R/generic.R

In aftgee: Accelerated Failure Time Model with Generalized Estimating Equations

#' @export
#' @noRd
coef.aftsrr <- function(object, ...){
    z <- object
    if (!is.aftsrr(z)) stop("Most be aftsrr class")
    ans <- z["call"]
    out <- z$beta
    names(out) <- z$vari.name
    out
}

#' @export
#' @noRd
residuals.aftsrr <- function(object, ...){
    z <- object
    if (!is.aftsrr(z)) stop("Most be aftsrr class")
    ans <- z["call"]
    out <- log(z$y[,1]) - as.matrix(z$x) %*% z$beta
    out
}

#' @export
#' @noRd
vcov.aftsrr <- function(object, ...){
    z <- object
    if (!is.aftsrr(z)) stop("Most be aftsrr class")
    ans <- z["call"]
    var.meth <- z$var.meth[z$var.meth %in% c("MB", "ZLCF", "ZLMB", "sHCF", "sHMB", "ISCF", "ISMB", "js")]
    se.count <- length(var.meth)
    se.name <- match(var.meth, names(z$covmat))
    p <- length(z$beta)
    TAB.srr <- NULL
    out <- list(NULL)
    out[se.count + 1] <- NULL
    names(out) <- z$var.meth
    for (i in 1:se.count) {
        se.srr <- z$covmat[[se.name[i]]]
        rownames(se.srr) <- z$vari.name
        colnames(se.srr) <- z$vari.name
        out[[i]] <- se.srr
    }
    out
}

#' @export
#' @noRd
coef.aftgee <- function(object, ...){
    z <- object
    if (!is.aftgee(z)) stop("Most be aftgee class")
    ans <- z["call"]
    out <- z$coef.res
    out
}

#' @export
#' @noRd
vcov.aftgee <- function(object, ...){
    z <- object
    if (!is.aftgee(z)) stop("Most be aftgee class")
    ans <- z["call"]
    out <- z$var.res
    out
}

#' @export
#' @noRd
residuals.aftgee <- function(object, ...){
    z <- object
    if (!is.aftgee(z)) stop("Most be aftgee class")
    if ("(Intercept)" %in% attr(object$coef.res, "names"))
        z$data$x <- as.matrix(cbind(1, z$data$x))
    else z$data$x <- as.matrix(z$data$x)
    ans <- z["call"]
    out <- log(z$data$y) - z$data$x %*% z$coef.res
    out
}

#' @export
#' @noRd
predict.aftsrr <- function(object, newdata = NULL, se.fit = FALSE, type = "lp", ...){
    z <- object
    out <- NULL
    z$x <- as.matrix(z$x)
    if (is.null(newdata)) {
        out$fit <- as.numeric(z$x %*% z$beta)
        if (type == "response") {
            out$fit <- as.numeric(exp(out$fit))
        }
    }
    if (!is.null(newdata)) {
        newdata0 <- as.matrix(newdata, ncol = length(z$beta))
        out$fit <- as.numeric(newdata0 %*% z$beta)
        if (type == "response") {
            out$fit <- as.numeric(exp(out$fit))
        }
    }
    if (se.fit == TRUE) {
        var.meth <- z$var.meth[z$var.meth %in% c("MB", "ZLCF", "ZLMB", "sHCF", "sHMB", "ISCF", "ISMB", "js")]
        se.count <- length(var.meth)
        se.name <- match(var.meth, names(z$covmat))
        p <- length(z$beta)
        TAB.srr <- NULL
        var <- list(NULL)
        var[se.count + 1] <- NULL
        names(var) <- z$var.meth
        for (i in 1:se.count) {
            se.srr <- z$covmat[[se.name[i]]]
            if (is.null(newdata)) {
                var[[i]] <- as.numeric(sqrt(diag(z$x %*% se.srr %*% t(z$x))))
            }
            if (!is.null(newdata)) {
                var[[i]] <- as.numeric(sqrt(diag(newdata0 %*% se.srr %*% t(newdata0))))
            }
        }
        out$se.fit <- var
        if (type == "response") {
            out$se.fit <- lapply(out$se.fit, function(x) out$fit * x)
        }
    }
    out
}

#' @export
#' @noRd
predict.aftgee <- function(object, newdata = NULL, se.fit = FALSE, ...){
    z <- object
    out <- NULL
    if ("(Intercept)" %in% attr(object$coef.res, "names")) z$data$x <- as.matrix(cbind(1, z$data$x))
    else z$data$x <- as.matrix(z$data$x)
    if (!is.aftgee(z)) stop("Most be aftgee class")
    ans <- z["call"]
    if (is.null(newdata)) {
        out$fit <- exp(drop(z$data$x %*% z$coef.res)) # originally on log scale
        if (se.fit == TRUE) {
            out$se.fit <- sqrt(diag(z$data$x %*% z$var.res %*% t(z$data$x)))
        }
    }
    if (!is.null(newdata)) {
        newdata0 <- as.matrix(newdata, ncol = length(z$coef.res))
        if (z$intercept == TRUE & ncol(newdata0) < length(z$coef.res)) {
            newdata0 <- cbind(1, newdata0)
        }
        out$fit <- exp(drop(newdata0 %*% z$coef.res))
        if (se.fit == TRUE) {
            out$se.fit <- sqrt(diag(newdata0 %*% z$var.res %*% t(newdata0)))
        }
    }
    out
}