Add cumulative count and summary stats for categories for exposure duration analysis

Usage

extend_exp_duration(
  outdata,
  category_section_label = paste0(metalite::collect_adam_mapping(outdata$meta,
    outdata$parameter)$label, " (extend)"),
  duration_category_list = extract_duration_category_ranges(duration_category_labels),
  duration_category_labels =
    levels(outdata$meta$data_population[[metalite::collect_adam_mapping(outdata$meta,
    outdata$parameter)$vargroup]])
)

Arguments

outdata: An outdata object created by prepare_exp_duration().
category_section_label: A character value of section label. If NULL, the parameter label is used with "(cumulative)".
duration_category_list: A list of duration category ranges. Must be real numbers and may overlap or be mutually exclusive. A list should be in the form of list(c(low1, high1), c(low2, high2), ...). If NA is included in the range, it is treated as -Inf or Inf. The range is defined as low <= x < high for each.
duration_category_labels: A character vector of internal labels. Labels to be displayed for the duration_category_list values. Must be the same length as duration_category_list.

Value

A list of analysis raw datasets.

Examples

meta <- metalite::meta_adam(
  population = metalite_sl_adexsum,
  observation = metalite_sl_adexsum
) |>
  metalite::define_plan(metalite::plan(
    analysis = "exp_dur", population = "apat",
    observation = "apat", parameter = "expdur"
  )) |>
  metalite::define_population(
    name = "apat", group = "TRTA", subset = APERIOD == 1 & AVAL > 0
  ) |>
  metalite::define_parameter(
    name = "expdur", subset = PARAMCD == "TRTDURD", var = "AVAL",
    label = "Exposure Duration (Days)", vargroup = "EXDURGR"
  ) |>
  metalite::define_analysis(
    name = "exp_dur", title = "Summary of Exposure Duration",
    label = "exposure duration table"
  ) |>
  metalite::meta_build()

outdata <- meta |> prepare_exp_duration()
outdata |>
  extend_exp_duration(
    duration_category_list = list(c(1, NA), c(7, NA), c(28, NA), c(12 * 7, NA), c(24 * 7, NA)),
    duration_category_labels = c(">=1 day", ">=7 days", ">=28 days", ">=12 weeks", ">=24 weeks")
  )
#> List of 19
#>  $ meta            :List of 7
#>  $ population      : chr "apat"
#>  $ observation     : chr "apat"
#>  $ parameter       : chr "expdur"
#>  $ n               :'data.frame':	1 obs. of  6 variables:
#>  $ order           : NULL
#>  $ group           : chr "TRTA"
#>  $ reference_group : NULL
#>  $ char_n          :List of 1
#>  $ char_var        : chr "AVAL"
#>  $ char_prop       :List of 1
#>  $ var_type        :List of 1
#>  $ group_label     : Factor w/ 3 levels "Placebo","Low Dose",..: 1 3 2
#>  $ analysis        : chr "exp_dur"
#>  $ char_stat_groups:List of 5
#>  $ char_n_cum      :List of 1
#>  $ char_prop_cum   :List of 1
#>  $ char_stat_cums  :List of 5
#>  $ extend_call     :List of 1