R/print.multivPenal.R
In socale/frailtypack: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
#' Print a Short Summary of parameter estimates of a multivariate frailty model
#'
#' Prints a short summary of parameter estimates of a multivariate frailty
#' model, or more generally an object of class 'multivPenal'.
#'
#'
#' @usage \method{print}{multivPenal}(x, digits = max(options()$digits - 4, 6),
#' ...)
#' @param x the result of a call to the multivPenal function
#' @param digits number of digits to print
#' @param \dots other unused arguments
#' @return
#'
#' Print, separately for each type of event (recurrent1, recurrent2 and
#' terminal), the parameter estimates of the survival or hazard functions.
#' @seealso \code{\link{multivPenal}}
#' @keywords methods multiv
##' @export
"print.multivPenal" <- function (x, digits = max(options()$digits - 4, 6), ...)
{
if (!is.null(cl <- x$call)){
cat("Call:\n")
dput(cl)
# if (x$type == "counting"){
# cat("\n left truncated structure used")
# }
if (x$AG == TRUE){
cat("\n Calendar timescale")
}
cat("\n")
}
if (!is.null(x$fail)) {
cat(" multivPenal failed.", x$fail, "\n")
return()
}
savedig <- options(digits = digits)
on.exit(options(savedig))
coef <- x$coef
nvar <- length(x$coef)
if (is.null(coef)){
x$varH<-matrix(x$varH)
x$varHIH<-matrix(x$varHIH)
}
#AD:
if (x$typeof == 0){
if (all(x$n.knots.temp < 4)){
cat("\n")
cat(" The minimum number of knots is 4","\n")
cat("\n")
}
if (all(x$n.knots.temp > 20)){
cat("\n")
cat(" The maximum number of knots is 20","\n")
}
}else{
if ((x$typeof == 1) & (x$indic.nb.int1 == 1)) cat(" The maximum number of time intervals nb.int[1] is 20","\n")
if ((x$typeof == 1) & (x$indic.nb.int2 == 1)) cat(" The maximum number of time intervals nb.int[2] is 20","\n")
if ((x$typeof == 1) & (x$indic.nb.int3 == 1)) cat(" The maximum number of time intervals nb.int[3] is 20","\n")
}
#AD
if (x$istop == 1){
if (!is.null(coef)){
seH <- sqrt(diag(x$varH))[-c(1,2)]
seHIH <- sqrt(diag(x$varHIH))[-c(1,2)]
if (x$typeof == 0){
tmp <- cbind(coef, exp(coef), seH, seHIH, coef/seH, ifelse(signif(1 - pchisq((coef/seH)^2, 1), digits - 1) == 0, "< 1e-16", signif(1 - pchisq((coef/seH)^2, 1), digits - 1)))
if(x$global_chisq.test==1) tmpwald <- cbind(x$global_chisq, x$dof_chisq, ifelse(x$p.global_chisq == 0, "< 1e-16", x$p.global_chisq))
if(x$global_chisq.test_d==1) tmpwalddc <- cbind(x$global_chisq_d, x$dof_chisq_d, ifelse(x$p.global_chisq_d == 0, "< 1e-16", x$p.global_chisq_d))
if(x$global_chisq.test2==1) tmpwald2 <- cbind(x$global_chisq2, x$dof_chisq2, ifelse(x$p.global_chisq2 == 0, "< 1e-16", x$p.global_chisq2))
}else{
tmp <- cbind(coef, exp(coef), seH, coef/seH, ifelse(signif(1 - pchisq((coef/seH)^2, 1), digits - 1) == 0, "< 1e-16", signif(1 - pchisq((coef/seH)^2, 1), digits - 1)))
