Fix code for print_priors

Author: giabaio

R/print.survHE.R

@@ -13,8 +13,8 @@
 #' significant digits to be shown in the summary table (default = 6);
 #' \code{original} = a flag to say whether the *original* table
 #' from either \code{flexsurv} or \code{INLA} or \code{rstan} should be printed;
-#' \code{print_priors} = a flag to sy whether the Stan table should also 
-#' include a summary of the prior used in the HMC model
+#' \code{print_priors} = a flag to say whether the distributional assumptions 
+#' for the HMC model (only)
 #' 
 #' @author Gianluca Baio
 #' @template refs
@@ -37,7 +37,7 @@ print.survHE <- function(x,mod=1,...) {
   # ... optional arguments
   # digits = number of *significant* digits to be shown in the summary table (default = 6)
   # original = a flag to say whether the *original* table from either INLA or MCMC should be printed
-  # print_priors = a flag to say whether the Stan table should also print a summary of the prior distributions
+  # print_priors = a flag to say whether the distributional assumptions for the HMC model (only)
 
   exArgs <- list(...)
 
@@ -49,13 +49,14 @@ print.survHE <- function(x,mod=1,...) {
   if(!exists("original",where=exArgs)){original=FALSE} else {original=exArgs$original}
   # Aliases for 'original'
   if(exists("orig",exArgs)){original=exArgs$orig}
+  if(!exists("print_priors",where=exArgs)){print_priors=FALSE} else {print_priors=exArgs$print_priors}
 
   # Now computes the stats, using different helpers depending on the underlying method
   # Can ask for the original output from either 'flexsurv', 'inla' or 'rstan'
   if(original==TRUE) {
     do.call(
       paste0("original_table_",x$method),
-      args=list(x,mod,digits,...)
+      args=list(x,mod,digits,print_priors)
     )
   } # If not, go with the default formatting using the standardised 'survHE' output
   else {

R/utils_print_survHE.R

@@ -616,7 +616,7 @@ add_effects_hmc <- function(table,x) {
 #' @references Baio (2020). survHE
 #' @keywords MLE
 #' @noRd 
-original_table_mle <- function(x,mod,digits,...) {
+original_table_mle <- function(x,mod,digits,print_priors) {
   print(x$models[[mod]],digits=digits)
 }
 
@@ -630,7 +630,7 @@ original_table_mle <- function(x,mod,digits,...) {
 #' @references Baio (2020). survHE
 #' @keywords INLA
 #' @noRd 
-original_table_inla <- function(x,mod,digits,...) {
+original_table_inla <- function(x,mod,digits,print_priors) {
   print(summary(x$models[[mod]]),digits=digits)
   cat("\n")
   cat("NB: notice that INLA models are fitted to data rescaled in [0-1] for computational stability.")
@@ -648,9 +648,7 @@ original_table_inla <- function(x,mod,digits,...) {
 #' @references Baio (2020). survHE
 #' @keywords HMC
 #' @noRd 
-original_table_hmc <- function(x,mod,digits,...) {
-  exArgs=list(...)
-  if(!exists("print_priors",where=exArgs)){print_priors=FALSE} else {print_priors=exArgs$print_priors}
+original_table_hmc <- function(x,mod,digits,print_priors) {
   print(x$models[[mod]],digits=digits)
   if (print_priors==TRUE) {
     cat("\nPrior modelling assumptions")