R/coef.ate.R

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

### coef.ate.R --- 
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## Author: Brice Ozenne
## Created: Oct 16 2024 (11:47) 
## Version: 
## Last-Updated: Oct 16 2024 (11:47) 
##           By: Brice Ozenne
##     Update #: 2
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### Commentary: 
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### Change Log:
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### Code:

## * coef.ate (documentation)
##' @title Estimated Average Treatment Effect.
##' @description Estimated average treatment effect.
##'
##' @param object A \code{ate} object, i.e. output of the \code{ate} function.
##' @param contrasts [character vector] levels of the treatment variable for which the estimates should be assessed or compared. Default is to consider all levels.
##' @param times [numeric vector] The timepoints at which the estimates should be displayed. Default is to consider all timepoints.
##' @param estimator [character] The type of estimator relative to which the estimates should be displayed. 
##' @param type [character] should the average risk per treatment be displayed (\code{"meanRisk"}),
##' or the difference in average risk between any two pairs of treatments (\code{"diffRisk"}),
##' or the ratio in average risk between any two pairs of treatments (\code{"ratioRisk"}).
##' @param ... Not used. For compatibility with the generic method.
##'
##' @return A numeric vector.
##' 
##' @author Brice Ozenne \email{broz@@sund.ku.dk}

## * coef.ate (code)
##' @export
coef.ate <- function(object, contrasts = NULL, times = NULL, estimator = NULL, type = NULL, ...){

    ## *** normalize user input
    if(is.null(estimator)){
        estimator <- object$estimator[1]
    }else{
        estimator <- match.arg(estimator, object$estimator)
    }
    if(is.null(contrasts)){
        contrasts <- object$contrasts
    }else{
        contrasts.original <- contrasts
        contrasts <- match.arg(contrasts, object$contrasts, several.ok = TRUE)
        if(length(contrasts.original)!=length(contrasts)){
            stop("Unknown value ",paste(setdiff(contrasts.original,object$contrasts), collapse = ", ")," in argument \'contrasts\'. \n",
                 "Valid values: ",paste(object$contrasts, collapse = ", "),". \n")
        }
    }
    if(is.null(times)){
        times <- object$eval.times
    }else{
        if(any(times %in% object$eval.times == FALSE)){
            stop("Unknown timepoint ",paste(setdiff(times,object$eval.times), collapse = ", ")," in argument \'times\'. \n",
                 "Valid timepoints: ",paste(object$eval.times, collapse = ", "),". \n")
        }
    }
    if(is.null(type)){
        type <- "meanRisk"
    }else{
        type <- match.arg(type, c("meanRisk","diffRisk","ratioRisk"))
    }

    dots <- list(...)
    if(length(dots)>0){
        stop("Unknown argument(s) \'",paste(names(dots),collapse="\' \'"),"\'. \n")
    }

    ## *** extract
    object.table1 <- object[[type]][object[[type]]$estimator==estimator,,drop=FALSE]
    out.times <- object.table1$time %in% times
    
    if(type == "meanRisk"){
        out <- setNames(object.table1$estimate, paste0(object.table1$treatment,"(t=",object.table1$time,")"))
        out.contrasts <- object.table1$treatment %in% contrasts
    }else if(type == "diffRisk"){
        out <-setNames(object.table1$estimate, paste0(object.table1$B,"-",object.table1$A,"(t=",object.table1$time,")"))
        out.contrasts <- (object.table1$B %in% contrasts) & (object.table1$A %in% contrasts)
    }else if(type == "ratioRisk"){
        out <- setNames(object.table1$estimate, paste0(object.table1$B,"/",object.table1$A,"(t=",object.table1$time,")"))
        out.contrasts <- (object.table1$B %in% contrasts) & (object.table1$A %in% contrasts)
    }

    ## *** export
    return(out[out.times & out.contrasts])
}


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### coef.ate.R ends here