if(x$global_chisq.test==1) tmpwald <- cbind(x$global_chisq, x$dof_chisq, ifelse(x$p.global_chisq == 0, "< 1e-16", x$p.global_chisq))
if(x$global_chisq.test_d==1) tmpwalddc <- cbind(x$global_chisq_d, x$dof_chisq_d, ifelse(x$p.global_chisq_d == 0, "< 1e-16", x$p.global_chisq_d))
if(x$global_chisq.test2==1) tmpwald2 <- cbind(x$global_chisq2, x$dof_chisq2, ifelse(x$p.global_chisq2 == 0, "< 1e-16", x$p.global_chisq2))
}
cat("\n")
cat(" Multivariate joint gaussian frailty model for two survival outcomes and a terminal event","\n")
if (x$typeof == 0){
cat(" using a Penalized Likelihood on the hazard function","\n")
}else{
cat(" using a Parametrical approach for the hazard function","\n")
}
if (x$typeof == 0){
if(x$global_chisq.test==1){
dimnames(tmpwald) <- list(x$names.factor,c("chisq", "df", "global p"))
}
if(x$global_chisq.test_d==1){
dimnames(tmpwalddc) <- list(x$names.factordc,c("chisq", "df", "global p"))
}
if(x$global_chisq.test2==1){
dimnames(tmpwald2) <- list(x$names.factor2,c("chisq", "df", "global p"))
}
dimnames(tmp) <- list(names(coef), c("coef", "exp(coef)",
"SE coef (H)", "SE coef (HIH)", "z", "p"))
}else{
if(x$global_chisq.test==1){
dimnames(tmpwald) <- list(x$names.factor,c("chisq", "df", "global p"))
}
if(x$global_chisq.test_d==1){
dimnames(tmpwalddc) <- list(x$names.factordc,c("chisq", "df", "global p"))
}
if(x$global_chisq.test2==1){
dimnames(tmpwald2) <- list(x$names.factor2,c("chisq", "df", "global p"))
}
dimnames(tmp) <- list(names(coef), c("coef", "exp(coef)",
"SE coef (H)", "z", "p"))
}
if (x$noVar[1] == 0){
cat("\n")
cat("Recurrences 1:\n")
cat("------------ \n")
prmatrix(tmp[1:x$nvar[1], ,drop=FALSE])
if(x$global_chisq.test==1){
cat("\n")
prmatrix(tmpwald)
}
}
cat("\n")
if (x$noVar[3] == 0){
cat("Recurrences 2:\n")
cat("------------- \n")
ntmp <- sum(x$nvar[1:2])
prmatrix(tmp[-c(1:ntmp), ,drop=FALSE])
if(x$global_chisq.test2==1){
cat("\n")
prmatrix(tmpwald2)
}
cat("\n")
if (x$noVar[2] == 0){
cat("Terminal event:\n")
cat("---------------- \n")
ntmp <- sum(x$nvar[1:2])
ntmp2 <- sum(x$nvar)
prmatrix(tmp[-c(1:x$nvar[1],(ntmp+1):ntmp2), ,drop=FALSE])
if(x$global_chisq.test_d==1){
cat("\n")
prmatrix(tmpwalddc)
}
cat("\n")
}
}
}
#theta
theta1 <- x$theta1
temp <- diag(x$varH)[1]
seH.theta1 <- sqrt(((2 * (theta1^0.5))^2) * temp)
temp <- diag(x$varHIH)[1]
seHIH.theta1 <- sqrt(((2 * (theta1^0.5))^2) * temp)
#eta
theta2 <- x$theta2
temp <- diag(x$varH)[2]
seH.theta2 <- sqrt(((2 * (theta2^0.5))^2) * temp)
temp <- diag(x$varHIH)[2]
seHIH.theta2 <- sqrt(((2 * (theta2^0.5))^2) * temp)
#AD:
if (x$noVar[1] == 1){
cat("\n")
cat(" Recurrences: No covariates \n")
cat(" ----------- \n")
}
if (x$noVar[2] == 1){
cat("\n")
cat(" Terminal event: No covariates \n")
cat(" -------------- \n")
cat("\n")
