Create CSV with DALYs for an uploaded burden estimate set

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 an output pq file 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.