rm_survtime: Display survival rates and events for specified times

Description

This is a wrapper for the survfit function to output a tidy display for reporting. Either Kaplan Meier or Cox Proportional Hazards models may be used to estimate the survival probabilities.

Usage

rm_survtime(
  data,
  time,
  status,
  covs = NULL,
  strata = NULL,
  type = "KM",
  survtimes,
  survtimeunit,
  strata.prefix = NULL,
  survtimesLbls = NULL,
  showCols = c("At Risk", "Events", "Censored"),
  CIwidth = 0.95,
  conf.type = "log",
  na.action = "na.omit",
  showCounts = TRUE,
  digits = getOption("reportRmd.digits", 2),
  caption = NULL,
  tableOnly = FALSE,
  fontsize
)

Value

A character vector of the survival 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
covs: character vector with the names of variables to adjust for in coxph fit
strata: string indicating the variable to group observations by. If this is left as NULL (the default) then event counts and survival rates are provided for the entire cohort.
type: survival function, if no covs are specified defaults to Kaplan-Meier, otherwise the Cox PH model is fit. Use type='PH' to fit a Cox PH model with no covariates.
survtimes: numeric vector specifying when survival probabilities should be calculated.
survtimeunit: unit of time to suffix to the time column label if survival probabilities are requested, should be plural
strata.prefix: character value describing the grouping variable
survtimesLbls: if supplied, a vector the same length as survtimes with descriptions (useful for displaying years with data provided in months)
showCols: character vector specifying which of the optional columns to display, defaults to c('At Risk','Events','Censored')
CIwidth: width of the survival probabilities, default is 95%
conf.type: type of confidence interval see survfit for details. Default is 'log'.
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
digits: the number of digits in the survival rate, default is 2.
caption: table caption for markdown output
tableOnly: should a dataframe or a formatted object be returned
fontsize: PDF/HTML output only, manually set the table fontsize

Details

If covariates are supplied then a Cox proportional hazards model is fit for the entire cohort and each strata. Otherwise the default is for Kaplan-Meier estimates. Setting type = 'PH' will force a proportional hazards model.

Examples

Run this code

# Kaplan-Mieir survival probabilities with time displayed in years
data("pembrolizumab")
rm_survtime(data=pembrolizumab,time='os_time',status='os_status',
strata="cohort",type='KM',survtimes=seq(12,72,12),
survtimesLbls=seq(1,6,1),
survtimeunit='years')

# Cox Proportional Hazards survivial probabilities
rm_survtime(data=pembrolizumab,time='os_time',status='os_status',
strata="cohort",type='PH',survtimes=seq(12,72,12),survtimeunit='months')

# Cox Proportional Hazards survivial probabilities controlling for age
rm_survtime(data=pembrolizumab,time='os_time',status='os_status',
covs='age',strata="cohort",survtimes=seq(12,72,12),survtimeunit='months')