}
if (x$noVar[3] == 1){
cat("\n")
cat(" Recurrences2: No covariates \n")
cat(" ----------- \n")
}
#AD:
cat(" Parameters associated with Frailties: \n")
# if (x$typeof == 0){
# cat(" theta1 :", theta1, "(SE (H):", seH.theta1, ")", "(SE (HIH):", seHIH.theta1, ")", "\n")
# cat(" theta2 :", theta2, "(SE (H):", seH.theta2, ")", "(SE (HIH):", seHIH.theta2, ")", "\n")
# cat(" alpha1 :", x$alpha1, "(SE (H):", sqrt(diag(x$varH))[3], ")", "(SE (HIH):", sqrt(diag(x$varHIH))[3],")", "\n")
# cat(" alpha2 :", x$alpha2, "(SE (H):", sqrt(diag(x$varH))[4], ")", "(SE (HIH):", sqrt(diag(x$varHIH))[4],")", "\n")
# cat(" rho :", x$rho, "(SE (H):", sqrt(diag(x$varH))[5], ")", "(SE (HIH):", sqrt(diag(x$varHIH))[5],")", "\n")
# cat(" \n")
# }else{
# cat(" theta1 :", theta1, "(SE (H):", seH.theta1, ")", "\n")
# cat(" theta2 :", theta2, "(SE (H):", seH.theta2, ")", "\n")
# cat(" alpha1 :", x$alpha1, "(SE (H):", sqrt(diag(x$varH))[3], ")", "\n")
# cat(" alpha2 :", x$alpha2, "(SE (H):", sqrt(diag(x$varH))[4], ")", "\n")
# cat(" rho :", x$rho, "(SE (H):", sqrt(diag(x$varH))[5], ")", "\n")
# cat(" \n")
# }
cat(" theta1 :", theta1, "(SE (H):", seH.theta1, ")", "p =", ifelse(signif(1 - pnorm(theta1/seH.theta1), digits - 1) == 0, "< 1e-16", signif(1 - pnorm(theta1/seH.theta1))), "\n")
cat(" theta2 :", theta2, "(SE (H):", seH.theta2, ")", "p =", ifelse(signif(1 - pnorm(theta2/seH.theta2), digits - 1) == 0, "< 1e-16", signif(1 - pnorm(theta2/seH.theta2))), "\n")
cat(" alpha1 :", x$alpha1, "(SE (H):", sqrt(diag(x$varH))[3], ")", "p =", ifelse(signif(1 - pchisq((x$alpha1/sqrt(diag(x$varH))[3])^2,1) , digits - 1) == 0, "< 1e-16", signif(1 - pchisq((x$alpha1/sqrt(diag(x$varH))[3])^2,1) , digits - 1)), "\n")
cat(" alpha2 :", x$alpha2, "(SE (H):", sqrt(diag(x$varH))[4], ")", "p =", ifelse(signif(1 - pchisq((x$alpha2/sqrt(diag(x$varH))[4])^2,1), digits - 1) == 0, "< 1e-16", signif(1 - pchisq((x$alpha2/sqrt(diag(x$varH))[4])^2,1), digits - 1)), "\n")
cat(" rho :", x$rho, "(SE (H):", sqrt(diag(x$varH))[5], ")", "\n")
cat(" \n")
if (x$typeof == 0){
cat(paste(" penalized marginal log-likelihood =", round(x$logLikPenal,2)))
cat("\n")
cat(" LCV = the approximate likelihood cross-validation criterion\n")
cat(" in the semi parametric case =",x$LCV,"\n")
}else{
cat(paste(" marginal log-likelihood =", round(x$logLik,2)))
cat("\n")
# cat(" LCV = the approximate likelihood cross-validation criterion\n")
# cat(" in the parametric case =",x$LCV,"\n")
cat(" AIC = Aikaike information Criterion =",x$AIC,"\n")
cat("\n")
cat("The expression of the Aikaike Criterion is:","\n")
cat(" 'AIC = (1/n)[np - l(.)]'","\n")
if (x$typeof == 2){
cat("\n")
cat(" Scale for the weibull hazard function is :",round(x$scale.weib[1],2),round(x$scale.weib[2],2),round(x$scale.weib[3],2),"\n")
