Improved printing for illparms()

For the case of single fits and no ill-defined parameters found

7 files changed, 80 insertions, 24 deletions

diff --git a/NAMESPACE b/NAMESPACE
index 877fc744..9f87fce6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -44,7 +44,9 @@ S3method(plot,mkinfit)
 S3method(plot,mmkin)
 S3method(plot,nafta)
 S3method(print,illparms.mhmkin)
+S3method(print,illparms.mkinfit)
 S3method(print,illparms.mmkin)
+S3method(print,illparms.saem.mmkin)
 S3method(print,mhmkin)
 S3method(print,mixed.mmkin)
 S3method(print,mkinds)
diff --git a/R/illparms.R b/R/illparms.R
index 931d8f05..003c6db1 100644
--- a/R/illparms.R
+++ b/R/illparms.R
@@ -22,8 +22,9 @@
 #' tested?
 #' @return For [mkinfit] or [saem] objects, a character vector of parameter
 #' names. For [mmkin] or [mhmkin] objects, a matrix like object of class
-#' 'illparms.mmkin' or 'illparms.mhmkin'. The latter objects have a suitable
-#' printing method.
+#' 'illparms.mmkin' or 'illparms.mhmkin'.
+#' @note All objects have printing methods. For the single fits, printing
+#' does not output anything in the case no ill-defined parameters are found.
 #' @export
 illparms <- function(object, ...)
 {
@@ -39,7 +40,18 @@ illparms.mkinfit <- function(object, conf.level = 0.95, ...) {
   p_values <- suppressWarnings(summary(object)$bpar[, "Pr(>t)"])
   na <- is.na(p_values)
   failed <- p_values > 1 - conf.level
-  names(parms(object))[na | failed]
+  ret <- names(parms(object))[na | failed]
+  class(ret) <- "illparms.mkinfit"
+  return(ret)
+}
+
+#' @rdname
+#' @export
+print.illparms.mkinfit <- function(x, ...) {
+  class(x) <- NULL
+  if (length(x) > 0) {
+    print(as.character(x))
+  }
 }
 
 #' @rdname illparms
@@ -82,7 +94,7 @@ print.illparms.mmkin <- function(x, ...) {
 #' @export
 illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) {
   if (inherits(object, "try-error")) {
-    return(NA)
+    failed <- NA
   } else {
     ints <- intervals(object, conf.level = conf.level)
     failed <- NULL
@@ -95,9 +107,13 @@ illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod
       failed <- c(failed, names(which(failed_errmod)))
     }
   }
+  class(failed) <- "illparms.saem.mmkin"
   return(failed)
 }
 
+#' @export
+print.illparms.saem.mmkin <- print.illparms.mkinfit
+
 #' @rdname illparms
 #' @export
 illparms.mhmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) {
diff --git a/log/check.log b/log/check.log
index 36bd30ca..4092108e 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,5 +1,5 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.2.1 (2022-06-23)
+* using R version 4.2.2 (2022-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
@@ -43,7 +43,7 @@ The Date field is over a month old.
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... OK
+* checking R code for possible problems ... [14s/14s] OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -59,7 +59,7 @@ The Date field is over a month old.
 * checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... OK
+* checking examples ... [15s/15s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
diff --git a/log/test.log b/log/test.log
index bb81dd43..7152c3fe 100644
--- a/log/test.log
+++ b/log/test.log
@@ -5,18 +5,27 @@
 ✔ |         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 [31.9s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.6s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [4.9s]
+✔ |        14 | Error model fitting [4.8s]
 ✔ |         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 [0.3s]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [15.8s]
+✖ | 1       7 | Batch fitting and diagnosing hierarchical kinetic models [14.4s]
+────────────────────────────────────────────────────────────────────────────────
+Failure (test_mhmkin.R:27:3): Multiple hierarchical kinetic models can be fitted and diagnosed
+illparms(hfit_sfo_tc) not equal to character(0).
+Attributes: < Modes: list, NULL >
+Attributes: < Lengths: 1, 0 >
+Attributes: < names for target but not for current >
+Attributes: < current is not list-like >
+target is illparms.saem.mmkin, current is character
+────────────────────────────────────────────────────────────────────────────────
 ✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits
@@ -27,14 +36,38 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |         7 | Multistart method for saem.mmkin models [36.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.4s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.9s]
-✔ |        16 | Plotting [9.9s]
+✔ |         7 | Multistart method for saem.mmkin models [35.7s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.3s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.6s]
+✔ |        16 | Plotting [10.1s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [72.6s]
+✖ | 3   1  34 | saemix parent models [70.9s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_saemix_parent.R:152:3): We can also use mkin solution methods for saem
+Failure (test_saemix_parent.R:12:3): Parent fits using saemix are correctly implemented
+illparms(sfo_saem_1) not equal to "sd(parent_0)".
+Attributes: < Modes: list, NULL >
+Attributes: < Lengths: 1, 0 >
+Attributes: < names for target but not for current >
+Attributes: < current is not list-like >
+target is illparms.saem.mmkin, current is character
+
+Failure (test_saemix_parent.R:14:3): Parent fits using saemix are correctly implemented
+illparms(sfo_saem_1_reduced) not equal to character(0).
+Attributes: < Modes: list, NULL >
+Attributes: < Lengths: 1, 0 >
+Attributes: < names for target but not for current >
+Attributes: < current is not list-like >
+target is illparms.saem.mmkin, current is character
+
+Failure (test_saemix_parent.R:25:3): Parent fits using saemix are correctly implemented
+illparms(sfo_saem_1_mkin) not equal to "sd(parent_0)".
+Attributes: < Modes: list, NULL >
+Attributes: < Lengths: 1, 0 >
+Attributes: < names for target but not for current >
+Attributes: < current is not list-like >
+target is illparms.saem.mmkin, current is character
+
+Skip (test_saemix_parent.R:153:3): 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]
@@ -42,16 +75,16 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ✔ |         7 | Fitting the SFORB model [3.7s]
 ✔ |         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 [8.1s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
+✔ |         9 | Hypothesis tests [8.0s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 209.2 s
+Duration: 204.9 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
 • Fitting with saemix takes around 10 minutes when using deSolve (1)
 • This still takes almost 2.5 minutes although we do not solve ODEs (1)
 
