Adapt tests, vignettes and examples

- Write the NEWS
- Static documentation rebuilt by pkgdown
- Adapt mkinerrmin
- Fix (hopefully all) remaining problems in mkinfit

1 files changed, 22 insertions, 17 deletions

diff --git a/test.log b/test.log
index 79813341..58c819f4 100644
--- a/test.log
+++ b/test.log
@@ -2,40 +2,45 @@ Loading mkin
 Testing mkin
 ✔ | OK F W S | Context
 
⠏ |  0       | Export dataset for reading into CAKE
⠋ |  1       | Export dataset for reading into CAKE
✔ |  1       | Export dataset for reading into CAKE
-
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
✔ |  2       | Calculation of FOCUS chi2 error levels [2.4 s]
-
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ |  7       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠇ |  9       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠏ | 10       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 11       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 12       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 13       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ | 13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [8.0 s]
-
⠏ |  0       | Test fitting the decline of metabolites from their maximum
⠋ |  1       | Test fitting the decline of metabolites from their maximum
⠙ |  2       | Test fitting the decline of metabolites from their maximum
⠹ |  3       | Test fitting the decline of metabolites from their maximum
✔ |  3       | Test fitting the decline of metabolites from their maximum [0.6 s]
-
⠏ |  0       | Iteratively reweighted least squares (IRLS) fitting
⠋ |  1       | Iteratively reweighted least squares (IRLS) fitting
⠙ |  2       | Iteratively reweighted least squares (IRLS) fitting
⠹ |  2     1 | Iteratively reweighted least squares (IRLS) fitting
✔ |  2     1 | Iteratively reweighted least squares (IRLS) fitting [16.0 s]
+
⠏ |  0       | Error model fitting
⠋ |  1       | Error model fitting
⠙ |  2       | Error model fitting
⠹ |  3       | Error model fitting
⠸ |  4       | Error model fitting
⠼ |  5       | Error model fitting
⠴ |  6       | Error model fitting
⠦ |  7       | Error model fitting
⠧ |  8       | Error model fitting
⠇ |  9       | Error model fitting
⠏ |  9   1   | Error model fitting
⠋ | 10   1   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting
⠙ | 10   2   | Error model fitting

⠙ | 10   2  ⠙ | 10    | Error model fitting2   | Error model fitting
⠙ | 11   1   | Error model fitting
⠹ | 12   1   | Error model fitting
✔ | 12   1   | Error model fitting [163.7 s]
 ────────────────────────────────────────────────────────────────────────────────
-test_irls.R:48: skip: Reweighting method 'tc' works
-Too much trouble with datasets that are randomly generated
+test_error_models.R:148: warning: Reweighting method 'tc' produces reasonable variance estimates
+Observations with value of zero were removed from the data
 ────────────────────────────────────────────────────────────────────────────────
-
⠏ |  0       | Fitting the logistic model
⠋ |  1       | Fitting the logistic model
⠙ |  1     1 | Fitting the logistic model
✔ |  1     1 | Fitting the logistic model [0.5 s]
+
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
⠹ |  3       | Calculation of FOCUS chi2 error levels
✔ |  3       | Calculation of FOCUS chi2 error levels [2.4 s]
+
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ |  7       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠇ |  9       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠏ | 10       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 11       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 12       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 13       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ | 13     1 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ | 13     1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [8.3 s]
+────────────────────────────────────────────────────────────────────────────────
+test_FOCUS_D_UBA_expertise.R:89: skip: The t-value for fits using internal transformations corresponds with results from FME, synthetic data
+Hessian matrices and df calculations differ from those in FME
+────────────────────────────────────────────────────────────────────────────────
+
⠏ |  0       | Test fitting the decline of metabolites from their maximum
⠋ |  1       | Test fitting the decline of metabolites from their maximum
⠙ |  2       | Test fitting the decline of metabolites from their maximum
⠹ |  3       | Test fitting the decline of metabolites from their maximum
⠸ |  4       | Test fitting the decline of metabolites from their maximum
⠼ |  5       | Test fitting the decline of metabolites from their maximum
⠴ |  6       | Test fitting the decline of metabolites from their maximum
✔ |  6       | Test fitting the decline of metabolites from their maximum [0.9 s]
+
⠏ |  0       | Fitting the logistic model
⠋ |  1       | Fitting the logistic model
⠙ |  1     1 | Fitting the logistic model
✔ |  1     1 | Fitting the logistic model [0.9 s]
 ────────────────────────────────────────────────────────────────────────────────
 test_logistic.R:41: skip: The logistic fit can be done via differential equation
 Skip slow fit of logistic model using deSolve without compilation
 ────────────────────────────────────────────────────────────────────────────────
 