cat(" Shape for the weibull hazard function is :",round(x$shape.weib[1],2),round(x$shape.weib[2],2),round(x$shape.weib[3],2),"\n")
cat("\n")
cat("The expression of the Weibull hazard function is:","\n")
cat(" 'lambda(t) = (shape.(t^(shape-1)))/(scale^shape)'","\n")
cat("The expression of the Weibull survival function is:","\n")
cat(" 'S(t) = exp[- (t/scale)^shape]'")
cat("\n")
}
}
#AD:
cat("\n")
cat(" n=", x$n)
if (length(x$na.action)){
cat(" (", length(x$na.action), " observation deleted due to missing) \n")
}else{
cat("\n")
}
cat(" n recurrent events of type 1=", x$n.events, " n subjects=", x$groups)
cat("\n")
cat(" n recurrent events of type 2=", x$n.events2)
cat("\n")
cat(" n terminal events=", x$n.deaths)
cat("\n")
cat(" number of iterations: ", x$n.iter,"\n")
if ((x$typeof == 1) & (x$indic.nb.int1 == 1)){
cat(" Exact number of intervals recurrent of type 1 used for hazard: 20","\n")
}else{
if (x$typeof == 1) cat(" Exact number of intervals for recurrent of type 1 used for hazard: ",x$nbintervR,"\n")
}
if ((x$typeof == 1) & (x$indic.nb.int3 == 1)){
cat(" Exact number of intervals for recurrent of type 2 used for hazard: 20","\n")
}else{
if (x$typeof == 1) cat(" Exact number of intervals for recurrent of type 2 used for hazard: ",x$nbintervR2,"\n")
}
if ((x$typeof == 1) & (x$indic.nb.int2 == 1)){
cat(" Exact number of intervals for terminal event used for hazard: 20","\n")
}else{
if (x$typeof == 1) cat(" Exact number of intervals for terminal event used for hazard: ",x$nbintervDC,"\n")
}
if (x$typeof == 0){
cat("\n")
cat(" Exact number of knots used: ", x$n.knots[1]," ",x$n.knots[2]," ",x$n.knots[3], "\n")
cat(" Value of the smoothing parameters: ", x$kappa, sep=" ")
cat("\n")
}
}else{
if (!is.null(coef)){
cat("\n")
cat(" Multivariate joint gaussian frailty model for two survival outcomes and a terminal event","\n")
if (x$typeof == 0){
cat(" using a Penalized Likelihood on the hazard function","\n")
}else{
cat(" using a Parametrical approach for the hazard function","\n")
}
if (x$noVar[1] == 1){
cat("\n")
cat(" Recurrences: No covariates \n")
cat(" ----------- \n")
}
if (x$noVar[3] == 1){
cat("\n")
cat(" Recurrences 2: No covariates \n")
cat(" -------------- \n")
cat("\n")
}
if (x$noVar[2] == 1){
cat("\n")
cat(" Terminal event: No covariates \n")
cat(" -------------- \n")
cat("\n")
}
cat("\n")
cat(" n=", x$n)
if (length(x$na.action)){
cat(" (", length(x$na.action), " observation deleted due to missing) \n")
}else{
cat("\n")
}
cat(" n recurrent events of type 1=", x$n.events, " n subjects=", x$groups)
cat("\n")
cat(" n recurrent events of type 2 =", x$n.events2)
cat("\n")
cat(" n terminal events=", x$n.deaths)
cat("\n")
}
}
invisible()
}
socale/frailtypack documentation built on June 15, 2021, 3:37 a.m.
