: check_properties .. automethod:: do_effects_of_treatment_and_return_outcome .. automethod:: record_sought_care_for_alri .. automethod:: get_imci_classification_based_on_symptoms .. automethod:: _ultimate_treatment_indicated_for_patient .. automethod:: do_at_generic_first_appt .. automethod:: do_at_generic_first_appt_emergency .. autoclass:: AlriPollingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} fraction_of_year_between_polling_event : **Functions (defined or overridden in class AlriPollingEvent):** .. automethod:: __init__ .. automethod:: get_probs_of_acquiring_pathogen .. automethod:: get_persons_for_new_alri .. automethod:: apply .. autoclass:: AlriIncidentCase Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class AlriIncidentCase):** .. automethod:: __init__ .. automethod:: determine_nature_of_the_case .. automethod:: apply_characteristics_of_the_case .. automethod:: apply .. autoclass:: AlriNaturalRecoveryEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class AlriNaturalRecoveryEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: AlriCureEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class AlriCureEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: AlriDeathEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class AlriDeathEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Alri_Treatment Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} _is_as_in_patient : **Functions (defined or overridden in class HSI_Alri_Treatment):** .. automethod:: __init__ .. automethod:: _as_out_patient .. automethod:: _as_in_patient .. automethod:: _refer_to_next_level_up .. automethod:: _refer_to_become_inpatient .. automethod:: _schedule_follow_up_following_treatment_failure .. automethod:: _get_cons .. automethod:: _get_cons_group .. automethod:: _get_cons_with_backups .. automethod:: _assess_and_treat .. automethod:: _has_staph_aureus .. automethod:: _get_imci_classification_based_on_symptoms .. automethod:: _get_imci_classification_by_SpO2_measure .. automethod:: _get_classification_given_by_health_worker .. automethod:: _get_disease_classification_for_treatment_decision .. automethod:: _do_action_given_classification .. automethod:: _provide_bronchodilator_if_wheeze .. automethod:: do_on_follow_up_following_treatment_failure .. automethod:: apply .. automethod:: never_ran .. autoclass:: AlriLoggingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class AlriLoggingEvent):** .. automethod:: __init__ .. automethod:: new_case .. automethod:: new_recovered_case .. automethod:: new_cured_case .. automethod:: new_death .. automethod:: new_seeking_care .. automethod:: new_treated .. automethod:: new_pulmonary_complication_case .. automethod:: new_systemic_complication_case .. automethod:: new_hypoxaemic_case .. automethod:: apply .. autoclass:: AlriCheckPropertiesEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class AlriCheckPropertiesEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: AlriIndividualLoggingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class AlriIndividualLoggingEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: AlriPropertiesOfOtherModules Bases: :class:`tlo.core.Module` **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - hv_inf - BOOL - temporary property * - hv_art - CATEGORICAL - temporary property. Possible values are: [not, on_VL_suppressed, on_not_VL_suppressed, ] * - nb_low_birth_weight_status - CATEGORICAL - temporary property. Possible values are: [extremely_low_birth_weight, very_low_birth_weight, low_birth_weight, normal_birth_weight, ] * - nb_breastfeeding_status - CATEGORICAL - temporary property. Possible values are: [none, non_exclusive, exclusive, ] * - va_pneumo_all_doses - BOOL - temporary property * - va_hib_all_doses - BOOL - temporary property * - va_measles_all_doses - BOOL - temporary property * - un_clinical_acute_malnutrition - CATEGORICAL - temporary property. Possible values are: [MAM, SAM, well, ] **Class attributes:** ALTERNATIVE_TO : {'Hiv', 'Wasting', 'Epi'} INIT_DEPENDENCIES : {'Demography'} **Functions (defined or overridden in class AlriPropertiesOfOtherModules):** .. automethod:: read_parameters .. automethod:: initialise_population .. automethod:: initialise_simulation .. automethod:: on_birth .. autoclass:: AlriIncidentCase_Lethal_DangerSigns_Pneumonia Bases: :class:`tlo.methods.alri.AlriIncidentCase`, :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class AlriIncidentCase_Lethal_DangerSigns_Pneumonia):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: AlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia Bases: :class:`tlo.methods.alri.AlriIncidentCase`, :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class AlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia):** .. automethod:: __init__ .. automethod:: apply