calculate_excess_time_series_by_group: Calculate time series of excess mortality across multiple...
In njhenry/covidemr: Tools for Mapping COVID Excess Mortality

Description Usage Arguments Value

Given draws of baseline mortality, observed starting population, and observed deaths by week, calculate excess mortality across many sub-population groupings. Sub-populations are identified by unique sets of ID columns. This is a wrapper for 'calculate_excess_time_series()', which calculates excess-adjusted population, excess deaths, and SMRs for a single population subgroup.

calculate_excess_time_series_by_group(
  experiment_draw_dt,
  baseline_draw_cols,
  group_cols,
  week_col = "week",
  obs_death_col = "deaths",
  pop_col = "pop"
)

`experiment_draw_dt`	data.table containing the experimental data ONLY for the time period when excess mortality is to be calculated. Should contain all of the fields specificied by the other parameters.
`baseline_draw_cols`	[character] columns in 'experiment_draw_dt' that contain the draws for predicted baseline mortality rate.
`group_cols`	[character] columns in 'experiment_draw_dt' with unique grouping identifiers. There should be no NULLs in any of these columns.
`week_col`	[character] name of the column containing week ID
`obs_death_col`	[character] name of the column containing observed deaths by week
`pop_col`	[character] name of the column containing estimated population by week, not adjusted (yet) to account for excess mortality.

Named list of three items: - 'baseline_deaths': Data.table of baseline death draws with identifiers - 'smrs': Data.table of SMR draws with identifiers - 'excess_deaths': Data.table of excess death draws with identifiers

njhenry/covidemr documentation built on Feb. 2, 2022, 2:31 a.m.