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.  library(mets) options(warn=-1) set.seed(1000) # to control output in simulatins for p-values below. data(bmt) bmttime <- bmt$time+runif(nrow(bmt))*0.01 # logistic regresion with IPCW binomial regression out <- binreg(Event(time,cause)~tcell+platelet,bmt,time=50) summary(out)  We can also compute predictions using the estimates  predict(out,data.frame(tcell=c(0,1),platelet=c(1,1)),se=TRUE)  Further the censoring model can depend on strata  outs <- binreg(Event(time,cause)~tcell+platelet,bmt,time=50,cens.model=~strata(tcell,platelet)) summary(outs)  # Absolute risk differences and ratio Now for illustrations I wish to consider the absolute risk difference depending on tcell  outs <- binreg(Event(time,cause)~tcell,bmt,time=50,cens.model=~strata(tcell)) summary(outs)  the risk difference is ps <- predict(outs,data.frame(tcell=c(0,1)),se=TRUE) ps sum( c(1,-1) * ps[,1])  Getting the standard errors are easy enough since the two-groups are independent. In the case where we in addition had adjusted for other covariates, however, we would need the to apply the delta-theorem thus using the relevant covariances along the lines of dd <- data.frame(tcell=c(0,1)) p <- predict(outs,dd) riskdifratio <- function(p,contrast=c(1,-1)) { outs$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

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.

 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

sessionInfo()


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mets documentation built on Jan. 17, 2023, 5:12 p.m.