Improve logLik.mkinfit to attach nobs attribute

The lack of that attribute lead to a failure to calculate the BIC in
test_AIC.R on R-devel from yesterday.

2 files changed, 33 insertions, 29 deletions

diff --git a/R/logLik.mkinfit.R b/R/logLik.mkinfit.R
index 7cc10234..abf8517c 100644
--- a/R/logLik.mkinfit.R
+++ b/R/logLik.mkinfit.R
@@ -37,6 +37,7 @@ logLik.mkinfit <- function(object, ...) {
   val <- object$logLik
   # Number of estimated parameters
   attr(val, "df") <- length(object$bparms.optim) + length(object$errparms)
+  attr(val, "nobs") <- nobs(object)
   class(val) <- "logLik"
   return(val)
 }
diff --git a/log/test_dev.log b/log/test_dev.log
index 24905a1a..527d28ed 100644
--- a/log/test_dev.log
+++ b/log/test_dev.log
@@ -1,54 +1,57 @@
-ℹ Loading mkin
-Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [14.6s]
+✔ |         5 | Analytical solutions for coupled models [3.2s]
 ✔ |         5 | Calculation of Akaike weights
-✔ |         2 | Export dataset for reading into CAKE
+✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-⠋ |         1 | Dimethenamid data from 2018                                     
-✔ |     1  27 | Dimethenamid data from 2018 [116.1s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.3s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+Skip ('test_dmta.R:98'): 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 [6.6s]
+✔ |        14 | Error model fitting [5.2s]
 ✔ |         5 | Time step normalisation
-✔ |         4 | Calculation of FOCUS chi2 error levels [0.8s]
-✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.6s]
-✔ |         1 | Fitting the logistic model [0.3s]
-⠋ |        11 | Nonlinear mixed-effects models                                  
-✔ |     1  14 | Nonlinear mixed-effects models [1.3s]
+✔ |         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]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [23.5s]
+✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
+Skip ('test_mixed.R:74'): 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 [0.6s]
-✔ |         3 | mkinfit features [1.1s]
+✔ |        10 | Special cases of mkinfit calls [0.5s]
+✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.1s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.7s]
-✔ |        16 | Plotting [1.4s]
+✔ |         9 | Multistart method for saem.mmkin models [35.2s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.3s]
+✔ |        16 | Plotting [10.0s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        23 | saemix parent models [28.4s]
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.0s]
-✔ |         7 | Fitting the SFORB model [16.9s]
+✔ |     1  36 | saemix parent models [63.3s]
+────────────────────────────────────────────────────────────────────────────────
+Skip ('test_saemix_parent.R:143'): 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 [1.3s]
+✔ |        11 | Processing of residue series
+✔ |        10 | Fitting the SFORB model [3.5s]
 ✔ |         1 | Summaries of old mkinfit objects
-✔ |         4 | Summary [0.1s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [18.1s]
-✔ |         9 | Hypothesis tests [78.9s]
-✔ |         2 | tffm0
+✔ |         5 | Summary [0.2s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
+✔ |         9 | Hypothesis tests [7.5s]
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 315.9 s
+Duration: 204.4 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 2 | PASS 240 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 269 ]