rm_cifsum: Summarize cumulative incidence by group

In reportRmd: Tidy Presentation of Clinical Reporting

Summarize cumulative incidence by group

Description

Displays event counts and event rates at specified time points for the entire cohort and by group. Gray's test of differences in cumulative incidence is displayed.

Usage

rm_cifsum(
  data,
  time,
  status,
  group = NULL,
  eventcode = 1,
  cencode = 0,
  eventtimes,
  eventtimeunit,
  eventtimeLbls = NULL,
  CIwidth = 0.95,
  unformattedp = FALSE,
  na.action = "na.omit",
  showCounts = TRUE,
  showGraystest = TRUE,
  digits = 2,
  caption = NULL,
  tableOnly = FALSE
)

Arguments

data	data frame containing survival data
time	string indicating survival time variable
status	string indicating event status variable; must have at least 3 levels, e.g. 0 = censor, 1 = event, 2 = competing risk
group	string or character vector indicating the variable to group observations by
eventcode	numerical variable indicating event, default is 1
cencode	numerical variable indicating censored observation, default is 0
eventtimes	numeric vector specifying when event probabilities should be calculated
eventtimeunit	unit of time to suffix to the time column label if event probabilities are requested, should be plural
eventtimeLbls	if supplied, a vector the same length as eventtimes with descriptions (useful for displaying years with data provided in months)
CIwidth	width of the event probabilities, default is 95%
unformattedp	boolean indicating if you would like the p-value to be returned unformatted (ie not rounded or prefixed with '<'). Should be used in conjunction with the digits argument.
na.action	default is to omit missing values, but can be set to throw and error using na.action='na.fail'
showCounts	boolean indicating if the at risk, events and censored columns should be output, default is TRUE
showGraystest	boolean indicating Gray's test should be included in the final table, default is TRUE
digits	the number of digits to report in the event probabilities, default is 2.
caption	table caption for markdown output
tableOnly	should a dataframe or a formatted object be returned

Value

A character vector of the event table source code, unless tableOnly=TRUE in which case a data frame is returned

Examples

library(survival)
data(pbc)

# Event probabilities at various time points with replacement time labels
rm_cifsum(data=pbc,time='time',status='status',
eventtimes=c(1825,3650),eventtimeLbls=c(5,10),eventtimeunit='yr')

# Event probabilities by one group
rm_cifsum(data=pbc,time='time',status='status',group='trt',
eventtimes=c(1825,3650),eventtimeunit='day')


# Event probabilities by multiple groups
rm_cifsum(data=pbc,time='time',status='status',group=c('trt','sex'),
eventtimes=c(1825,3650),eventtimeunit='day')

reportRmd documentation built on April 4, 2025, 2:03 a.m.