Refactor mkinfit, infrastructure work

mkinfit objects now include an ll() function to calculate the
log-likelihood. Part of the code was refactored, hopefully making it
easier to read and maintain. IRLS is currently the default algorithm for
the error model "obs", for no particular reason. This may be subject
to change when I get around to investigate.

Slow tests are now in a separate subdirectory and will probably
only be run by my own Makefile target.

Formatting of test logs is improved.

Roundtripping error model parameters works with a precision of 10% when
we use lots of replicates in the synthetic data (see slow tests). This
is not new in this commit, but as I think it is reasonable this
closes #7.

1 files changed, 21 insertions, 21 deletions

diff --git a/test.log b/test.log
index 361359cf..79ff8ba7 100644
--- a/test.log
+++ b/test.log
@@ -1,30 +1,30 @@
 Loading mkin
 Testing mkin
 ✔ |  OK F W S | Context
-
⠏ |   0       | Export dataset for reading into CAKE
✔ |   1       | Export dataset for reading into CAKE
-
⠏ |   0       | Error model fitting
⠋ |   1       | Error model fitting
⠹ |   3       | Error model fitting
⠸ |   4       | Error model fitting
⠼ |   5       | Error model fitting
⠴ |   6       | Error model fitting
⠧ |   8       | Error model fitting
⠏ |  10       | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  10   1   | Error model fitting
⠋ |  11       | Error model fitting
⠹ |  13       | Error model fitting
⠸ |  14       | Error model fitting
⠼ |  15       | Error model fitting
⠴ |  16       | Error model fitting
⠦ |  17       | Error model fitting
⠧ |  18       | Error model fitting
⠇ |  19       | Error model fitting
⠏ |  20       | Error model fitting
✔ |  20       | Error model fitting [413.8 s]
-
⠏ |   0       | Calculation of FOCUS chi2 error levels
⠋ |   1       | Calculation of FOCUS chi2 error levels
⠹ |   3       | Calculation of FOCUS chi2 error levels
⠼ |   5       | Calculation of FOCUS chi2 error levels
✔ |   5       | Calculation of FOCUS chi2 error levels [3.5 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)
⠸ |   4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠇ |   9       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s]
-
⠏ |   0       | Test fitting the decline of metabolites from their maximum
⠋ |   1       | Test fitting the decline of metabolites from their maximum
⠹ |   3       | 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 [0.9 s]
-
⠏ |   0       | Fitting the logistic model
⠋ |   1       | Fitting the logistic model
✔ |   1       | Fitting the logistic model [0.9 s]
-
⠏ |   0       | 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
⠇ |   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       | Special cases of mkinfit calls [2.7 s]
-
⠏ |   0       | 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
✔ |   3       | Model predictions with mkinpredict [0.3 s]
-
⠏ |   0       | Evaluations according to 2015 NAFTA guidance
⠙ |   2       | Evaluations according to 2015 NAFTA guidance
⠇ |   9       | Evaluations according to 2015 NAFTA guidance
⠏ |  10       | Evaluations according to 2015 NAFTA guidance
⠴ |  16       | Evaluations according to 2015 NAFTA guidance
✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.0 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
⠴ |  16       | Fitting of parent only models
⠧ |  18       | Fitting of parent only models
⠏ |  20       | Fitting of parent only models
✔ |  21       | Fitting of parent only models [40.6 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) [2.2 s]
-
⠏ |   0       | Summary
✔ |   1       | Summary
-
⠏ |   0       | Plotting
⠹ |   3       | Plotting
✔ |   4       | Plotting [0.3 s]
-
⠏ |   0       | 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 [5.2 s]
-
⠏ |   0       | Summaries of old mkinfit objects
✔ |   1       | Summaries of old mkinfit objects
-
⠏ |   0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |   1       | 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) [7.2 s]
+✔ |   1       | Export dataset for reading into CAKE
+✔ |   2       | Confidence intervals and p-values [5.6 s]
+✔ |  11       | Error model fitting [53.4 s]
+✔ |   5       | Calculation of FOCUS chi2 error levels [3.5 s]
+✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s]
+✔ |   6       | Test fitting the decline of metabolites from their maximum [0.9 s]
+✔ |   1       | Fitting the logistic model [0.9 s]
+✔ |   1       | Test dataset class mkinds used in gmkin
+✔ |  12       | Special cases of mkinfit calls [2.7 s]
+✔ |   9       | mkinmod model generation and printing [0.2 s]
+✔ |   3       | Model predictions with mkinpredict [0.3 s]
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.0 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
+✔ |   1       | Summary
+✔ |   4       | Plotting [0.3 s]
+✔ |   2       | AIC calculation
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.2 s]
+✔ |   1       | Summaries of old mkinfit objects
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 491.0 s
+Duration: 95.5 s
 
-OK:       126
+OK:       98
 Failed:   0
 Warnings: 0
 Skipped:  0