lbt05: 'LBT05' Table 1 (Default) Laboratory Abnormalities with...

In chevron: Standard TLGs for Clinical Trials Reporting

LBT05 Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.

Description

LBT05 Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.

Usage

lbt05_main(
  adam_db,
  arm_var = "ACTARM",
  lbl_overall = NULL,
  map = lab_paramcd_abn_dir(),
  ...
)

lbt05_pre(adam_db, ...)

lbt05_post(tlg, prune_0 = FALSE, keep = "Any Abnormality", ...)

lbt05

lab_paramcd_abn_dir()

Arguments

adam_db	(list of data.frames) object containing the ADaM datasets
arm_var	(string) variable used for column splitting
lbl_overall	(string) label used for overall column, if set to NULL the overall column is omitted
map	(data.frame) with two columns mapping of parameters code (PARAMCD) to directions of abnormality (ABN_DIR). If a parameter is not in the map or if map is NULL, both directions are analyzed.
...	not used.
tlg	(TableTree, Listing or ggplot) object typically produced by a main function.
prune_0	(flag) remove 0 count rows
keep	(character) the levels to keep in the table even if they are empty. If NULL, all levels are pruned.

Format

An object of class chevron_t of length 1.

Details

• Does not remove rows with zero counts by default.

• Lab test results with missing AVAL values are excluded.

• Split columns by arm, typically ACTARM.

Value

the main function returns an rtables object.

the preprocessing function returns a list of data.frame.

the postprocessing function returns an rtables object or an ElementaryTable (null report).

a data.frame with the direction of abnormality of each lab parameter code.

Functions

• lbt05_main(): Main TLG function

• lbt05_pre(): Preprocessing

• lbt05_post(): Postprocessing

• lab_paramcd_abn_dir():

Note

• adam_db object must contain an adlb table with columns "ONTRTFL", "PARCAT2", "PARAM", "ANRIND", "AVALCAT1", and column specified by arm_var.

Examples

run(lbt05, syn_data)

map <- data.frame(PARAMCD = c("ALT", "ALT", "CRP", "CRP", "IGA", "XXX"), ABN_DIR = c("Low", "High"))
run(lbt05, syn_data, map = map)
# example code
head(lab_paramcd_abn_dir())

chevron documentation built on June 20, 2025, 5:08 p.m.