-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 261 ]
+[ FAIL 4 | WARN 0 | SKIP 3 | PASS 259 ]
diff --git a/man/illparms.Rd b/man/illparms.Rd
index 90adf2bb..ebc3185a 100644
--- a/man/illparms.Rd
+++ b/man/illparms.Rd
@@ -41,8 +41,7 @@ tested?}
 \value{
 For \link{mkinfit} or \link{saem} objects, a character vector of parameter
 names. For \link{mmkin} or \link{mhmkin} objects, a matrix like object of class
-'illparms.mmkin' or 'illparms.mhmkin'. The latter objects have a suitable
-printing method.
+'illparms.mmkin' or 'illparms.mhmkin'.
 }
 \description{
 The method for generalised nonlinear regression fits as obtained
@@ -59,6 +58,10 @@ effects expressed as standard deviations include zero, and if
 the confidence intervals for the error model parameters include
 zero.
 }
+\note{
+All objects have printing methods. For the single fits, printing
+does not output anything in the case no ill-defined parameters are found.
+}
 \examples{
 fit <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE)
 illparms(fit)
diff --git a/tests/testthat/test_mhmkin.R b/tests/testthat/test_mhmkin.R
index fc588473..72b81fec 100644
--- a/tests/testthat/test_mhmkin.R
+++ b/tests/testthat/test_mhmkin.R
@@ -25,6 +25,7 @@ test_that("Multiple hierarchical kinetic models can be fitted and diagnosed", {
   hfit_sfo_tc <- update(hfits[["SFO", "tc"]],
     covariance.model = diag(c(0, 1)))
   expect_equal(illparms(hfit_sfo_tc), character(0))
+  expect_silent(print(illparms(hfit_sfo_tc)))
 
   test_summary <- summary(hfit_sfo_tc)
   test_summary$saemixversion <- "Dummy 0.0 for testing"
@@ -37,7 +38,7 @@ test_that("Multiple hierarchical kinetic models can be fitted and diagnosed", {
   expect_known_output(print(test_summary, digits = 1),
     "summary_hfit_sfo_tc.txt")
 
-  # It depends on the platform exactly which of the 
+  # It depends on the platform exactly which of the
   # SFO datasets fail to converge with FOMC
   skip_on_travis()
 
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index 39efa18f..e7574b01 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -12,6 +12,7 @@ test_that("Parent fits using saemix are correctly implemented", {
   expect_equal(illparms(sfo_saem_1), "sd(parent_0)")
   # So we have also done a fit without this variance
   expect_equal(illparms(sfo_saem_1_reduced), character(0))
+  expect_silent(print(illparms(sfo_saem_1_reduced)))
 
   # We cannot currently do the fit with completely fixed initial values
   mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100))