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.
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.
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
initial 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_prop_primary_edu
REAL
proportion of starting primary education at baseline age 5-12
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 given population 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 given population 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 exercise population 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 given population 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 given population 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 quantile
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 hand washing 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
CATEGORICAL
bmi: 1 (<18) 2 (18-24.9) 3 (25-29.9) 4 (30-34.9) 5 (35+)bmi is np.nan until age 15. Possible values are: [1, 2, 3, 4, 5, ]
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 to quit 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 : {}
__annotations__ : {}
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.
- pre_initialise_population()
Initialise the linear model class
- 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
- class LifestyleEvent(module)
Regular event that updates all lifestyle properties for population
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
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
schedule logging to repeat every 3 months
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