Rename 'convergence' method to 'status'

The reason is that it is misleading in the case of saem.mmkin objects,
because convergence is not really checked there.

9 files changed, 71 insertions, 75 deletions

diff --git a/NAMESPACE b/NAMESPACE
index 8ffa0425..37b6c74d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,10 +13,6 @@ S3method(aw,mmkin)
 S3method(aw,multistart)
 S3method(best,default)
 S3method(confint,mkinfit)
-S3method(convergence,mhmkin)
-S3method(convergence,mmkin)
-S3method(convergence,multistart)
-S3method(convergence,multistart.saem.mmkin)
 S3method(f_time_norm_focus,mkindsg)
 S3method(f_time_norm_focus,numeric)
 S3method(illparms,mhmkin)
@@ -44,9 +40,6 @@ S3method(plot,mixed.mmkin)
 S3method(plot,mkinfit)
 S3method(plot,mmkin)
 S3method(plot,nafta)
-S3method(print,convergence.mhmkin)
-S3method(print,convergence.mmkin)
-S3method(print,convergence.multistart)
 S3method(print,illparms.mhmkin)
 S3method(print,illparms.mmkin)
 S3method(print,mhmkin)
@@ -59,12 +52,18 @@ S3method(print,multistart)
 S3method(print,nafta)
 S3method(print,nlme.mmkin)
 S3method(print,saem.mmkin)
+S3method(print,status.mhmkin)
+S3method(print,status.mmkin)
+S3method(print,status.multistart)
 S3method(print,summary.mkinfit)
 S3method(print,summary.mmkin)
 S3method(print,summary.nlme.mmkin)
 S3method(print,summary.saem.mmkin)
 S3method(residuals,mkinfit)
 S3method(saem,mmkin)
+S3method(status,mmkin)
+S3method(status,multistart)
+S3method(status,multistart.saem.mmkin)
 S3method(summary,mkinfit)
 S3method(summary,mmkin)
 S3method(summary,nlme.mmkin)
@@ -87,7 +86,6 @@ export(add_err)
 export(aw)
 export(backtransform_odeparms)
 export(best)
-export(convergence)
 export(create_deg_func)
 export(endpoints)
 export(f_time_norm_focus)
@@ -138,6 +136,7 @@ export(saemix_model)
 export(set_nd_nq)
 export(set_nd_nq_focus)
 export(sigma_twocomp)
+export(status)
 export(transform_odeparms)
 export(which.best)
 import(deSolve)
diff --git a/R/mhmkin.R b/R/mhmkin.R
index 542bddf7..47b84b9d 100644
--- a/R/mhmkin.R
+++ b/R/mhmkin.R
@@ -133,11 +133,10 @@ mhmkin.list <- function(objects, backend = "saemix",
 print.mhmkin <- function(x, ...) {
   cat("<mhmkin> object\n")
   cat("Status of individual fits:\n\n")
-  print(convergence(x))
+  print(status(x))
 }
 
-#' @export
-convergence.mhmkin <- function(object, ...) {
+status.mhmkin <- function(object, ...) {
   if (inherits(object[[1]], "saem.mmkin")) {
     test_func <- function(fit) {
       if (inherits(fit$so, "try-error")) {
@@ -160,12 +159,12 @@ convergence.mhmkin <- function(object, ...) {
   dim(result) <- dim(object)
   dimnames(result) <- dimnames(object)
 
-  class(result) <- "convergence.mhmkin"
+  class(result) <- "status.mhmkin"
   return(result)
 }
 
 #' @export
-print.convergence.mhmkin <- function(x, ...) {
+print.status.mhmkin <- function(x, ...) {
   class(x) <- NULL
   print(x, quote = FALSE)
   cat("\n")
diff --git a/R/mmkin.R b/R/mmkin.R
index 247fd5fa..01e53290 100644
--- a/R/mmkin.R
+++ b/R/mmkin.R
@@ -171,7 +171,7 @@ mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets,
 print.mmkin <- function(x, ...) {
   cat("<mmkin> object\n")
   cat("Status of individual fits:\n\n")
-  print(convergence(x))
+  print(status(x))
 }
 
