survival: Interfaces to survival package for data science pipelines.

In rbertolusso/intubate: Interface to Popular R Functions for Data Science Pipelines

Description

Interfaces to survival functions that can be used in a pipeline implemented by magrittr.

Usage

ntbt_cch(data, ...)
ntbt_coxph(data, ...)
ntbt_pyears(data, ...)
ntbt_survConcordance(data, ...)
ntbt_survexp(data, ...)
ntbt_survfit(data, ...)
ntbt_survreg(data, ...)
ntbt_survSplit(data, ...)

Arguments

data	data frame, tibble, list, ...
...	Other arguments passed to the corresponding interfaced function.

Details

Interfaces call their corresponding interfaced function.

Value

Object returned by interfaced function.

Author(s)

Roberto Bertolusso

Examples

## Not run: 
library(intubate)
library(magrittr)
library(survival)

## cch
subcoh <- nwtco$in.subcohort
selccoh <- with(nwtco, rel==1|subcoh==1)
ccoh.data <- nwtco[selccoh,]
ccoh.data$subcohort <- subcoh[selccoh]
ccoh.data$histol <- factor(ccoh.data$histol,labels=c("FH","UH"))
ccoh.data$stage <- factor(ccoh.data$stage,labels=c("I","II","III","IV"))
ccoh.data$age <- ccoh.data$age/12 # Age in years

## Original function to interface
cch(Surv(edrel, rel) ~ stage + histol + age, data = ccoh.data,
    subcoh = ~subcohort, id=~seqno, cohort.size=4028)

## The interface reverses the order of data and formula
ntbt_cch(data = ccoh.data, Surv(edrel, rel) ~ stage + histol + age,
    subcoh = ~subcohort, id=~seqno, cohort.size=4028)

## so it can be used easily in a pipeline.
ccoh.data %>%
  ntbt_cch(Surv(edrel, rel) ~ stage + histol + age,
    subcoh = ~subcohort, id=~seqno, cohort.size=4028)
    
## coxph    
## Original function to interface
vet2 <- survSplit(Surv(time, status) ~., veteran,
                  cut = c(60, 120), episode = "timegroup")
coxph(Surv(tstart, time, status) ~ karno*strata(timegroup) +
                age + trt, data = vet2)

## The interface reverses the order of data and formula
vet2 <- ntbt_survSplit(veteran, Surv(time, status) ~.,
                       cut = c(60, 120), episode = "timegroup")
ntbt_coxph(data = vet2, Surv(tstart, time, status) ~
              karno*strata(timegroup) + age + trt)

## so it can be used easily in a pipeline.
veteran %>%
  ntbt_survSplit(Surv(time, status) ~.,
                 cut = c(60, 120), episode = "timegroup") %>%
  ntbt_coxph(Surv(tstart, time, status) ~ 
             karno*strata(timegroup) + age + trt)

## pyears
hearta <- by(heart, heart$id,  
             function(x)x[x$stop == max(x$stop),]) 
hearta <- do.call("rbind", hearta) 

## Original function to interface
pyears(Surv(stop/365.25, event) ~
         cut(age + 48, c(0,50,60,70,100)) + surgery,
       data = hearta, scale = 1)

## The interface reverses the order of data and formula
ntbt_pyears(data = hearta,
            Surv(stop/365.25, event) ~
              cut(age + 48, c(0,50,60,70,100)) + surgery,
            scale = 1)

## so it can be used easily in a pipeline.
hearta %>%
  ntbt_pyears(Surv(stop/365.25, event) ~
                cut(age + 48, c(0,50,60,70,100)) + surgery,
              scale = 1)

## survConcordance
## Original function to interface
survConcordance(Surv(time, status) ~ age, data=lung)

## The interface reverses the order of data and formula
ntbt_survConcordance(data=lung, Surv(time, status) ~ age)

## so it can be used easily in a pipeline.
lung %>%
  ntbt_survConcordance(Surv(time, status) ~ age)

## survexp
## Original function to interface
fit1 <- survexp(futime ~ 1,data=jasa, 
                rmap=list(sex="male", year=accept.dt,   
                          age=(accept.dt-birth.dt)),
                method='conditional')
summary(fit1, times=1:10*182.5, scale=365)

## The interface reverses the order of data and formula
fit1 <- ntbt_survexp(data=jasa, futime ~ 1,
                  rmap=list(sex="male", year=accept.dt,   
                            age=(accept.dt-birth.dt)),
                  method='conditional')
summary(fit1, times=1:10*182.5, scale=365)

## so it can be used easily in a pipeline.
jasa %>%
  ntbt_survexp(futime ~ 1,
            rmap=list(sex="male", year=accept.dt,   
                      age=(accept.dt-birth.dt)),
            method='conditional') %>%
  summary(times=1:10*182.5, scale=365)

## survfit
## Original function to interface
survfit(Surv(time, status) ~ x, data = aml)

## The interface reverses the order of data and formula
ntbt_survfit(data = aml, Surv(time, status) ~ x)

## so it can be used easily in a pipeline.
aml %>%
  ntbt_survfit(Surv(time, status) ~ x)

aml %>%
  ntbt_survfit(Surv(time, status) ~ x) %>%
  plot(lty = 2:3)


## survreg
## Original function to interface
survreg(Surv(time, status) ~ ph.ecog + age + strata(sex), lung)

## The interface reverses the order of data and formula
ntbt_survreg(lung, Surv(time, status) ~ ph.ecog + age + strata(sex))

## so it can be used easily in a pipeline.
lung %>%
  ntbt_survreg(Surv(time, status) ~ ph.ecog + age + strata(sex))

## survSplit
## Original function to interface
vet2 <- survSplit(Surv(time, status) ~., veteran,
                  cut = c(60, 120), episode = "timegroup")
coxph(Surv(tstart, time, status) ~ karno*strata(timegroup) +
                age + trt, data = vet2)

## The interface reverses the order of data and formula
vet2 <- ntbt_survSplit(veteran, Surv(time, status) ~.,
                       cut = c(60, 120), episode = "timegroup")
ntbt_coxph(data = vet2, Surv(tstart, time, status) ~
           karno*strata(timegroup) + age + trt)

## so it can be used easily in a pipeline.
veteran %>%
  ntbt_survSplit(Surv(time, status) ~.,
                 cut = c(60, 120),
                 episode = "timegroup") %>%
  ntbt_coxph(Surv(tstart, time, status) ~ 
             karno*strata(timegroup) + age + trt)

## End(Not run)

rbertolusso/intubate documentation built on May 27, 2019, 3 a.m.