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#' Print a Short Summary of parameter estimates of a multivariate frailty model
#'
#' Prints a short summary of parameter estimates of a multivariate frailty
#' model, or more generally an object of class 'multivPenal'.
#'
#'
#' @usage \method{print}{multivPenal}(x, digits = max(options()$digits - 4, 6),
#' ...)
#' @param x the result of a call to the multivPenal function
#' @param digits number of digits to print
#' @param \dots other unused arguments
#' @return
#'
#' Print, separately for each type of event (recurrent1, recurrent2 and
#' terminal), the parameter estimates of the survival or hazard functions.
#' @seealso \code{\link{multivPenal}}
#' @keywords methods multiv
##' @export
"print.multivPenal" <- function (x, digits = max(options()$digits - 4, 6), ...)
{
if (!is.null(cl <- x$call)){
cat("Call:\n")
dput(cl)
# if (x$type == "counting"){
# cat("\n left truncated structure used")
# }
if (x$AG == TRUE){
cat("\n Calendar timescale")
}
cat("\n")
}
if (!is.null(x$fail)) {
cat(" multivPenal failed.", x$fail, "\n")
return()
}
savedig <- options(digits = digits)
on.exit(options(savedig))
coef <- x$coef
nvar <- length(x$coef)
if (is.null(coef)){
x$varH<-matrix(x$varH)
x$varHIH<-matrix(x$varHIH)
}
#AD:
if (x$typeof == 0){
if (all(x$n.knots.temp < 4)){
cat("\n")
cat(" The minimum number of knots is 4","\n")
cat("\n")
}
if (all(x$n.knots.temp > 20)){
cat("\n")
cat(" The maximum number of knots is 20","\n")
}
}else{
if ((x$typeof == 1) & (x$indic.nb.int1 == 1)) cat(" The maximum number of time intervals nb.int[1] is 20","\n")
if ((x$typeof == 1) & (x$indic.nb.int2 == 1)) cat(" The maximum number of time intervals nb.int[2] is 20","\n")
if ((x$typeof == 1) & (x$indic.nb.int3 == 1)) cat(" The maximum number of time intervals nb.int[3] is 20","\n")
}
#AD
if (x$istop == 1){
if (!is.null(coef)){
seH <- sqrt(diag(x$varH))[-c(1,2)]
seHIH <- sqrt(diag(x$varHIH))[-c(1,2)]
if (x$typeof == 0){
tmp <- cbind(coef, exp(coef), seH, seHIH, coef/seH, ifelse(signif(1 - pchisq((coef/seH)^2, 1), digits - 1) == 0, "< 1e-16", signif(1 - pchisq((coef/seH)^2, 1), digits - 1)))
if(x$global_chisq.test==1) tmpwald <- cbind(x$global_chisq, x$dof_chisq, ifelse(x$p.global_chisq == 0, "< 1e-16", x$p.global_chisq))
if(x$global_chisq.test_d==1) tmpwalddc <- cbind(x$global_chisq_d, x$dof_chisq_d, ifelse(x$p.global_chisq_d == 0, "< 1e-16", x$p.global_chisq_d))
if(x$global_chisq.test2==1) tmpwald2 <- cbind(x$global_chisq2, x$dof_chisq2, ifelse(x$p.global_chisq2 == 0, "< 1e-16", x$p.global_chisq2))
}else{
tmp <- cbind(coef, exp(coef), seH, coef/seH, ifelse(signif(1 - pchisq((coef/seH)^2, 1), digits - 1) == 0, "< 1e-16", signif(1 - pchisq((coef/seH)^2, 1), digits - 1)))
