R/getInfluenceCurve.Brier.R

In tagteam/riskRegression: Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

### getInfluenceCurve.Brier.R --- 
#----------------------------------------------------------------------
## Author: Thomas Alexander Gerds
## Created: Jun  4 2024 (11:46) 
## Version: 
## Last-Updated: Jun 25 2024 (13:01) 
##           By: Thomas Alexander Gerds
##     Update #: 14
#----------------------------------------------------------------------
## 
### Commentary: 
##
## Compute influence function of Brier score estimator using weights of the reverse Cox model
## This function evaluates the part of influence function which is related to the IPCW weights
## The other part is IC0.
##
## \frac{1}{n}\sum_{i=1}^n
## m_{t,n}^{(1)}(X_i)
## [\frac{I_{T_i\leq t}\Delta_i}{G^2(T_i\vert Z_i)}IF_G(T_i,X_k; X_i)+\frac{I_{T_i>t}}{G^2(t|Z_i)}IF_G(t,X_k; X_i)]
## with
## IF_G(t,X_k; X_i)=-\exp(-\Lambda(t\vert Z_i))IF_{\Lambda}(t,X_k; X_i)
##
## IC_G(t,z;x_k) is an array with dimension (nlearn=N, gtimes, newdata)
## where gtimes = subject.times (Weights$IC$IC.subject) or times (Weights$IC$IC.times)
## and subject.times=Y[(((Y<=max(times))*status)==1)]
##
## don't square the weights because they will be multiplied with the
## residuals that are already weighted
##
### Change Log:
#----------------------------------------------------------------------
## 
### Code:
getInfluenceCurve.Brier <- function(t,
                                    time,
                                    IC0,
                                    residuals,
                                    IC.G,
                                    cens.model,
                                    nth.times=NULL,
                                    conservative,
                                    event){
    if (is.unsorted(time)){
        stop("Internal error. Time is not sorted in ascending order. ")
    }
    N <- length(residuals)
    if (conservative[[1]] || cens.model[[1]] == "none"){
        IC0
    }
    else if (cens.model[[1]]=="cox") {## Cox regression
        if (!IC.G$censoring.save.memory){
            ic.weights <- IC.G[["IC.weights"]][[nth.times]]
            IF.Brier <- IC0+as.numeric(rowSumsCrossprod(as.matrix(residuals),ic.weights,0)) / N
        }
        else {
            wdata <- IC.G[["wdata"]]
            fit <- IC.G[["fit"]]
            TiMinus <- IC.G[["TiMinus"]]
            res1 <- (time <= t & event != 0)*residuals
            res2 <- (time > t)*residuals
            IF.Brier <- IC0 + (predictCoxWeights(fit,newdata = wdata,times = TiMinus,diag=TRUE,weights=res1,isBeforeTau = TRUE, tau=t) + predictCoxWeights(fit,newdata = wdata,times = t,diag=FALSE,weights=res2,isBeforeTau = FALSE, tau=t))/N
        }
        IF.Brier
    }else if (cens.model[[1]] == "KaplanMeier"){
        IC0 + getInfluenceFunctionBrierKMCensoringTerm(t,time,residuals,event)
    }
    else {
        stop("Non conservative options with cens.model not being a Cox model or KaplanMeier are not implemented. ")
    }
}


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### getInfluenceCurve.Brier.R ends here