⠏ |  0       | Test dataset class mkinds used in gmkin
⠋ |  1       | Test dataset class mkinds used in gmkin
✔ |  1       | Test dataset class mkinds used in gmkin
-
⠏ |  0       | Special cases of mkinfit calls
⠋ |  1       | Special cases of mkinfit calls
⠙ |  2       | Special cases of mkinfit calls
⠹ |  3       | Special cases of mkinfit calls
⠸ |  4       | Special cases of mkinfit calls
⠼ |  5       | Special cases of mkinfit calls
⠴ |  6       | Special cases of mkinfit calls
⠦ |  7       | Special cases of mkinfit calls
⠧ |  8       | Special cases of mkinfit calls
⠇ |  9       | Special cases of mkinfit calls
⠏ | 10       | Special cases of mkinfit calls
⠋ | 11       | Special cases of mkinfit calls
⠙ | 12       | Special cases of mkinfit calls
⠹ | 12     1 | Special cases of mkinfit calls
⠸ | 13     1 | Special cases of mkinfit calls
⠼ | 14     1 | Special cases of mkinfit calls
⠴ | 15     1 | Special cases of mkinfit calls
⠦ | 16     1 | Special cases of mkinfit calls
✔ | 16     1 | Special cases of mkinfit calls [2.9 s]
+
⠏ |  0       | Special cases of mkinfit calls
⠋ |  1       | Special cases of mkinfit calls
⠙ |  2       | Special cases of mkinfit calls
⠹ |  3       | Special cases of mkinfit calls
⠸ |  4       | Special cases of mkinfit calls
⠼ |  5       | Special cases of mkinfit calls
⠴ |  6       | Special cases of mkinfit calls
⠦ |  7       | Special cases of mkinfit calls
⠧ |  8       | Special cases of mkinfit calls
⠇ |  8   1   | Special cases of mkinfit calls
⠏ |  9   1   | Special cases of mkinfit calls
⠋ | 10   1   | Special cases of mkinfit calls
⠙ | 11   1   | Special cases of mkinfit calls
⠹ | 12   1   | Special cases of mkinfit calls
✔ | 12   1   | Special cases of mkinfit calls [3.2 s]
 ────────────────────────────────────────────────────────────────────────────────
-test_mkinfit_errors.R:67: skip: mkinfit warns if the user chooses the SANN method
-The SANN algorithm takes very long with the default maximum number of iterations of 10000
+test_mkinfit_errors.R:59: warning: mkinfit stops early when a low maximum number of iterations is specified
+Optimisation did not converge:
+iteration limit reached without convergence (10)
 ────────────────────────────────────────────────────────────────────────────────
 
⠏ |  0       | mkinmod model generation and printing
⠋ |  1       | mkinmod model generation and printing
⠙ |  2       | mkinmod model generation and printing
⠹ |  3       | mkinmod model generation and printing
⠸ |  4       | mkinmod model generation and printing
⠼ |  5       | mkinmod model generation and printing
⠴ |  6       | mkinmod model generation and printing
⠦ |  7       | mkinmod model generation and printing
⠧ |  8       | mkinmod model generation and printing
⠇ |  9       | mkinmod model generation and printing
✔ |  9       | mkinmod model generation and printing [0.2 s]
 
