mahp: A model of alchohol harms and policies
In uvic-cisur/intermahp3: The International Model of Alcohol Harms and Policies

Description Input Fields Computed Fields Data Methods Evaluation Methods Results Methods

API for InterMAHP Shiny App

pc: A dataset of alcohol consumption and prevalence
mm: A dataset of mortality and morbidity counts
rr: A list of relative risk function evaluation datasets
sk: A dataset skeleton used to perform aaf computations
dg: A list of gender-stratified drinking groups
bb: Gender-stratified definition of binge drinking
scc: Gender-stratified propotion of squamous-cell carcinoma among oesophageal cancers (only SCC is alcohol-caused)
ub: Upper bound of alcohol consumption
mcn: Number of samples in Monte Carlo uncertainty estimation
pc_sample_vars: Which prevalence and consumption variables to sample
dg: List of all drinking groups (gender stratified)
sn: Vector of all scenarios as mult. changes in consumption.
ext: Character indicating whether relative risk functions are extrapolated linearly or capped after a consumption level of 150 grams per day
cal: Boolean indiciating whether to try to calibrate absolute risk curves for calibrable wholly attributable conditions
rr_choice: Character, relative risk source

af: A list of the wide fraction datasets described below
base_paf: A wide dataset of alcohol attributable fractions from partially attributable causes not affected by bingeing
base_former_paf: A wide dataset of alcohol attributable fractions from partially attributable causes not affected by bingeing that still affect former drinkers
binge_paf: A wide dataset of alcohol attributable fractions from partially attributable causes affected by bingeing
binge_former_paf: A wide dataset of alcohol attributable fractions from partially attributable causes affected by bingeing that still affect former drinkers
scaled_base_waf: A wide dataset of alcohol attributable fractions from wholly attributable causes not affected by binging whose attributable fractions are scaled forms of similar partially attributable forms
scaled_binge_waf: A wide dataset of alcohol attributable fractions from wholly attributable causes affected by binging whose attributable fractions are scaled forms of similar partially attributable forms
calibrated_waf: A wide dataset of alcohol attributable fractions from wholly attributable causes whose risk functions are calibrated from morbidity and mortality data

$new() Creates a new model object.

$add_pc() Prepares a prevalence and consumption dataset

$add_mm() Prepares a morbidity and mortality dataset

$choose_rr() Chooses a source for relative risk functions

$choose_project() Chooses a predefined set of project settings

$set_ext() Set risk extrapolation method (linear >> TRUE, capped >> FALSE)

$set_bb() Sets binge consumption definitions

$set_ub() Sets upper bound on consumption

$set_scc() Sets squamous cell carcinoma proportions

$update_rr() Updates relative risk function evaluations with latest parameters

$make_gamma() Makes base and binge gamma functions at the prescribed level of consumption

$init_fractions Initialize and populate fraction sheets

$def_scenario() Defines a scenario $rm_scenario $cmp_scenario() Adds new scenario attributable fractions and relative attributable fractions to the partially attributable fraction dataset $cmp_scenarios()

$def_group() Defines or redefines a group $rm_group $cmp_group() $cmp_groups()

$add_scenario() Adds new scenario attributable fractions and relative attributable fractions to the skeleton dataset for each existing drinking group

$add_group() Adds a new set of drinking groups for each existing scenario

$get_afs Provides all attributable fractions computed and evaluates scc correction if supplied

$get_long_afs Invokes get_afs and formats as long

$get_long_counts Invokes get_long_afs and applied afs to counts

uvic-cisur/intermahp3 documentation built on July 29, 2021, 5:11 p.m.