 #' @export
diff --git a/R/multistart.R b/R/multistart.R
index fc2dcd7d..29ccdc44 100644
--- a/R/multistart.R
+++ b/R/multistart.R
@@ -112,7 +112,7 @@ multistart.saem.mmkin <- function(object, n = 50, cores = 1,
 }
 
 #' @export
-convergence.multistart <- function(object, ...) {
+status.multistart <- function(object, ...) {
   all_summary_warnings <- character()
 
   result <- lapply(object,
@@ -124,12 +124,12 @@ convergence.multistart <- function(object, ...) {
   })
   result <- unlist(result)
 
-  class(result) <- "convergence.multistart"
+  class(result) <- "status.multistart"
   return(result)
 }
 
 #' @export
-convergence.multistart.saem.mmkin <- function(object, ...) {
+status.multistart.saem.mmkin <- function(object, ...) {
   all_summary_warnings <- character()
 
   result <- lapply(object,
@@ -141,12 +141,12 @@ convergence.multistart.saem.mmkin <- function(object, ...) {
   })
   result <- unlist(result)
 
-  class(result) <- "convergence.multistart"
+  class(result) <- "status.multistart"
   return(result)
 }
 
 #' @export
-print.convergence.multistart <- function(x, ...) {
+print.status.multistart <- function(x, ...) {
   class(x) <- NULL
   print(table(x, dnn = NULL))
   if (any(x == "OK")) cat("OK: Fit terminated successfully\n")
@@ -157,7 +157,7 @@ print.convergence.multistart <- function(x, ...) {
 #' @export
 print.multistart <- function(x, ...) {
   cat("<multistart> object with", length(x), "fits:\n")
-  print(convergence(x))
+  print(status(x))
 }
 
 #' @rdname multistart
diff --git a/R/convergence.R b/R/status.R
index e75bb1b1..44d2a9bc 100644
--- a/R/convergence.R
+++ b/R/status.R
@@ -1,18 +1,17 @@
-#' Method to get convergence information
+#' Method to get status information for fit array objects
 #'
 #' @param object The object to investigate
 #' @param x The object to be printed
 #' @param \dots For potential future extensions
-#' @return For [mkinfit] objects, a character vector containing
-#' For [mmkin] objects, an object of class 'convergence.mmkin' with a
+#' @return  An object with the same dimensions as the fit array
 #' suitable printing method.
 #' @export
-convergence <- function(object, ...)
+status <- function(object, ...)
 {
-  UseMethod("convergence", object)
+  UseMethod("status", object)
 }
 
-#' @rdname convergence
+#' @rdname status
 #' @export
 #' @examples
 #' \dontrun{
@@ -21,9 +20,9 @@ convergence <- function(object, ...)
 #'   list("FOCUS A" = FOCUS_2006_A,
 #'        "FOCUS B" = FOCUS_2006_C),
 #'   quiet = TRUE)
-#' convergence(fits)
+#' status(fits)
 #' }
-convergence.mmkin <- function(object, ...) {
+status.mmkin <- function(object, ...) {
   all_summary_warnings <- character()
   sww <- 0 # Counter for Shapiro-Wilks warnings
 
@@ -51,13 +50,13 @@ convergence.mmkin <- function(object, ...) {
 
   u_swn <- unique(names(all_summary_warnings))
   attr(result, "unique_warnings") <- all_summary_warnings[u_swn]
-  class(result) <- "convergence.mmkin"
+  class(result) <- "status.mmkin"
   return(result)
 }
 