⠏ |  0       | Model predictions with mkinpredict
⠋ |  1       | Model predictions with mkinpredict
⠙ |  2       | Model predictions with mkinpredict
⠹ |  3       | Model predictions with mkinpredict
✔ |  3       | Model predictions with mkinpredict [0.3 s]
-
⠏ |  0       | Evaluations according to 2015 NAFTA guidance
⠋ |  1       | Evaluations according to 2015 NAFTA guidance
⠙ |  2       | Evaluations according to 2015 NAFTA guidance
⠹ |  3       | Evaluations according to 2015 NAFTA guidance
⠸ |  4       | Evaluations according to 2015 NAFTA guidance
⠼ |  5       | Evaluations according to 2015 NAFTA guidance
⠴ |  6       | Evaluations according to 2015 NAFTA guidance
⠦ |  7       | Evaluations according to 2015 NAFTA guidance
⠧ |  8       | Evaluations according to 2015 NAFTA guidance
⠇ |  9       | Evaluations according to 2015 NAFTA guidance
⠏ | 10       | Evaluations according to 2015 NAFTA guidance
⠋ | 11       | Evaluations according to 2015 NAFTA guidance
⠙ | 12       | Evaluations according to 2015 NAFTA guidance
⠹ | 13       | Evaluations according to 2015 NAFTA guidance
⠸ | 14       | Evaluations according to 2015 NAFTA guidance
⠼ | 15       | Evaluations according to 2015 NAFTA guidance
⠴ | 16       | Evaluations according to 2015 NAFTA guidance
⠦ | 17       | Evaluations according to 2015 NAFTA guidance
✔ | 17       | Evaluations according to 2015 NAFTA guidance [2.2 s]
-
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [23.8 s]
+
⠏ |  0       | Evaluations according to 2015 NAFTA guidance
⠋ |  1       | Evaluations according to 2015 NAFTA guidance
⠙ |  2       | Evaluations according to 2015 NAFTA guidance
⠹ |  3       | Evaluations according to 2015 NAFTA guidance
⠸ |  4       | Evaluations according to 2015 NAFTA guidance
⠼ |  5       | Evaluations according to 2015 NAFTA guidance
⠴ |  6       | Evaluations according to 2015 NAFTA guidance
⠦ |  7       | Evaluations according to 2015 NAFTA guidance
⠧ |  8       | Evaluations according to 2015 NAFTA guidance
⠇ |  9       | Evaluations according to 2015 NAFTA guidance
⠏ | 10       | Evaluations according to 2015 NAFTA guidance
⠋ | 11       | Evaluations according to 2015 NAFTA guidance
⠙ | 12       | Evaluations according to 2015 NAFTA guidance
⠹ | 13       | Evaluations according to 2015 NAFTA guidance
⠸ | 14       | Evaluations according to 2015 NAFTA guidance
⠼ | 15       | Evaluations according to 2015 NAFTA guidance
⠴ | 16       | Evaluations according to 2015 NAFTA guidance
✔ | 16       | Evaluations according to 2015 NAFTA guidance [4.1 s]
+
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [58.6 s]
 
⠏ |  0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |  1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |  2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |  3       | Calculation of maximum time weighted average concentrations (TWAs)
⠸ |  4       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |  4       | Calculation of maximum time weighted average concentrations (TWAs) [3.7 s]
 
⠏ |  0       | Summary
⠋ |  1       | Summary
✔ |  1       | Summary
 
⠏ |  0       | Plotting
⠋ |  1       | Plotting
⠙ |  2       | Plotting
⠹ |  3       | Plotting
⠸ |  4       | Plotting
✔ |  4       | Plotting [0.3 s]
 
⠏ |  0       | AIC calculation
⠋ |  1       | AIC calculation
⠙ |  2       | AIC calculation
✔ |  2       | AIC calculation
-
⠏ |  0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |  1       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.9 s]
+
⠏ |  0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |  1       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.6 s]
 
⠏ |  0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 75.3 s
+Duration: 265.8 s
 
-OK:       106
+OK:       115
 Failed:   0
-Warnings: 0
-Skipped:  3
+Warnings: 2
+Skipped:  2