---
title: "Binomial Regression for Survival and Competing Risks Data"
author: Klaus Holst & Thomas Scheike
date: "`r Sys.Date()`"
output:
  rmarkdown::html_vignette:
    fig_caption: yes
    fig_width: 7.15
    fig_height: 5.5 
vignette: >
  %\VignetteIndexEntry{Binomial Regression for Survival and Competing Risks Data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(mets)
```

Binomial Regression for censored data 
=====================================

The binreg function does direct binomial regression for one time-point, $t$, 
fitting the model 
\begin{align*}
P(T \leq t, \epsilon=1 | X )  & = \mbox{expit}( X^T \beta) 
\end{align*}
the estimation is based on IPCW weighted EE
\begin{align*}
 U(\beta) = &  X ( \Delta(t) I(T \leq t, \epsilon=1 )/G_c(T_i- \wedge t) - \mbox{expit}( X^T \beta)) = 0 
\end{align*}
for IPCW adjusted responses and with $\Delta$ indicator of death and $G_c$ censoring survival
distribution. With $\Delta(t) = I( C_i > T_i \wedge t)$. 

The function logitIPCW instead considers 
\begin{align*}
 U(\beta) = &  X  \Delta(t) /G_c(T_i- \wedge t) ( I(T \leq t, \epsilon=1 ) - \mbox{expit}( X^T \beta)) = 0.
\end{align*}
The two score equations are quite similar, and exactly the same when the censoring model is fully-nonparametric.

Additional functions logitATE, and binregATE computes the average treatment effect, the average effect on treated (ATT), and 
the average effect on non-treated (ATC). We demonstrate this in another vignette. 

The function logitATE also works when there is no censoring and we thus have simple binary outcome. 

Variance is based on  sandwich formula with IPCW adjustment, and naive.var is variance 
under known censoring model. The influence functions are stored in the output. 


```{r}
 library(mets)
 options(warn=-1)
 set.seed(1000) # to control output in simulatins for p-values below.

 data(bmt)
 bmt$time <- bmt$time+runif(nrow(bmt))*0.01
 # logistic regresion with IPCW binomial regression 
 out <- binreg(Event(time,cause)~tcell+platelet,bmt,time=50)
 summary(out)
```

We can also compute predictions using the estimates 
```{r}
 predict(out,data.frame(tcell=c(0,1),platelet=c(1,1)),se=TRUE)
```

Further the censoring model can depend on strata 

```{r}
 outs <- binreg(Event(time,cause)~tcell+platelet,bmt,time=50,cens.model=~strata(tcell,platelet))
 summary(outs)
```

Absolute risk differences and ratio
===================================

Now for illustrations I wish to consider the absolute risk difference
depending on tcell 

```{r}
 outs <- binreg(Event(time,cause)~tcell,bmt,time=50,cens.model=~strata(tcell))
 summary(outs)
```

the risk difference is 

```{r}
ps <-  predict(outs,data.frame(tcell=c(0,1)),se=TRUE)
ps
sum( c(1,-1) * ps[,1])
```

Getting the standard errors are easy enough since the two-groups are
independent. In the case where we in addition had adjusted for other covariates, however, we would need 
the to apply the delta-theorem thus using the relevant covariances along the lines of 

```{r}
dd <- data.frame(tcell=c(0,1))
p <- predict(outs,dd)

riskdifratio <- function(p,contrast=c(1,-1)) {
   outs$coef <- p
   p <- predict(outs,dd)[,1]
   pd <- sum(contrast*p)
   r1 <- p[1]/p[2]
   r2 <- p[2]/p[1]
   return(c(pd,r1,r2))
}
     
estimate(outs,f=riskdifratio,dd,null=c(0,1,1))
```

same as 

```{r}
run <- 0
if (run==1) {
library(prodlim)
pl <- prodlim(Hist(time,cause)~tcell,bmt)
spl <- summary(pl,times=50,asMatrix=TRUE)
spl
}
```


Augmenting the Binomial Regression 
===================================

Rather than using a larger censoring model we can also compute an  augmentation term and
then fit the binomial regression model based on this augmentation term. 
Here we compute the augmentation based on stratified non-parametric estimates of $F_1(t,S(X))$, 
where $S(X)$ gives strata based on $X$ as a working model. 

 Computes  the augmentation term for each individual as well as the sum
\begin{align*}
 A & = \int_0^t H(u,X) \frac{1}{S^*(u,s)} \frac{1}{G_c(u)} dM_c(u)
\end{align*}
 with 
\begin{align*}
 H(u,X) & = F_1^*(t,S(X)) - F_1^*(u,S(X))
\end{align*}
using a KM for $G_c(t)$ and a working model for cumulative baseline
related to $F_1^*(t,s)$ and $s$ is strata, $S^*(t,s) = 1 - F_1^*(t,s) - F_2^*(t,s)$. 

 Standard errors computed under assumption of correct but estimated $G_c(s)$ model.

```{r}
 data(bmt)
 dcut(bmt,breaks=2) <- ~age 
 out1<-BinAugmentCifstrata(Event(time,cause)~platelet+agecat.2+
			  strata(platelet,agecat.2),data=bmt,cause=1,time=40)
 summary(out1)

 out2<-BinAugmentCifstrata(Event(time,cause)~platelet+agecat.2+
     strata(platelet,agecat.2)+strataC(platelet),data=bmt,cause=1,time=40)
 summary(out2)
```


SessionInfo
============

```{r}
sessionInfo()
```