tlo.methods.enhanced_lifestyle module

Lifestyle module Documentation: 04 - Methods Repository/Method_Lifestyle.xlsx

class Lifestyle(name=None, resourcefilepath=None)

Lifestyle module provides properties that are used by all disease modules if they are affected by urban/rural, wealth, tobacco usage etc.

Bases: tlo.core.Module

PARAMETERS:

Item	Type	Description
init_p_urban	REAL	initial proportion urban
init_p_wealth_urban	LIST	List of probabilities of category given urban
init_p_wealth_rural	LIST	List of probabilities of category given rural
init_p_bmi_urban_m_not_high_sugar_age1529_not_tob_wealth1	LIST	List of probabilities of bmi categories for urban men age 15-29 with not high sugar, not tobacco, wealth level 1
init_or_higher_bmi_f	REAL	odds ratio higher BMI if female
init_or_higher_bmi_rural	REAL	odds ratio higher BMI if rural
init_or_higher_bmi_high_sugar	REAL	odds ratio higher BMI if high sugar intake
init_or_higher_bmi_age3049	REAL	odds ratio higher BMI if age 30-49
init_or_higher_bmi_agege50	REAL	odds ratio higher BMI if age ge 50
init_or_higher_bmi_tob	REAL	odds ratio higher BMI if use tobacco
init_or_higher_bmi_per_higher_wealth	REAL	odds ratio higher BMI per higer wealth level
init_or_higher_bmi_per_higher_wealth_level	REAL	odds ratio for higher initial bmi category per higher wealth level
init_p_high_sugar	REAL	initital proportion with high sugar intake
init_p_high_salt_urban	REAL	initital proportion with high salt intake
init_or_high_salt_rural	REAL	odds ratio high salt if rural
init_p_ex_alc_m	REAL	initital proportion of men with excess alcohol use
init_p_ex_alc_f	REAL	initital proportion of women with excess alcohol use
init_p_low_ex_urban_m	REAL	initital proportion of men with low exercise urban
init_or_low_ex_rural	REAL	odds ratio low exercise rural
init_or_low_ex_f	REAL	odds ratio low exercise female
init_p_tob_age1519_m_wealth1	REAL	initital proportion of 15-19 year old men using tobacco, wealth level 1
init_or_tob_f	REAL	odds ratio tobacco use females
init_or_tob_age2039_m	REAL	odds ratio tobacco use age2039 in men
init_or_tob_agege40_m	REAL	odds ratio tobacco use age40+ in men
init_or_tob_wealth2	REAL	odds ratio tobacco use wealth level 2
init_or_tob_wealth3	REAL	odds ratio tobacco use wealth level 3
init_or_tob_wealth4	REAL	odds ratio tobacco use wealth level 4
init_or_tob_wealth5	REAL	odds ratio tobacco use wealth level 5
init_dist_mar_stat_age1520	LIST	proportions never, current, div_wid age 15-20 baseline
init_dist_mar_stat_age2030	LIST	proportions never, current, div_wid age 20-30 baseline
init_dist_mar_stat_age3040	LIST	proportions never, current, div_wid age 30-40 baseline
init_dist_mar_stat_age4050	LIST	proportions never, current, div_wid age 40-50 baseline
init_dist_mar_stat_age5060	LIST	proportions never, current, div_wid age 50-60 baseline
init_dist_mar_stat_agege60	LIST	proportions never, current, div_wid age 60+ baseline
init_age2030_w5_some_ed	REAL	proportions of low wealth 20-30 year olds with some education at baseline
init_or_some_ed_age0513	REAL	odds ratio of some education at baseline age 5-13
init_or_some_ed_age1320	REAL	odds ratio of some education at baseline age 13-20
init_or_some_ed_age2030	REAL	odds ratio of some education at baseline age 20-30
init_or_some_ed_age3040	REAL	odds ratio of some education at baseline age 30-40
init_or_some_ed_age4050	REAL	odds ratio of some education at baseline age 40-50
init_or_some_ed_age5060	REAL	odds ratio of some education at baseline age 50-60
init_or_some_ed_per_higher_wealth	REAL	odds ratio of some education at baseline per higher wealth level
init_prop_age2030_w5_some_ed_sec	REAL	proportion of low wealth aged 20-30 with some education who have secondary education at baseline
init_or_some_ed_sec_age1320	REAL	odds ratio of secondary education age 13-20