if(x$global_chisq.test==1) tmpwald <- cbind(x$global_chisq, x$dof_chisq, ifelse(x$p.global_chisq == 0, "< 1e-16", x$p.global_chisq))
if(x$global_chisq.test_d==1) tmpwalddc <- cbind(x$global_chisq_d, x$dof_chisq_d, ifelse(x$p.global_chisq_d == 0, "< 1e-16", x$p.global_chisq_d))
if(x$global_chisq.test2==1) tmpwald2 <- cbind(x$global_chisq2, x$dof_chisq2, ifelse(x$p.global_chisq2 == 0, "< 1e-16", x$p.global_chisq2))
}
cat("\n")
cat(" Multivariate joint gaussian frailty model for two survival outcomes and a terminal event","\n")
if (x$typeof == 0){
cat(" using a Penalized Likelihood on the hazard function","\n")
}else{
cat(" using a Parametrical approach for the hazard function","\n")
}
if (x$typeof == 0){
if(x$global_chisq.test==1){
dimnames(tmpwald) <- list(x$names.factor,c("chisq", "df", "global p"))
}
if(x$global_chisq.test_d==1){
dimnames(tmpwalddc) <- list(x$names.factordc,c("chisq", "df", "global p"))
}
if(x$global_chisq.test2==1){
dimnames(tmpwald2) <- list(x$names.factor2,c("chisq", "df", "global p"))
}
dimnames(tmp) <- list(names(coef), c("coef", "exp(coef)",
"SE coef (H)", "SE coef (HIH)", "z", "p"))
}else{
if(x$global_chisq.test==1){
dimnames(tmpwald) <- list(x$names.factor,c("chisq", "df", "global p"))
}
if(x$global_chisq.test_d==1){
dimnames(tmpwalddc) <- list(x$names.factordc,c("chisq", "df", "global p"))
}
if(x$global_chisq.test2==1){
dimnames(tmpwald2) <- list(x$names.factor2,c("chisq", "df", "global p"))
}
dimnames(tmp) <- list(names(coef), c("coef", "exp(coef)",
"SE coef (H)", "z", "p"))
}
if (x$noVar[1] == 0){
cat("\n")
cat("Recurrences 1:\n")
cat("------------ \n")
prmatrix(tmp[1:x$nvar[1], ,drop=FALSE])
if(x$global_chisq.test==1){
cat("\n")
prmatrix(tmpwald)
}
}
cat("\n")
if (x$noVar[3] == 0){
cat("Recurrences 2:\n")
cat("------------- \n")
ntmp <- sum(x$nvar[1:2])
prmatrix(tmp[-c(1:ntmp), ,drop=FALSE])
if(x$global_chisq.test2==1){
cat("\n")
prmatrix(tmpwald2)
}
cat("\n")
if (x$noVar[2] == 0){
cat("Terminal event:\n")
cat("---------------- \n")
ntmp <- sum(x$nvar[1:2])
ntmp2 <- sum(x$nvar)
prmatrix(tmp[-c(1:x$nvar[1],(ntmp+1):ntmp2), ,drop=FALSE])
if(x$global_chisq.test_d==1){
cat("\n")
prmatrix(tmpwalddc)
}
cat("\n")
}
}
}
#theta
theta1 <- x$theta1
temp <- diag(x$varH)[1]
seH.theta1 <- sqrt(((2 * (theta1^0.5))^2) * temp)
temp <- diag(x$varHIH)[1]
seHIH.theta1 <- sqrt(((2 * (theta1^0.5))^2) * temp)
#eta
theta2 <- x$theta2
temp <- diag(x$varH)[2]
seH.theta2 <- sqrt(((2 * (theta2^0.5))^2) * temp)
temp <- diag(x$varHIH)[2]
seHIH.theta2 <- sqrt(((2 * (theta2^0.5))^2) * temp)
#AD:
if (x$noVar[1] == 1){
cat("\n")
cat(" Recurrences: No covariates \n")
cat(" ----------- \n")
}
if (x$noVar[2] == 1){
cat("\n")
cat(" Terminal event: No covariates \n")
cat(" -------------- \n")
cat("\n")
}
if (x$noVar[3] == 1){
