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Start a hierarchical table from the data

Source: R/first_table.R
first_hierarchy_table.Rd

The other kind of table the app's "first table" form starts: counts of subjects by a hierarchy of terms – adverse events by system organ class and preferred term (AEBODSYS | AEDECOD), and the same for medications or medical history by their own – in the columns of a group, the percents of the analysis set's subjects. It writes the rows every sheet says them in, as a table made by hand has them:

Usage

first_hierarchy_table(
  x,
  output_id,
  path,
  data,
  subjects_path,
  subjects,
  population,
  group,
  hierarchy = c("AEBODSYS", "AEDECOD"),
  where = NA_character_,
  total = NA_character_,
  grade = NA_character_,
  description = NA_character_
)

Arguments

x

A tflplanner.

output_id

The report.

path

The records' data file (data/adam/adae.rds), relative to the study folder.

data

Its data.

subjects_path

The subject-level data file (data/adam/adsl.rds).

subjects

Its data.

population

The analysis set flag column of the subject-level data (SAFFL).

group

The column of the groups (TRT01A).

hierarchy

The terms, outermost first (c("AEBODSYS", "AEDECOD")).

where

The records counted (TRTEMFL == "Y"); NA all of them.

total

The heading of a Total column ("Total"); NA none.

grade

A severity or grade column (AESEV, ATOXGR) to count by too, in the columns under each group; NA none. Each subject is counted once, at the worst: the grade's levels are written in order (a code list), and cards counts a subject at the last level it has – of the SOC for the SOC row, of the PT for the PT row. Not with a Total column.

description

The report's description.

Value

The tflplanner.

Details

  • the datasets (added to the data catalog when missing) and the analysis set (population flag == "Y" of the subject-level data);

  • two analysis data of the report: the analysis set's subjects (adsl_saf), and the records kept to them and to where (adae_saf);

  • one hierarchical analysis by the group, over the hierarchy, its denominator the analysis set (over_variables = TRUE: the "any event" row, named in the table's overall_label: "Any TEAE");

  • the table: the group as columns, the outer terms as groups and the innermost as rows, by frequency (most first) within each group;

  • the column header (the standards' "Arm (N=n) n (%), SOC / PT"), a page not splitting a group (22 rows a page, unless the study says), and a Total column when total is given.