init_or_some_ed_sec_age3040	REAL	odds ratio of secondary education age 30-40
init_or_some_ed_sec_age4050	REAL	odds ratio of secondary education age 40-50
init_or_some_ed_sec_age5060	REAL	odds ratio of secondary education age 50-60
init_or_some_ed_sec_agege60	REAL	odds ratio of secondary education age 60+
init_or_some_ed_sec_per_higher_wealth	REAL	odds ratio of secondary education per higher wealth level
init_p_unimproved_sanitation_urban	REAL	initial probability of unimproved_sanitation given urban
init_or_unimproved_sanitation_rural	REAL	initial odds ratio of unimproved_sanitation if rural
init_p_no_clean_drinking_water_urban	REAL	initial probability of no_clean_drinking_water given urban
init_or_no_clean_drinking_water_rural	REAL	initial odds ratio of no clean drinking_water if rural
init_p_wood_burn_stove_urban	REAL	initial probability of wood_burn_stove given urban
init_or_wood_burn_stove_rural	REAL	initial odds ratio of wood_burn_stove if rural
init_p_no_access_handwashing_wealth1	REAL	initial probability of no_access_handwashing given wealth 1
init_or_no_access_handwashing_per_lower_wealth	REAL	initial odds ratio of no_access_handwashing per lower wealth level
init_rp_some_ed_age0513	REAL	relative prevalence of some education at baseline age 5-13
init_rp_some_ed_age1320	REAL	relative prevalence of some education at baseline age 13-20
init_rp_some_ed_age2030	REAL	relative prevalence of some education at baseline age 20-30
init_rp_some_ed_age3040	REAL	relative prevalence of some education at baseline age 30-40
init_rp_some_ed_age4050	REAL	relative prevalence of some education at baseline age 40-50
init_rp_some_ed_age5060	REAL	relative prevalence of some education at baseline age 50-60
init_rp_some_ed_per_higher_wealth	REAL	relative prevalence of some education at baseline per higher wealth level
init_rp_some_ed_sec_age1320	REAL	relative prevalence of secondary education age 15-20
init_rp_some_ed_sec_age3040	REAL	relative prevalence of secondary education age 30-40
init_rp_some_ed_sec_age4050	REAL	relative prevalence of secondary education age 40-50
init_rp_some_ed_sec_age5060	REAL	relative prevalence of secondary education age 50-60
init_rp_some_ed_sec_agege60	REAL	relative prevalence of secondary education age 60+
init_rp_some_ed_agege60	REAL	relative prevalence of some education at baseline age age 60+
init_rp_some_ed_sec_per_higher_wealth	REAL	relative prevalence of secondary education per higher wealth level
r_urban	REAL	probability per 3 months of change from rural to urban
r_rural	REAL	probability per 3 months of change from urban to rural
r_higher_bmi	REAL	probability per 3 months of increase in bmi category if rural male age15-29 not using tobacoo with wealth level 1 with not high sugar intake
rr_higher_bmi_urban	REAL	probability per 3 months of increase in bmi category if
rr_higher_bmi_f	REAL	rate ratio for increase in bmi category for females
rr_higher_bmi_age3049	REAL	rate ratio for increase in bmi category for age 30-49
rr_higher_bmi_agege50	REAL	rate ratio for increase in bmi category for age ge 50
rr_higher_bmi_tob	REAL	rate ratio for increase in bmi category for tobacco users
rr_higher_bmi_per_higher_wealth	REAL	rate ratio for increase in bmi category per higher wealth level
rr_higher_bmi_high_sugar	REAL	rate ratio for increase in bmi category for high sugar intake
r_lower_bmi	REAL	probability per 3 months of decrease in bmi category in non tobacco users
rr_lower_bmi_tob	REAL	rate ratio for lower bmi category for tobacco users
rr_lower_bmi_pop_advice_weight	REAL	probability per 3 months of decrease in bmi category given population advice/campaign on weight
r_high_salt_urban	REAL	probability per 3 months of high salt intake if urban
rr_high_salt_rural	REAL	rate ratio for high salt if rural
r_not_high_salt	REAL	probability per 3 months of not high salt intake