cat("\n")
cat(" Recurrences2: No covariates \n")
cat(" ----------- \n")
}
#AD:
cat(" Parameters associated with Frailties: \n")
# if (x$typeof == 0){
# cat(" theta1 :", theta1, "(SE (H):", seH.theta1, ")", "(SE (HIH):", seHIH.theta1, ")", "\n")
# cat(" theta2 :", theta2, "(SE (H):", seH.theta2, ")", "(SE (HIH):", seHIH.theta2, ")", "\n")
# cat(" alpha1 :", x$alpha1, "(SE (H):", sqrt(diag(x$varH))[3], ")", "(SE (HIH):", sqrt(diag(x$varHIH))[3],")", "\n")
# cat(" alpha2 :", x$alpha2, "(SE (H):", sqrt(diag(x$varH))[4], ")", "(SE (HIH):", sqrt(diag(x$varHIH))[4],")", "\n")
# cat(" rho :", x$rho, "(SE (H):", sqrt(diag(x$varH))[5], ")", "(SE (HIH):", sqrt(diag(x$varHIH))[5],")", "\n")
# cat(" \n")
# }else{
# cat(" theta1 :", theta1, "(SE (H):", seH.theta1, ")", "\n")
# cat(" theta2 :", theta2, "(SE (H):", seH.theta2, ")", "\n")
# cat(" alpha1 :", x$alpha1, "(SE (H):", sqrt(diag(x$varH))[3], ")", "\n")
# cat(" alpha2 :", x$alpha2, "(SE (H):", sqrt(diag(x$varH))[4], ")", "\n")
# cat(" rho :", x$rho, "(SE (H):", sqrt(diag(x$varH))[5], ")", "\n")
# cat(" \n")
# }
cat(" theta1 :", theta1, "(SE (H):", seH.theta1, ")", "p =", ifelse(signif(1 - pnorm(theta1/seH.theta1), digits - 1) == 0, "< 1e-16", signif(1 - pnorm(theta1/seH.theta1))), "\n")
cat(" theta2 :", theta2, "(SE (H):", seH.theta2, ")", "p =", ifelse(signif(1 - pnorm(theta2/seH.theta2), digits - 1) == 0, "< 1e-16", signif(1 - pnorm(theta2/seH.theta2))), "\n")
cat(" alpha1 :", x$alpha1, "(SE (H):", sqrt(diag(x$varH))[3], ")", "p =", ifelse(signif(1 - pchisq((x$alpha1/sqrt(diag(x$varH))[3])^2,1) , digits - 1) == 0, "< 1e-16", signif(1 - pchisq((x$alpha1/sqrt(diag(x$varH))[3])^2,1) , digits - 1)), "\n")
cat(" alpha2 :", x$alpha2, "(SE (H):", sqrt(diag(x$varH))[4], ")", "p =", ifelse(signif(1 - pchisq((x$alpha2/sqrt(diag(x$varH))[4])^2,1), digits - 1) == 0, "< 1e-16", signif(1 - pchisq((x$alpha2/sqrt(diag(x$varH))[4])^2,1), digits - 1)), "\n")
cat(" rho :", x$rho, "(SE (H):", sqrt(diag(x$varH))[5], ")", "\n")
cat(" \n")
if (x$typeof == 0){
cat(paste(" penalized marginal log-likelihood =", round(x$logLikPenal,2)))
cat("\n")
cat(" LCV = the approximate likelihood cross-validation criterion\n")
cat(" in the semi parametric case =",x$LCV,"\n")
}else{
cat(paste(" marginal log-likelihood =", round(x$logLik,2)))
cat("\n")
# cat(" LCV = the approximate likelihood cross-validation criterion\n")
# cat(" in the parametric case =",x$LCV,"\n")
cat(" AIC = Aikaike information Criterion =",x$AIC,"\n")
cat("\n")
cat("The expression of the Aikaike Criterion is:","\n")
cat(" 'AIC = (1/n)[np - l(.)]'","\n")
if (x$typeof == 2){
cat("\n")
cat(" Scale for the weibull hazard function is :",round(x$scale.weib[1],2),round(x$scale.weib[2],2),round(x$scale.weib[3],2),"\n")
