aggregate_summarize_excess: Aggregate and summarize excess mortality estimates
In njhenry/covidemr: Tools for Mapping COVID Excess Mortality

Description Usage Arguments Value

Given draws of baseline death COUNTS (not rates) and observed death counts, calculate summary metrics of excess mortality, optionally grouping by fields in the data

aggregate_summarize_excess(
  baseline_deaths_dt,
  aggregate = FALSE,
  group_cols = NULL,
  baseline_draw_cols = paste0("draw", 1:1000),
  obs_death_col = "deaths",
  alpha = 0.05
)

`baseline_deaths_dt`	data.table containing draws of baseline death COUNTS (not rates), observed death counts, and optional identifier columns for the period when excess mortality is being calculated
`aggregate`	[bool, default FALSE] should the data be aggregated across grouping columns?
`group_cols`	[char, default NULL] If 'aggregate' is TRUE, group by these columns when aggregating baseline and observed deaths. If aggregation is specified and this argument is left as NULL, the aggregation will occur across all rows
`baseline_draw_cols`	[character, default c('draw1', ... 'draw1000')] columns in 'baseline_deaths_dt' that contain the draws for predicted baseline death counts
`obs_death_col`	[character, default 'deaths'] name of the column in 'baseline_deaths_dt' containing observed deaths by week
`alpha`	[numeric, default 0.05] Cutoff for two-tailed uncertainty interval. For example, the default of 0.05 will use the 95 interval for each outcome

data.table containing at least the following fields: - Any grouping columns, if specified - 'obs_death_col' as specified in the function argument - 'bl_<mean/lower/upper>': Mean and UI bounds for baseline death counts - 'smr_<mean/lower/upper>': Mean and UI bounds for Standardized Mortality Ratios, calculated as observed / baseline - 'ex_d_<mean/lower/upper>': Mean and UI bounds for Excess Deaths, calculated as observed - baseline - 'sig_under1': Did the observed deaths fall BELOW the baseline deaths UI? - 'sig_over1': Did the observed deaths fall ABOVE the baseline deaths UI?

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