sstable.ae: Create an adverse event summary table

In oucru-biostats/C306: Collection of useful R codes for data analysis from the Biostatistics group at OUCRU

Create an adverse event summary table

Description

A function to create a simple adverse event summary table.

Usage

sstable.ae(
  ae_data,
  fullid_data,
  group_data = NULL,
  id.var,
  aetype.var,
  grade.var = NULL,
  group.var = NULL,
  group.var.priority = NULL,
  arm.var,
  sort.by,
  digits = 0,
  test = TRUE,
  pdigits = 3,
  pcutoff = 0.001,
  chisq.test = FALSE,
  correct = FALSE,
  simulate.p.value = FALSE,
  B = 2000,
  workspace = 1e+06,
  hybrid = FALSE,
  print.aetype.header = length(aetype.var) > 1 | any(length(names(aetype.var)) > 0) |
    any(isTRUE(nchar(names(aetype.var)) > 0)),
  na.text = "(Missing)",
  footer = NULL,
  flextable = TRUE,
  bg = "#F2EFEE"
)

Arguments

ae_data	a data frame contains adverse event data.
fullid_data	a data frame contains treatment arm data of all participants (not just those had adverse event).
group_data	a reference data frame contains the group name of each ae.
id.var	a character specifies name of study id variable (exists in both adverse event data and treatment arm data).
aetype.var	a character specifies name of adverse event type variable (exists in adverse event data).
grade.var	NULL or character specifies name of adverse event grade variable (exists in adverse event data).
group.var	a character specifies group (exists in adverse event data if group_data = NULL or group_data otherwise).
group.var.priority	a vector that specifies which groups will be appear first in the table.
arm.var	a character specifies name of treatment arm variable (exists in treatment arm data).
sort.by	An unquoted formula of sorting options. Available options are 'ep', 'pt', 'p', or a combination of them (eg ep+pt-p); A minus sign indicates a descending order.
digits	a number specifies number of significant digits for numeric statistics.
test	a logical value specifies whether a statistical test will be performed to compare between treatment arms.
pdigits	a number specifies number of significant digits for p value.
pcutoff	a number specifies threshold value of p value to be displayed as "< pcutoff".
chisq.test	a logical value specifies whether Chi-squared test or Fisher's exact test will be used to compare between treatment arms. Be aware that even when chisq.test==TRUE, if expected values are < 1, the later test will take over.
correct	a parameter for chisq.test().
simulate.p.value	a parameter for chisq.test() and fisher.test().
B	a parameter for chisq.test() and fisher.test().
workspace	a parameter for fisher.test().
hybrid	a parameter for fisher.test().
print.aetype.header	a logical value, whether to print the label of aetype.header.
na.text	['(Missing)'] in-placed text for missing AE
footer	a vector of strings to be used as footnote of table.
flextable	a logical value specifies whether output will be a flextable-type table.
bg	a character specifies color of the odd rows in the body of flextable-type table.

Value

a flextable-type table or a list with values/headers/footers

oucru-biostats/C306 documentation built on July 16, 2024, 2:33 p.m.