README.md

In fei-heng/cmprskPH: Cause-specific proportional hazards model for competing risks analysis

Cause-specific proportional hazards model for competing risks analysis (cmprskPH)

Authors: Fei Heng ([e-mail]), Yanqing Sun ([e-mail]), and Peter B. Gilbert

R package for the paper `Estimation and Hypothesis Testing of Strain-Specific Vaccine Efficacy Adjusted for Covariate Effects with Missing Causes'

Installation

Requires Rtools on windows and development tools (+Xcode) for Mac OS X: ```{r eval=F} devtools::install_github("fei-heng/cmprskPH")

## Code Examples
### Example 1: for 2 causes
```{r eval=F}
library(cmprskPH)

## Approach 1
data(sim2cs)
res.aipw <- markPH.aipw(cmprskPHformula=cbind(time,delta,cause)~z1+z2,
            trtpos=1,
            strata="strata",
            missformula=~z1+A,
            markformula=~time+z1+A,
            data=sim2cs,
            VEnull=0.3,
            maxit=15)
res.aipw # print the result

res.ipw <- markPH.ipw(cmprskPHformula=cbind(time,delta,cause)~z1+z2,
                   trtpos=1,
                   strata="strata",
                   missformula=~z1+A,
                   data=sim2cs,
                   VEnull=0.3,
                   maxit=15)
res.ipw # print the result

## Approach 2
data(sim2cs)
threshold <- 0.5
sim2cs$cause[(sim2cs$delta==1)&(sim2cs$A<threshold)] <- 3

res.aipw2 <- markPH.aipw2(cmprskPHformula=cbind(time,delta,cause)~z1+z2,
            trtpos=1,
            strata="strata",
            causelevels=c(1,2,3),
            missmodel=c(T,T,F),
            missformula=~z1+A,
            markformula=~time+z1+A,
            data=sim2cs,
            VEnull=0.3,
            maxit=15)
res.aipw2

res.ipw2 <- markPH.ipw2(cmprskPHformula=cbind(time,delta,cause)~z1+z2,
                   trtpos=1,
                   strata="strata",
                   causelevels=c(1,2,3),
                   missmodel=c(T,T,F),
                   missformula=~z1+A,
                   data=sim2cs,
                   VEnull=0.3,
                   maxit=15)
res.ipw2

Example 2: for 3 causes

```{r eval=F} library(cmprskPH)

Approach 1

data(sim3cs) res.aipw <- markPH.aipw(cmprskPHformula=cbind(time,delta,cause)~z1+z2, trtpos=1, strata="strata", missformula=~z1+A, markformula=~time+z1+A, data=sim3cs, VEnull=0.3, maxit=15) res.aipw

res.ipw <- markPH.ipw(cmprskPHformula=cbind(time,delta,cause)~z1+z2, trtpos=1, strata="strata", missformula=~z1+A, data=sim3cs, VEnull=0.3, maxit=15) res.ipw

Approach 2

data(sim3cs) threshold <- 0.5 sim3cs$cause[(sim3cs$delta==1)&(sim3cs$A<threshold)] <- 4

res.aipw2 <- markPH.aipw2(cmprskPHformula=cbind(time,delta,cause)~z1+z2, trtpos=1, strata="strata", causelevels=c(1,2,3,4), missmodel=c(T,T,T,F), missformula=~z1+A, markformula=~time+z1+A, data=sim3cs, VEnull=0.3, maxit=15) res.aipw2

res.ipw2 <- markPH.ipw2(cmprskPHformula=cbind(time,delta,cause)~z1+z2, trtpos=1, strata="strata", causelevels=c(1,2,3,4), missmodel=c(T,T,T,F), missformula=~z1+A, data=sim3cs, VEnull=0.3, maxit=15) res.ipw2 ```

fei-heng/cmprskPH documentation built on May 24, 2023, 3:54 p.m.