reportRmd (version 0.1.0)

rm_cifsum: 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
)

Value

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

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

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')