library(metalite)
library(metalite.sl)

## Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
##   object 'type_sum.accel' not found

Create Exposure Duration Table

The exposure duration analysis aims to provide table to summarize by each identified duration category. The development of exposure duration analysis involves functions:

meta_sl_exposure_example: build the metadata (meta object) for analysis.
prepare_exp_duration: prepare analysis raw datasets.
format_exp_duration: prepare analysis outdata with proper format.
rtf_exp_duration: transfer (mock) output dataset to RTF table.

Build a metadata

There are two steps in meta_sl_exposure_example function in order to build the metadata (meta object): processing the ADaM dataset and save meta information for A&R reporting.

Step1: ADEXSUM, the ADaM dataset for Drug Exposrue Summary Data, is utilized to:

Sum up duration by STUDYID SITENUM USUBJID SUBJID APERIOD EXTRT ADOSEFRM PARAMCD.
Subset the exposure data by upcase(trim(left(paramcd))) = "TRTDUR".
Get the exposure duration adexsum$AVAL for all participants.
Assign duration category adexsum$EXDURGR i.e.”>=1 day”, “>=7 days”,“>=28 days”, “>=12 weeks” and “>=24 weeks”.

adsl <- r2rtf::r2rtf_adsl
adexsum <- data.frame(USUBJID = adsl$USUBJID)
adexsum$TRTA <- factor(adsl$TRT01A,
  levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
  labels = c("Placebo", "Low Dose", "High Dose")
)

adexsum$APERIODC <- "Base"
adexsum$APERIOD <- 1

set.seed(123) # Set a seed for reproducibility
adexsum$AVAL <- sample(x = 0:(24 * 7), size = length(adexsum$USUBJID), replace = TRUE)
adexsum$EXDURGR <- "not treated"
adexsum$EXDURGR[adexsum$AVAL >= 1] <- ">=1 day"
adexsum$EXDURGR[adexsum$AVAL >= 7] <- ">=7 days"
adexsum$EXDURGR[adexsum$AVAL >= 28] <- ">=28 days"
adexsum$EXDURGR[adexsum$AVAL >= 12 * 7] <- ">=12 weeks"
adexsum$EXDURGR[adexsum$AVAL >= 24 * 7] <- ">=24 weeks"

adexsum$EXDURGR <- factor(adexsum$EXDURGR,
  levels = c("not treated", ">=1 day", ">=7 days", ">=28 days", ">=12 weeks", ">=24 weeks")
)
unique(adexsum$EXDURGR)

## [1] >=12 weeks  >=7 days    >=28 days   >=1 day     >=24 weeks  not treated
## Levels: not treated >=1 day >=7 days >=28 days >=12 weeks >=24 weeks

Step2: Save analysis plan and metadata(parameter and analysis) information, then build meta object.

plan <- metalite::plan(
  analysis = "exp_dur", population = "apat",
  observation = "apat", parameter = "expdur"
)

meta <- metalite::meta_adam(
  population = adexsum,
  observation = adexsum
) |>
  metalite::define_plan(plan) |>
  metalite::define_population(
    name = "apat",
    group = "TRTA",
    subset = quote(APERIOD == 1 & AVAL > 0)
  ) |>
  metalite::define_parameter(
    name = "expdur",
    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()

Analysis preparation

The input of the function prepare_exp_duration() is a meta object created by the metalite package. The resulting output comprises a collection of raw datasets for analysis and reporting.

outdata <- prepare_exp_duration(meta)
outdata

## List of 14
##  $ 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"

Number of participants in population

outdata$n[, 1:5]

##                         name n_1 n_2 n_3 n_9999
## 1 Participants in population  86  83  84    253

Exposure Duration Table

Create Exposure Duration Table

Build a metadata

Analysis preparation

Format output

Output as RTF