Nothing
##' @export
##'
summary.JMMLSM <- function(object, process = c("longitudinal", "survival"), digits = 4, ...) {
if (!inherits(object, "JMMLSM"))
stop("Use only with 'JMMLSM' objects.\n")
if (process == "longitudinal") {
##Estimates of betas
Estimate <- object$beta
SE <- object$sebeta
LowerLimit <- Estimate - 1.96 * SE
UpperLimit <- Estimate + 1.96 * SE
zval = (Estimate/SE)
pval = 2 * pnorm(-abs(zval))
out <- data.frame(Estimate, SE, LowerLimit, UpperLimit, pval)
out <- cbind(paste0("Mean_", rownames(out)), out)
rownames(out) <- NULL
colnames(out)[1] <- "Parameter"
##Estimates of tau
Estimate <- object$tau
SE <- object$setau
LowerLimit <- Estimate - 1.96 * SE
UpperLimit <- Estimate + 1.96 * SE
zval = (Estimate/SE)
pval = 2 * pnorm(-abs(zval))
out2 <- data.frame(Estimate, SE, LowerLimit, UpperLimit, pval)
out2 <- cbind(paste0("Var_", rownames(out2)), out2)
rownames(out2) <- NULL
colnames(out2)[1] <- "Parameter"
out3 <- rbind(out, out2)
rownames(out3) <- NULL
names(out3) <- c("Longitudinal", "coef", "SE", "95%Lower", "95%Upper", "p-values")
out3[, 2:ncol(out3)] <- round(out3[, 2:ncol(out3)], digits = digits)
out3[, ncol(out3)] <- format(out3[, ncol(out3)], scientific = FALSE)
return(out3)
} else if (process == "survival") {
##gamma
Estimate <- object$gamma1
SE <- object$segamma1
LowerLimit <- Estimate - 1.96 * SE
expLL <- exp(LowerLimit)
UpperLimit <- Estimate + 1.96 * SE
expUL <- exp(UpperLimit)
zval = (Estimate/SE)
pval = 2 * pnorm(-abs(zval))
out <- data.frame(Estimate, exp(Estimate), SE, LowerLimit, UpperLimit, expLL, expUL, pval)
out <- cbind(rownames(out), out)
rownames(out) <- NULL
colnames(out)[1] <- "Parameter"
if (object$CompetingRisk) {
Estimate <- object$gamma2
SE <- object$segamma2
LowerLimit <- Estimate - 1.96 * SE
expLL <- exp(LowerLimit)
UpperLimit <- Estimate + 1.96 * SE
expUL <- exp(UpperLimit)
zval = (Estimate/SE)
pval = 2 * pnorm(-abs(zval))
out2 <- data.frame(Estimate, exp(Estimate), SE, LowerLimit, UpperLimit, expLL, expUL, pval)
out2 <- cbind(rownames(out2), out2)
rownames(out2) <- NULL
colnames(out2)[1] <- "Parameter"
outgamma <- rbind(out, out2)
names(outgamma) <- c("Survival", "coef", "exp(coef)", "SE(coef)", "95%Lower", "95%Upper",
"95%exp(Lower)", "95%exp(Upper)", "p-values")
} else {
outgamma <- out
names(outgamma) <- c("Survival", "coef", "exp(coef)", "SE(coef)", "95%Lower", "95%Upper",
"95%exp(Lower)", "95%exp(Upper)", "p-values")
}
##alpha
Estimate <- object$alpha1
for (i in 1:length(Estimate)) names(Estimate)[i] <- paste0("alpha1_b", i-1)
SE <- object$sealpha1
LowerLimit <- Estimate - 1.96 * SE
expLL <- exp(LowerLimit)
UpperLimit <- Estimate + 1.96 * SE
expUL <- exp(UpperLimit)
zval = (Estimate/SE)
pval = 2 * pnorm(-abs(zval))
out <- data.frame(Estimate, exp(Estimate), SE, LowerLimit, UpperLimit, expLL, expUL, pval)
out <- cbind(rownames(out), out)
rownames(out) <- NULL
colnames(out)[1] <- "Parameter"
if (object$CompetingRisk) {
Estimate <- object$alpha2
for (i in 1:length(Estimate)) names(Estimate)[i] <- paste0("alpha2_b", i-1)
SE <- object$sealpha2
LowerLimit <- Estimate - 1.96 * SE
expLL <- exp(LowerLimit)
UpperLimit <- Estimate + 1.96 * SE
expUL <- exp(UpperLimit)
zval = (Estimate/SE)
pval = 2 * pnorm(-abs(zval))
out2 <- data.frame(Estimate, exp(Estimate), SE, LowerLimit, UpperLimit, expLL, expUL, pval)
out2 <- cbind(rownames(out2), out2)
rownames(out2) <- NULL
colnames(out2)[1] <- "Parameter"
outalpha <- rbind(out, out2)
names(outalpha) <- c("Survival", "coef", "exp(coef)", "SE(coef)", "95%Lower", "95%Upper",
"95%exp(Lower)", "95%exp(Upper)", "p-values")
} else {
outalpha <- out
names(outalpha) <- c("Survival", "coef", "exp(coef)", "SE(coef)", "95%Lower", "95%Upper",
"95%exp(Lower)", "95%exp(Upper)", "p-values")
}
#vee
Estimate <- object$vee1
names(Estimate) <- "alpha1_w0"
SE <- object$sevee1
LowerLimit <- Estimate - 1.96 * SE
expLL <- exp(LowerLimit)
UpperLimit <- Estimate + 1.96 * SE
expUL <- exp(UpperLimit)
zval = (Estimate/SE)
pval = 2 * pnorm(-abs(zval))
out <- data.frame(Estimate, exp(Estimate), SE, LowerLimit, UpperLimit, expLL, expUL, pval)
out <- cbind(rownames(out), out)
rownames(out) <- NULL
colnames(out)[1] <- "Parameter"
if (object$CompetingRisk) {
Estimate <- object$vee2
names(Estimate) <- "alpha2_w0"
SE <- object$sevee2
LowerLimit <- Estimate - 1.96 * SE
expLL <- exp(LowerLimit)
UpperLimit <- Estimate + 1.96 * SE
expUL <- exp(UpperLimit)
zval = (Estimate/SE)
pval = 2 * pnorm(-abs(zval))
out2 <- data.frame(Estimate, exp(Estimate), SE, LowerLimit, UpperLimit, expLL, expUL, pval)
out2 <- cbind(rownames(out2), out2)
rownames(out2) <- NULL
colnames(out2)[1] <- "Parameter"
outnu <- rbind(out, out2)
names(outnu) <- c("Survival", "coef", "exp(coef)", "SE(coef)", "95%Lower", "95%Upper",
"95%exp(Lower)", "95%exp(Upper)", "p-values")
} else {
names(out) <- c("Survival", "coef", "exp(coef)", "SE(coef)", "95%Lower", "95%Upper",
"95%exp(Lower)", "95%exp(Upper)", "p-values")
outnu <- out
}
out <- rbind(outgamma, outalpha, outnu)
out[, 2:ncol(out)] <- round(out[, 2:ncol(out)], digits = digits)
out[, ncol(out)] <- format(out[, ncol(out)], scientific = FALSE)
return(out)
}
}
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