Summary method for mmkin objects

Also, add a method for gathering convergence information
and a method for gathering information on ill-defined parameters

1 files changed, 15 insertions, 32 deletions

diff --git a/test.log b/test.log
index 55a56153..03755ce5 100644
--- a/test.log
+++ b/test.log
@@ -3,20 +3,20 @@ Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.2s]
+✔ |         5 | Analytical solutions for coupled models [3.4s]
 ✔ |         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 [32.1s]
+✔ |     1  12 | Dimethenamid data from 2018 [34.2s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [4.8s]
+✔ |        14 | Error model fitting [5.1s]
 ✔ |         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]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.4s]
 ✔ |         1 | Fitting the logistic model [0.2s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.2s]
 ────────────────────────────────────────────────────────────────────────────────
@@ -27,42 +27,25 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |        10 | Special cases of mkinfit calls [0.4s]
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.4s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.1s]
-✖ | 2      14 | Plotting [10.5s]
-────────────────────────────────────────────────────────────────────────────────
-Failure (test_plot.R:56:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed
-Run `testthat::snapshot_review('plot/')` to review changes
-Backtrace:
- 1. vdiffr::expect_doppelganger(...)
-      at test_plot.R:56:2
- 3. testthat::expect_snapshot_file(...)
-
-Failure (test_plot.R:64:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Snapshot of `testcase` to 'plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed
-Run `testthat::snapshot_review('plot/')` to review changes
-Backtrace:
- 1. vdiffr::expect_doppelganger(...)
-      at test_plot.R:64:2
- 3. testthat::expect_snapshot_file(...)
-────────────────────────────────────────────────────────────────────────────────
+✔ |         3 | Model predictions with mkinpredict [0.3s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.7s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.5s]
+✔ |        16 | Plotting [10.2s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        25 | saemix parent models [171.7s]
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.3s]
+✔ |        25 | saemix parent models [175.0s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
 ✔ |         7 | Fitting the SFORB model [3.6s]
 ✔ |         1 | Summaries of old mkinfit objects
-✔ |         4 | Summary [0.1s]
+✔ |         5 | Summary [0.2s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
-✔ |         9 | Hypothesis tests [7.7s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s]
+✔ |         9 | Hypothesis tests [7.8s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 254.3 s
+Duration: 260.5 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)
 
-[ FAIL 2 | WARN 0 | SKIP 2 | PASS 222 ]
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 225 ]