cat(" Shape for the weibull hazard function is :",round(x$shape.weib[1],2),round(x$shape.weib[2],2),round(x$shape.weib[3],2),"\n")
cat("\n")
cat("The expression of the Weibull hazard function is:","\n")
cat(" 'lambda(t) = (shape.(t^(shape-1)))/(scale^shape)'","\n")
cat("The expression of the Weibull survival function is:","\n")
cat(" 'S(t) = exp[- (t/scale)^shape]'")
cat("\n")
}
}
#AD:
cat("\n")
cat(" n=", x$n)
if (length(x$na.action)){
cat(" (", length(x$na.action), " observation deleted due to missing) \n")
}else{
cat("\n")
}
cat(" n recurrent events of type 1=", x$n.events, " n subjects=", x$groups)
cat("\n")
cat(" n recurrent events of type 2=", x$n.events2)
cat("\n")
cat(" n terminal events=", x$n.deaths)
cat("\n")
cat(" number of iterations: ", x$n.iter,"\n")
if ((x$typeof == 1) & (x$indic.nb.int1 == 1)){
cat(" Exact number of intervals recurrent of type 1 used for hazard: 20","\n")
}else{
if (x$typeof == 1) cat(" Exact number of intervals for recurrent of type 1 used for hazard: ",x$nbintervR,"\n")
}
if ((x$typeof == 1) & (x$indic.nb.int3 == 1)){
cat(" Exact number of intervals for recurrent of type 2 used for hazard: 20","\n")
}else{
if (x$typeof == 1) cat(" Exact number of intervals for recurrent of type 2 used for hazard: ",x$nbintervR2,"\n")
}
if ((x$typeof == 1) & (x$indic.nb.int2 == 1)){
cat(" Exact number of intervals for terminal event used for hazard: 20","\n")
}else{
if (x$typeof == 1) cat(" Exact number of intervals for terminal event used for hazard: ",x$nbintervDC,"\n")
}
if (x$typeof == 0){
cat("\n")
cat(" Exact number of knots used: ", x$n.knots[1]," ",x$n.knots[2]," ",x$n.knots[3], "\n")
cat(" Value of the smoothing parameters: ", x$kappa, sep=" ")
cat("\n")
}
}else{
if (!is.null(coef)){
cat("\n")
cat(" Multivariate joint gaussian frailty model for two survival outcomes and a terminal event","\n")
if (x$typeof == 0){
cat(" using a Penalized Likelihood on the hazard function","\n")
}else{
cat(" using a Parametrical approach for the hazard function","\n")
}
if (x$noVar[1] == 1){
cat("\n")
cat(" Recurrences: No covariates \n")
cat(" ----------- \n")
}
if (x$noVar[3] == 1){
cat("\n")
cat(" Recurrences 2: No covariates \n")
cat(" -------------- \n")
cat("\n")
}
if (x$noVar[2] == 1){
cat("\n")
cat(" Terminal event: No covariates \n")
cat(" -------------- \n")
cat("\n")
}
cat("\n")
cat(" n=", x$n)
if (length(x$na.action)){
cat(" (", length(x$na.action), " observation deleted due to missing) \n")
}else{
cat("\n")
}
cat(" n recurrent events of type 1=", x$n.events, " n subjects=", x$groups)
cat("\n")
cat(" n recurrent events of type 2 =", x$n.events2)
cat("\n")
cat(" n terminal events=", x$n.deaths)
cat("\n")
}
}
invisible()
}
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