Add functionality to plot the error model

by plotting squared residuals against predicted values, and
showing the variance function used in the fitted error model.

Rebuild docs

1 files changed, 13 insertions, 18 deletions

diff --git a/test.log b/test.log
index 230aaf7b..0fcca094 100644
--- a/test.log
+++ b/test.log
@@ -2,33 +2,28 @@ 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
⠋ |  11       | Error model fitting
✔ |  12       | Error model fitting [214.9 s]
-
⠏ |   0       | Calculation of FOCUS chi2 error levels
⠋ |   1       | 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)
⠸ |   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       | 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
⠋ |  11       | Error model fitting
✔ |  12       | Error model fitting [214.1 s]
+
⠏ |   0       | Calculation of FOCUS chi2 error levels
⠋ |   1       | Calculation of FOCUS chi2 error levels
⠹ |   3       | Calculation of FOCUS chi2 error levels
✔ |   3       | Calculation of FOCUS chi2 error levels [2.3 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) [3.8 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
⠋ |  10 1     | Special cases of mkinfit calls
⠙ |  11 1     | Special cases of mkinfit calls
✖ |  11 1     | Special cases of mkinfit calls [2.8 s]
-────────────────────────────────────────────────────────────────────────────────
-test_mkinfit_errors.R:72: failure: We get reproducible output if quiet = FALSE
-`mkinfit("DFOP", FOCUS_2006_C, reweight.method = "tc", trace_parms = TRUE)` has changed from known value recorded in 'DFOP_FOCUS_C_messages.txt'.
-Lengths differ: 165 is not 410
-────────────────────────────────────────────────────────────────────────────────
-
⠏ |   0       | mkinmod model generation and printing
⠇ |   9       | mkinmod model generation and printing
✔ |   9       | mkinmod model generation and printing [0.1 s]
+
⠏ |   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 [2.9 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 [40.5 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       | 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 [4.1 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
⠴ |  16       | Fitting of parent only models
⠧ |  18       | Fitting of parent only models
⠏ |  20       | Fitting of parent only models
✔ |  21       | Fitting of parent only models [40.1 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) [2.3 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 [5.3 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)
⠹ |   3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 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 [5.2 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)
⠹ |   3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.0 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 291.1 s
+Duration: 289.7 s
 
-OK:       114
-Failed:   1
+OK:       115
+Failed:   0
 Warnings: 0
 Skipped:  0