PAFcalc.RdUses [tobalcepi::RRFunc()] and [tobalcepi::subgroupRisk()] to calculate population attributable fractions based on the survey data provided.
PAFcalc(
data = NULL,
rrdata = NULL,
substance,
tob_include_risk_in_former_smokers = TRUE,
alc_protective = TRUE,
alc_wholly_chronic_thresholds = c(2, 2),
alc_wholly_acute_thresholds = c(3, 4),
grams_ethanol_per_unit = 8,
use_weights = FALSE,
year_range = "all",
pool = FALSE,
subgroups = c("sex", "age_cat"),
tobalc_include_int = FALSE,
within_model = FALSE,
mort_or_morb = c("mort", "morb")[1],
country = c("England", "Scotland")[1],
other_lag_function = "Cancers",
oesoph_subtypes = FALSE
)Data table of individual characteristics. Defaults to NULL.
Optional - data table containing individual tobacco and alcohol consumption characteristics with relative risks of disease already assigned. This could be useful for increasing efficiency - saving computer processing time. Defaults to NULL.
Whether to compute relative risks for just alcohol ("alc"), just tobacco ("tob") or joint risks for tobacco and alcohol ("tobalc").
Logical - whether the residual risks of smoking in former smokers should be considered (defaults to TRUE).
Logical - whether to include the protective effects of alcohol in the risk function. Defaults to TRUE. If TRUE, then the part of the risk function < 1 is set to equal 1.
Numeric vector - the thresholds in UK standard units of alcohol per day over which individuals begin to experience an elevated risk for chronic diseases that are wholly attributable to alcohol. Input in the order c(female, male). Defaults to the current UK healthy drinking threshold of 14 units/week for females and males, or 2 units/day.
Numeric vector - the thresholds in UK standard units of alcohol /day over which individuals begin to experience an elevated risk for acute diseases that are wholly attributable to alcohol. Input in the form c(female, male). Defaults to 3 units/day for females and 4 units/day for males.
Numeric value giving the conversion factor for the number of grams of pure ethanol in one UK standard unit of alcohol.
Logical - should the calculation account for survey weights. Defaults to FALSE. Weight variable must be called "wt_int".
Either an integer vector of the years to be selected or "all". Defaults to "all".
Logical - should the years selected be pooled. Defaults to FALSE.
Character vector - the variable names of the subgroups used to stratify the estimates.
Logical - in computing joint relative risks for tobacco and alcohol, should a (synergistic/multiplicative) interaction between exposure to tobacco and alcohol be included. Defaults to FALSE. If TRUE, then only interactive effects for oesophageal, pharynx, oral cavity and larynx cancers are considered.
Logical - is the function being used to calculate PAFs from the results of a STAPM model simulation. Defaults to FALSE.
Character string - whether the risk functions for conditions with separate mortality and morbidity risk functions should refer to mortality or morbidity. Values could be "mort" or "morb". Default is "mort".
Character string - "England" or "Scotland"
Character - the name of the lag function to use for tobacco related conditions that are not categorised as CVD, COPD, or Cancer. Options: c("Cancers", "CVD", "COPD", "immediate"). The default is "Cancers", which gives the most conservative (i.e. slowest) estimate of the rate of decline in the risk of disease after quitting smoking.
Logical - should the attributable fractions for oesophageal cancer be multiplied by the proportions of each subtype. Defaults to FALSE.
Returns a data.table containing the estimated PAFs.
if (FALSE) {
tobacco_pafs <- PAFcalc(
data = test_data,
substance = "tob",
tob_include_risk_in_former_smokers = TRUE,
use_weights = TRUE,
year_range = "all",
pool = TRUE,
subgroups = c("sex", "age_cat", "imd_quintile")
)
}