---
title: "Mediation Analysis for survival 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{Mediation Analysis for survival data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  #dev="png",
  comment = "#>"  
)
fullVignette <- Sys.getenv("_R_FULL_VIGNETTE_") %in% c("1","TRUE")
library(mets)
```

Overview 
========

We fit

 * binomial regression with IPCW: `binreg`
 * additive Lin-Ying model: `aalenMets`
 * Cox model: `phreg`
 * standard logistic regression via `binreg`

in the context of mediation analysis using mediation weights as in the `medFlex` package.
We thus fit natural effects models; for example, on the binary scale:
\begin{align*}
\mbox{logit}(P(Y(x,M(x^*))=1| Z)  = \beta_0+ \beta_1 x + \beta_2 x^* + \beta_3^T Z,
\end{align*}
In this case the Natural Direct Effect (NDE) for fixed covariates $Z$ is
\begin{align*}
 \mbox{OR}_{1,0|Z}^{\mbox{NDE}} = \frac{\mbox{odds}(Y(1,M(x))|Z)}{\mbox{odds}(Y(0,M(x))|Z)}  = \exp(\beta_1),
\end{align*}
and the Natural Indirect Effect (NIE) for fixed covariates $Z$ is
\begin{align*}
 \mbox{OR}_{1,0|Z}^{\mbox{NIE}} = \frac{\mbox{odds}(Y(x,M(1))|Z)}{\mbox{odds}(Y(x,M(0))|Z)} = \exp(\beta_2).
\end{align*}
See the `medFlex` package for additional discussion of the parametrisation.

The mediator can be:

 * binomial, using `glm` with family `binomial`.
 * multinomial, via the `mlogit` function in `mets`.

Both mediator and exposure must be coded as factors.

In the example below:

 * mediator: `gp.f`
 * exposure: `dnr.f`

The outcome model concerns the risk/hazard of cause 2.

Standard errors are computed using i.i.d. influence functions and a Taylor expansion to account for uncertainty in the
mediation weights.


Simulated Data 
==============

First we simulate data that mimics the dataset from Kumar et al. (2012),
which consists of multiple myeloma patients treated with allogeneic stem cell
transplantation from the Center for International Blood and Marrow Transplant Research
(CIBMTR). The data cover patients transplanted from 1995 to
2005, comparing outcomes between transplant periods: 2001--2005 ($N=488$)
versus 1995--2000 ($N=375$). The two competing events were
relapse (cause 2) and treatment-related mortality (TRM, cause 1),
defined as death without relapse.
Kumar et al. (2012) considered the following risk covariates:
transplant period (`gp`, the main variable of interest: 1 for 2001--2005, 0 for 1995--2000),
donor type (`dnr`: 1 for unrelated or other related donor ($N=280$), 0 for HLA-identical sibling ($N=584$)),
prior autologous transplant (`preauto`: 1 for auto+allo transplant ($N=399$), 0 for allogeneic alone ($N=465$)),
and time to transplant (`ttt24`: 1 for more than 24 months ($N=289$), 0 for 24 months or less ($N=575$)).

The interest is in the effect of transplant period (`gp`) and possible mediation
via the proportion of unrelated or related donors (`dnr`) — a somewhat artificial example.
All analyses are adjusted for other important confounders.

```{r}
 library(mets)
 runb <- 0
 options(warn=-1)
 set.seed(1000) # to control output in simulations for p-values below.

n <- 200; k.boot <- 10; 

dat <- kumarsimRCT(n,rho1=0.5,rho2=0.5,rct=2,censpar=c(0,0,0,0),
          beta = c(-0.67, 0.59, 0.55, 0.25, 0.98, 0.18, 0.45, 0.31),
    treatmodel = c(-0.18, 0.56, 0.56, 0.54),restrict=1)
dfactor(dat) <- dnr.f~dnr
dfactor(dat) <- gp.f~gp
drename(dat) <- ttt24~"ttt24*"
dat$id <- 1:n
dat$ftime <- 1
```


Mediation Weights
=================

We compute the mediation weights based on a model for the mediator:

```{r}
weightmodel <- fit <- glm(gp.f~dnr.f+preauto+ttt24,data=dat,family=binomial)
wdata <- medweight(fit,data=dat)
```

Binomial Regression 
===================

A simple multivariate regression of the probability of relapse at 50 months with both
exposure and mediator (given the other covariates):

```{r}
aaMss2 <- binreg(Event(time,status)~gp+dnr+preauto+ttt24+cluster(id),data=dat,time=50,cause=2)
summary(aaMss2)
```

Binomial regression IPCW Mediation Analysis
===========================================

We first look at the probability of relapse at 50 months:

