Export status method for mhmkin, move to status.R

5 files changed, 70 insertions, 59 deletions

diff --git a/NAMESPACE b/NAMESPACE
index 37b6c74d..a5691eee 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -61,6 +61,7 @@ S3method(print,summary.nlme.mmkin)
 S3method(print,summary.saem.mmkin)
 S3method(residuals,mkinfit)
 S3method(saem,mmkin)
+S3method(status,mhmkin)
 S3method(status,mmkin)
 S3method(status,multistart)
 S3method(status,multistart.saem.mmkin)
diff --git a/R/mhmkin.R b/R/mhmkin.R
index 47b84b9d..7f3ff9fa 100644
--- a/R/mhmkin.R
+++ b/R/mhmkin.R
@@ -136,45 +136,6 @@ print.mhmkin <- function(x, ...) {
   print(status(x))
 }
 
-status.mhmkin <- function(object, ...) {
-  if (inherits(object[[1]], "saem.mmkin")) {
-    test_func <- function(fit) {
-      if (inherits(fit$so, "try-error")) {
-        return("E")
-      } else {
-        if (!is.null(fit$FIM_failed)) {
-          return_values <- c("fixed effects" = "Fth",
-            "random effects and error model parameters" = "FO")
-          return(paste(return_values[fit$FIM_failed], collapse = ", "))
-        } else {
-          return("OK")
-        }
-      }
-    }
-  } else {
-    stop("Only mhmkin objects containing saem.mmkin objects currently supported")
-  }
-  result <- lapply(object, test_func)
-  result <- unlist(result)
-  dim(result) <- dim(object)
-  dimnames(result) <- dimnames(object)
-
-  class(result) <- "status.mhmkin"
-  return(result)
-}
-
-#' @export
-print.status.mhmkin <- function(x, ...) {
-  class(x) <- NULL
-  print(x, quote = FALSE)
-  cat("\n")
-  if (any(x == "OK")) cat("OK: Fit terminated successfully\n")
-  if (any(x == "Fth")) cat("Fth: Could not invert FIM for fixed effects\n")
-  if (any(x == "FO")) cat("FO: Could not invert FIM for random effects and error model parameters\n")
-  if (any(x == "Fth, FO")) cat("Fth, FO: Could not invert FIM for fixed effects, nor for random effects and error model parameters\n")
-  if (any(x == "E")) cat("E: Error\n")
-}
-
 #' @export
 AIC.mhmkin <- function(object, ..., k = 2) {
   if (inherits(object[[1]], "saem.mmkin")) {
diff --git a/R/status.R b/R/status.R
index 44d2a9bc..8bcd3a16 100644
--- a/R/status.R
+++ b/R/status.R
@@ -68,3 +68,46 @@ print.status.mmkin <- function(x, ...) {
   if (any(x == "OK")) cat("OK: No warnings\n")
   if (any(x == "E")) cat("E: Error\n")
 }
+
+#' @rdname status
+#' @export
+status.mhmkin <- function(object, ...) {
+  if (inherits(object[[1]], "saem.mmkin")) {
+    test_func <- function(fit) {
+      if (inherits(fit$so, "try-error")) {
+        return("E")
+      } else {
+        if (!is.null(fit$FIM_failed)) {
+          return_values <- c("fixed effects" = "Fth",
+            "random effects and error model parameters" = "FO")
+          return(paste(return_values[fit$FIM_failed], collapse = ", "))
+        } else {
+          return("OK")
+        }
+      }
+    }
+  } else {
+    stop("Only mhmkin objects containing saem.mmkin objects currently supported")
+  }
+  result <- lapply(object, test_func)
+  result <- unlist(result)
+  dim(result) <- dim(object)
+  dimnames(result) <- dimnames(object)
+
+  class(result) <- "status.mhmkin"
+  return(result)
+}
+
+#' @rdname status
+#' @export
+print.status.mhmkin <- function(x, ...) {
+  class(x) <- NULL
+  print(x, quote = FALSE)
+  cat("\n")
+  if (any(x == "OK")) cat("OK: Fit terminated successfully\n")
+  if (any(x == "Fth")) cat("Fth: Could not invert FIM for fixed effects\n")
+  if (any(x == "FO")) cat("FO: Could not invert FIM for random effects and error model parameters\n")
+  if (any(x == "Fth, FO")) cat("Fth, FO: Could not invert FIM for fixed effects, nor for random effects and error model parameters\n")
+  if (any(x == "E")) cat("E: Error\n")
+}
+
diff --git a/log/test.log b/log/test.log
index dee62073..429a2e02 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,53 +1,53 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.4s]
+✔ |         5 | Analytical solutions for coupled models [3.3s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [32.5s]
+✔ |     1  12 | Dimethenamid data from 2018 [43.2s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [5.0s]
+✔ |        14 | Error model fitting [11.5s]
 ✔ |         5 | Time step normalisation
-✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
-✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.4s]
-✔ |         1 | Fitting the logistic model [0.2s]
-✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.5s]
-✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
+✔ |         4 | Calculation of FOCUS chi2 error levels [1.3s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.9s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.9s]
+✔ |         1 | Fitting the logistic model [0.6s]
+✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [30.9s]
+✔ |     1  12 | Nonlinear mixed-effects models [0.4s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        10 | Special cases of mkinfit calls [0.4s]
-✔ |         3 | mkinfit features [0.7s]
-✔ |         8 | mkinmod model generation and printing [0.2s]
+✔ |        10 | Special cases of mkinfit calls [0.7s]
+✔ |         3 | mkinfit features [1.0s]
+✔ |         8 | mkinmod model generation and printing [0.3s]
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |         7 | Multistart method for saem.mmkin models [37.6s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.3s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.7s]
+✔ |         7 | Multistart method for saem.mmkin models [39.8s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.6s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.8s]
 ✔ |        16 | Plotting [10.1s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [72.8s]
+✔ |     1  36 | saemix parent models [72.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_saemix_parent.R:152:3): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
 ✔ |        11 | Processing of residue series
-✔ |         7 | Fitting the SFORB model [3.7s]
+✔ |         7 | Fitting the SFORB model [3.8s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
-✔ |         9 | Hypothesis tests [8.3s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s]
+✔ |         9 | Hypothesis tests [8.0s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 210.4 s
+Duration: 249.3 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/man/status.Rd b/man/status.Rd
index 8ff3531b..1cadbfcc 100644
--- a/man/status.Rd
+++ b/man/status.Rd
@@ -4,6 +4,8 @@
 \alias{status}
 \alias{status.mmkin}
 \alias{print.status.mmkin}
+\alias{status.mhmkin}
+\alias{print.status.mhmkin}
 \title{Method to get status information for fit array objects}
 \usage{
 status(object, ...)
@@ -11,6 +13,10 @@ status(object, ...)
 \method{status}{mmkin}(object, ...)
 
 \method{print}{status.mmkin}(x, ...)
+
+\method{status}{mhmkin}(object, ...)
+
+\method{print}{status.mhmkin}(x, ...)
 }
 \arguments{
 \item{object}{The object to investigate}