chevron (version 0.2.12)

lbt05_main: 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()

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.

Format

An object of class chevron_t of length 1.

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.

Functions

• lbt05_main(): Main TLG function

• lbt05_pre(): Preprocessing

• lbt05_post(): Postprocessing

• lab_paramcd_abn_dir():

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.

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())