```{r, label=firstmodel}
### binomial regression ###########################################################
aaMss <- binreg(Event(time,status)~dnr.f0+dnr.f1+preauto+ttt24+cluster(id),data=wdata,
		time=50,weights=wdata$weights,cause=2)
summary(aaMss)

ll <- mediatorSurv(aaMss,fit,data=dat,wdata=wdata)
summary(ll)
if (runb>0) { bll <- BootmediatorSurv(aaMss,fit,data=dat,k.boot=k.boot); summary(bll)}
```

The estimated NDE is $1.40$ (95% CI: $0.72$, $2.76$) and the NIE is $1.32$ (95% CI: $1.05$, $1.66$).

Mediation Analysis
====================

We illustrate how to use the other models mentioned above.

```{r, label=multiplemodels}
### lin-ying model ################################################################
aaMss <- aalenMets(Surv(time/100,status==2)~dnr.f0+dnr.f1+preauto+ttt24+cluster(id),data=wdata,
		   weights=wdata$weights)
ll <- mediatorSurv(aaMss,fit,data=dat,wdata=wdata)
summary(ll)
if (runb>0) { bll <- BootmediatorSurv(aaMss,fit,data=dat,k.boot=k.boot); summary(bll)}

### cox model ###############################################################################
aaMss <- phreg(Surv(time,status==2)~dnr.f0+dnr.f1+preauto+ttt24+cluster(id),data=wdata,
	       weights=wdata$weights)
summary(aaMss)
ll <- mediatorSurv(aaMss,fit,data=dat,wdata=wdata)
summary(ll)
if (runb>0) { bll <- BootmediatorSurv(aaMss,fit,data=dat,k.boot=k.boot); summary(bll)}

### Fine-Gray #############################################################3
aaMss <- cifreg(Event(time,status)~dnr.f0+dnr.f1+preauto+ttt24+cluster(id),data=wdata,
		weights=wdata$weights,propodds=NULL,cause=2)
summary(aaMss)
ll <- mediatorSurv(aaMss,fit,data=dat,wdata=wdata)
summary(ll)
if (runb>0) { bll <- BootmediatorSurv(aaMss,fit,data=dat,k.boot=k.boot); summary(bll)}

### logit model  #############################################################3
aaMss <- cifreg(Event(time,status)~dnr.f0+dnr.f1+preauto+ttt24+cluster(id),data=wdata,
		weights=wdata$weights,cause=2)
summary(aaMss)
ll <- mediatorSurv(aaMss,fit,data=dat,wdata=wdata)
summary(ll)
if (runb>0) { bll <- BootmediatorSurv(aaMss,fit,data=dat,k.boot=k.boot); summary(bll)}

### binomial outcome  ############################
aaMss <- binreg(Event(ftime,status)~dnr.f0+dnr.f1+preauto+ttt24+cluster(id),data=wdata,
		time=50,weights=wdata$weights,cens.weights=1,cause=2)
summary(aaMss)
ll <- mediatorSurv(aaMss,fit,data=dat,wdata=wdata)
summary(ll)
if (runb>0) { bll <- BootmediatorSurv(aaMss,fit,data=dat,k.boot=k.boot); summary(bll)}
```


Multinomial regression
======================

Also works with a mediator with more than two levels:

 * mediator: `wmi` in 4 categories
 * exposure: `age` in 4 categories

```{r, label=multinom, cache=TRUE, eval=fullVignette}
library(mets)
data(tTRACE)
dcut(tTRACE) <- ~. 

weightmodel <- fit <- mlogit(wmicat.4 ~agecat.4+vf+chf,data=tTRACE,family=binomial)
wdata <- medweight(fit,data=tTRACE)

aaMss <- binreg(Event(time,status)~agecat.40+ agecat.41+ vf+chf+cluster(id),data=wdata,
		time=7,weights=wdata$weights,cause=9)
summary(aaMss)
MultMed <- mediatorSurv(aaMss,fit,data=tTRACE,wdata=wdata)
summary(MultMed)
```

```{r  results="hide", echo=FALSE }
## To save time building the vignettes on CRAN, we cache time consuming computations
if (fullVignette) {
  MultMed[c('iid','iid.w','iid.surv')] <- NULL
  saveRDS(MultMed, "data/MultMed.rds")
} else {
  MultMed <- readRDS("data/MultMed.rds")
}
```

```{r}
summary(MultMed)
```

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


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