stoner_dalys_for_db: Create CSV with DALYs for an uploaded burden estimate set

In vimc/stoner: Support for Building VIMC Montagu Touchstones, using Dettl

Create CSV with DALYs for an uploaded burden estimate set

Description

When a group has uploaded a burden estimate set without DALYs, this function can retrieve that burden estimate set, extend it with DALYs, and write a new CSV file ready for uploading through the Montagu portal.

Usage

stoner_dalys_for_db(
  con,
  dalys_params,
  modelling_group = NULL,
  disease = NULL,
  touchstone = NULL,
  scenario = NULL,
  burden_estimate_set_id = NULL,
  output_file = NULL,
  life_table = NULL,
  year_min = 2000,
  year_max = 2100
)

Arguments

con	DBI connection to a Montagu database, for retrieving the burden_estimate set.
dalys_params	A data.frame containing how to calculate dalys; each row represents a condition, and the four columns describe how to calculate the cost of that condition across the population in that year. For each condition, the outcome column must provide a burden outcome (which will be a column name in data). The proportion is the proportion of people reported as that outcome, who suffer this condition. average_duration is the number of years for which the condition is suffered, set to greater than 120 for a life-long period. And disability_weight is a measure of how severe the implications are of this particular condition. See http://ghdx.healthdata.org/record/ihme-data/gbd-2017-disability-weights for where these figures come from; the final figures are decided in discussion with the groups.
modelling_group	If the modelling group, disease, touchstone and scenario are all provided, then we lookup the current (most recently uploaded) burden estimate set matching those details.
disease	If specified, the name of the disease in question
touchstone	If specified, the touchstone (including version) for the set.
scenario	If specified, the name of the scenario for the set.
burden_estimate_set_id	Alternatively, if modelling_group, disease, touchstone and scenario are NULL, the numerical id of a particular burden estimate set can be specified here, to extend that estimate set with DALYs. Otherwise, leave as NULL to look up by the other four fields.
output_file	If provided, then write the output CSV with the additional DALYs field to this filename. The file will be ready to be uploaded to Montagu.
life_table	If provided, then re-use the life table provided by a previous call to this function. Otherwise, it can be left at NULL to generate the life-table.
year_min	The first year of the range in which to calculate DALYs. (Default 2000)
year_max	The final year of the range in which to calculate DALYs. (Default 2100)

Value

A list with two components, data is a data.frame of the complete DALYs extended data, and life_table is the life table used for calculating the DALYs, should that be required again.

vimc/stoner documentation built on May 16, 2024, 11:09 a.m.