rr_not_high_salt_pop_advice_salt	REAL	probability per 3 months of not high salt givenpopulation advice/campaign on salt
r_high_sugar	REAL	probability per 3 months of high sugar intake
r_not_high_sugar	REAL	probability per 3 months of not high sugar intake
rr_not_high_sugar_pop_advice_sugar	REAL	probability per 3 months of not high sugar givenpopulation advice/campaign on sugar
r_low_ex	REAL	probability per 3 months of change from not low exercise to low exercise
r_not_low_ex	REAL	probability per 3 months of change from low exercise to not low exercie
rr_not_low_ex_pop_advice_exercise	REAL	probability per 3 months of not low exercisepopulation advice/campaign on exercise
rr_low_ex_f	REAL	risk ratio for becoming low exercise if female rather than male
rr_low_ex_urban	REAL	risk ratio for becoming low exercise if urban rather than rural
r_tob	REAL	probability per 3 months of change from not using tobacco to using tobacco if male age 15-19 wealth level 1
r_not_tob	REAL	probability per 3 months of change from tobacco using to not tobacco using
rr_tob_f	REAL	rate ratio tobacco if female
rr_tob_age2039	REAL	risk ratio for tobacco using if age 20-39 compared with 15-19
rr_tob_agege40	REAL	risk ratio for tobacco using if age >= 40 compared with 15-19
rr_tob_wealth	REAL	risk ratio for tobacco using per 1 higher wealth level (higher wealth level = lower wealth)
rr_not_tob_pop_advice_tobacco	REAL	probability per 3 months of quitting tobacco givenpopulation advice/campaign on tobacco
r_ex_alc	REAL	probability per 3 months of change from not excess alcohol to excess alcohol
r_not_ex_alc	REAL	probability per 3 months of change from excess alcohol to not excess alcohol
rr_ex_alc_f	REAL	risk ratio for becoming excess alcohol if female rather than male
rr_not_ex_alc_pop_advice_alcohol	REAL	probability per 3 months of not excess alcohol givenpopulation advice/campaign on alcohol
r_mar	REAL	probability per 3 months of marriage when age 15-30
r_div_wid	REAL	probability per 3 months of becoming divorced or widowed, amongst those married
r_stop_ed	REAL	probabilities per 3 months of stopping education if wealth level 5
rr_stop_ed_lower_wealth	REAL	relative rate of stopping education per 1 lower wealth quintile
p_ed_primary	REAL	probability at age 5 that start primary education if wealth level 5
rp_ed_primary_higher_wealth	REAL	relative probability of starting school per 1 higher wealth level
p_ed_secondary	REAL	probability at age 13 that start secondary education at 13 if in primary education and wealth level 5
rp_ed_secondary_higher_wealth	REAL	relative probability of starting secondary school per 1 higher wealth level
r_improved_sanitation	REAL	probability per 3 months of change from unimproved_sanitation true to false
r_clean_drinking_water	REAL	probability per 3 months of change from drinking_water true to false
r_non_wood_burn_stove	REAL	probability per 3 months of change from wood_burn_stove true to false
r_access_handwashing	REAL	probability per 3 months of change from no_access_handwashing true to false
start_date_campaign_exercise_increase	DATE	Date of campaign start for increased exercise
start_date_campaign_quit_smoking	DATE	Date of campaign start to quit smoking
start_date_campaign_alcohol_reduction	DATE	Date of campaign start for alcohol reduction
proportion_of_men_that_are_assumed_to_be_circumcised_at_birth	REAL	Proportion of men that are assumed to be circumcised at birth.The men are assumed to be circumcised at birth.
proportion_of_men_circumcised_at_initiation	REAL	Proportion of men (of all ages) that are assumed to be circumcised at the initiation of thesimulation.
proportion_female_sex_workers	REAL	proportion of women aged 15-49 years who are sex workers
fsw_transition	REAL	proportion of sex workers that stop being a sex worker each year

