rm_survtime {reportRmd}

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
)

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.

Value

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

See Also

survfit

Examples

# 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')