-#' @rdname convergence
+#' @rdname status
 #' @export
-print.convergence.mmkin <- function(x, ...) {
+print.status.mmkin <- function(x, ...) {
   u_w <- attr(x, "unique_warnings")
   attr(x, "unique_warnings") <- NULL
   class(x) <- NULL
diff --git a/R/summary.mmkin.R b/R/summary.mmkin.R
index 5f4a048b..06472e18 100644
--- a/R/summary.mmkin.R
+++ b/R/summary.mmkin.R
@@ -1,6 +1,6 @@
 #' Summary method for class "mmkin"
 #'
-#' Shows convergence information on the [mkinfit] objects contained in the object
+#' Shows status information on the [mkinfit] objects contained in the object
 #' and gives an overview of ill-defined parameters calculated by [illparms].
 #'
 #' @param object an object of class [mmkin]
@@ -24,7 +24,7 @@ summary.mmkin <- function(object, conf.level = 0.95, ...) {
     err_mod = object[[1, 1]]$err_mod,
     time = attr(object, "time"),
     illparms = illparms(object),
-    convergence = convergence(object)
+    status = status(object)
   )
 
   class(ans) <- c("summary.mmkin")
@@ -43,8 +43,8 @@ print.summary.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...
   }
   cat("Fitted in", x$time[["elapsed"]],  "s\n")
 
-  cat("\nConvergence:\n")
-  print(x$convergence)
+  cat("\nStatus:\n")
+  print(x$status)
 
   if (any(x$illparms != "")) {
     cat("\nIll-defined parameters:\n")
diff --git a/man/convergence.Rd b/man/convergence.Rd
deleted file mode 100644
index 635eb9ae..00000000
--- a/man/convergence.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/convergence.R
-\name{convergence}
-\alias{convergence}
-\alias{convergence.mmkin}
-\alias{print.convergence.mmkin}
-\title{Method to get convergence information}
-\usage{
-convergence(object, ...)
-
-\method{convergence}{mmkin}(object, ...)
-
-\method{print}{convergence.mmkin}(x, ...)
-}
-\arguments{
-\item{object}{The object to investigate}
-
-\item{\dots}{For potential future extensions}
-
-\item{x}{The object to be printed}
-}
-\value{
-For \link{mkinfit} objects, a character vector containing
-For \link{mmkin} objects, an object of class 'convergence.mmkin' with a
-suitable printing method.
-}
-\description{
-Method to get convergence information
-}
-\examples{
-\dontrun{
-fits <- mmkin(
-  c("SFO", "FOMC"),
-  list("FOCUS A" = FOCUS_2006_A,
-       "FOCUS B" = FOCUS_2006_C),
-  quiet = TRUE)
-convergence(fits)
-}
-}
diff --git a/man/status.Rd b/man/status.Rd
new file mode 100644
index 00000000..8ff3531b
--- /dev/null
+++ b/man/status.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/status.R
+\name{status}
+\alias{status}
+\alias{status.mmkin}
+\alias{print.status.mmkin}
+\title{Method to get status information for fit array objects}
+\usage{
+status(object, ...)
+
+\method{status}{mmkin}(object, ...)
+
+\method{print}{status.mmkin}(x, ...)
+}
+\arguments{
+\item{object}{The object to investigate}
+
+\item{\dots}{For potential future extensions}
+
+\item{x}{The object to be printed}
+}
+\value{
+An object with the same dimensions as the fit array
+suitable printing method.
+}
+\description{
+Method to get status information for fit array objects
+}
+\examples{
+\dontrun{
+fits <- mmkin(
+  c("SFO", "FOMC"),
+  list("FOCUS A" = FOCUS_2006_A,
+       "FOCUS B" = FOCUS_2006_C),
+  quiet = TRUE)
+status(fits)
+}
+}
diff --git a/man/summary.mmkin.Rd b/man/summary.mmkin.Rd
index 69245621..32e5824f 100644
--- a/man/summary.mmkin.Rd
+++ b/man/summary.mmkin.Rd
@@ -21,7 +21,7 @@
 \item{digits}{number of digits to use for printing}
 }
 \description{
-Shows convergence information on the \link{mkinfit} objects contained in the object
+Shows status information on the \link{mkinfit} objects contained in the object
 and gives an overview of ill-defined parameters calculated by \link{illparms}.
 }
 \examples{