PROPERTIES:

Item	Type	Description
li_urban	BOOL	Currently urban
li_wealth	CATEGORICAL	wealth level: 1 (high) to 5 (low). Possible values are: [1, 2, 3, 4, 5, ]
li_bmi	INT	bmi: 1 (<18) 2 (18-24.9) 3 (25-29.9) 4 (30-34.9) 5 (35+)bmi is 0 until age 15
li_exposed_to_campaign_weight_reduction	BOOL	currently exposed to population campaign for weight reduction if BMI >= 25
li_low_ex	BOOL	currently low exercise
li_exposed_to_campaign_exercise_increase	BOOL	currently exposed to population campaign for increase exercise if low ex
li_high_salt	BOOL	currently high salt intake
li_exposed_to_campaign_salt_reduction	BOOL	currently exposed to population campaign for salt reduction if high salt
li_high_sugar	BOOL	currently high sugar intake
li_exposed_to_campaign_sugar_reduction	BOOL	currently exposed to population campaign for sugar reduction if high sugar
li_tob	BOOL	current using tobacco
li_date_not_tob	DATE	date last transitioned from tob to not tob
li_exposed_to_campaign_quit_smoking	BOOL	currently exposed to population campaign toquit smoking if tob
li_ex_alc	BOOL	current excess alcohol
li_exposed_to_campaign_alcohol_reduction	BOOL	currently exposed to population campaign for alcohol reduction if ex alc
li_mar_stat	CATEGORICAL	marital status {1:never, 2:current, 3:past (widowed or divorced)}. Possible values are: [1, 2, 3, ]
li_in_ed	BOOL	currently in education
li_ed_lev	CATEGORICAL	education level achieved as of now. Possible values are: [1, 2, 3, ]
li_unimproved_sanitation	BOOL	uninproved sanitation - anything other than own or shared latrine
li_no_access_handwashing	BOOL	no_access_handwashing - no water, no soap, no other cleaning agent - as in DHS
li_no_clean_drinking_water	BOOL	no drinking water from an improved source
li_wood_burn_stove	BOOL	wood (straw / crop)-burning stove
li_date_trans_to_urban	DATE	date transition to urban
li_date_acquire_improved_sanitation	DATE	date transition to urban
li_date_acquire_access_handwashing	DATE	date acquire access to handwashing
li_date_acquire_clean_drinking_water	DATE	date acquire clean drinking water
li_date_acquire_non_wood_burn_stove	DATE	date acquire non-wood burning stove
li_is_sexworker	BOOL	Is the person a sex worker
li_is_circ	BOOL	Is the person circumcised if they are male (False for all females)

Class attributes:

INIT_DEPENDENCIES : {‘Demography’}

METADATA : {}

Functions (defined or overridden in class Lifestyle):

__init__(name=None, resourcefilepath=None)

Construct a new disease module ready to be included in a simulation.

Initialises an empty parameters dictionary and module-specific random number generator.

Parameters:

name – the name to use for this module. Defaults to the concrete subclass’ name.

read_parameters(data_folder)

Read parameter values from file, if required.

Must be implemented by subclasses.

Parameters:

data_folder – path of a folder supplied to the Simulation containing data files. Typically, modules would read a particular file within here.

initialise_population(population)

Set our property values for the initial population. :param population: the population of individuals

initialise_simulation(sim)

Add lifestyle events to the simulation

on_birth(mother_id, child_id)

Initialise properties for a newborn individual. :param mother_id: the mother for this child :param child_id: the new child

determine_who_will_be_sexworker(months_since_last_poll)

Determine which women will be sex workers. This is called by initialise_population and the LifestyleEvent. Subject to the constraints: (i) Women who are in sex work may stop and there is a proportion that stop during each year. (ii) New women are ‘recruited’ to start sex work such that the overall proportion of women who are sex workers

does not fall below a given level.

compute_bmi_proportions_of_interest()

This is called by the logger and computes summary statistics about the bmi

class LifestyleEvent(module)

Regular event that updates all lifestyle properties for population

Bases: tlo.events.RegularEvent, tlo.events.Event, tlo.events.PopulationScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class LifestyleEvent):

__init__(module)

schedule to run every 3 months note: if change this offset from 3 months need to consider code conditioning on age.years_exact :param module: the module that created this event

apply(population)

Apply this event to the population. :param population: the current population

class LifestylesLoggingEvent(module)

Handles lifestyle logging

Bases: tlo.events.RegularEvent, tlo.events.Event, tlo.events.PopulationScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class LifestylesLoggingEvent):

__init__(module)

schedule logging to repeat every 3 months

apply(population)

Apply this event to the population. :param population: the current population