From 7e8d788d298b8e1492fd8f62d88456e99e0f5992 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 4 Jul 2019 08:10:33 +0200 Subject: Address failures of CRAN checks, improve NEWS Static documentation rebuilt by pkgdown --- DESCRIPTION | 2 +- NEWS.md | 6 +++-- docs/articles/FOCUS_D.html | 8 +++--- docs/articles/FOCUS_L.html | 40 ++++++++++++++-------------- docs/articles/mkin.html | 2 +- docs/articles/twa.html | 2 +- docs/articles/web_only/FOCUS_Z.html | 2 +- docs/articles/web_only/NAFTA_examples.html | 2 +- docs/articles/web_only/benchmarks.html | 24 ++++++++--------- docs/articles/web_only/compiled_models.html | 12 ++++----- docs/news/index.html | 9 ++++--- docs/reference/mkinfit.html | 28 +++++++++---------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +-- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 4 +-- tests/testthat/test_error_models.R | 13 +++++---- tests/testthat/test_nafta.R | 8 ++++-- vignettes/mkin_benchmarks.rda | Bin 877 -> 875 bytes 19 files changed, 91 insertions(+), 81 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index eab410b5..7af9ef7e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.49.5 -Date: 2019-07-03 +Date: 2019-07-04 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), diff --git a/NEWS.md b/NEWS.md index 37964fd9..853f6b56 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# mkin 0.9.49.5 (2019-07-03) +# mkin 0.9.49.5 (2019-07-04) - Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm 'd_3' tries direct minimization and a three-step procedure, and returns the model with the highest likelihood. @@ -14,7 +14,7 @@ - Add a simple benchmark vignette to document the impact on performance. -- The code for manual weighting was removed. This functionality might get added again at a later time. +- The code for manual weighting was removed. This functionality might get added again at a later time. For the time being, please use an earlier version, e.g. 0.9.48.1 if you want to do manual weighting. - The fitting time reported in the summary now includes the time used for calculation of the hessians @@ -22,6 +22,8 @@ - Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting in parallel via mmkin this could go unnoticed. +- Add example datasets obtained from risk assessment reports published by the European Food Safety Agency. + # mkin 0.9.48.1 (2019-03-04) - Add the function 'logLik.mkinfit' which makes it possible to calculate an AIC for mkinfit objects diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 88a3fa6a..ed41e555 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -88,7 +88,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2019-07-03

+

2019-07-04

@@ -168,8 +168,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed Jul  3 16:39:00 2019 
-## Date of summary: Wed Jul  3 16:39:00 2019 
+## Date of fit:     Thu Jul  4 08:04:23 2019 
+## Date of summary: Thu Jul  4 08:04:24 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,7 +177,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 0.977 s
+## Fitted using 389 model solutions performed in 0.982 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 1b54252f..0060bd69 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -88,7 +88,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2019-07-03

+            
2019-07-04

       
       
       
@@ -114,15 +114,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed Jul  3 16:39:02 2019 
-## Date of summary: Wed Jul  3 16:39:02 2019 
+## Date of fit:     Thu Jul  4 08:04:26 2019 
+## Date of summary: Thu Jul  4 08:04:26 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.279 s
+## Fitted using 133 model solutions performed in 0.278 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -216,8 +216,8 @@
 ## finite result is doubtful
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed Jul  3 16:39:04 2019 
-## Date of summary: Wed Jul  3 16:39:04 2019 
+## Date of fit:     Thu Jul  4 08:04:28 2019 
+## Date of summary: Thu Jul  4 08:04:28 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -229,7 +229,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.874 s
+## Fitted using 899 model solutions performed in 1.876 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -321,15 +321,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed Jul  3 16:39:05 2019 
-## Date of summary: Wed Jul  3 16:39:05 2019 
+## Date of fit:     Thu Jul  4 08:04:29 2019 
+## Date of summary: Thu Jul  4 08:04:29 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.485 s
+## Fitted using 239 model solutions performed in 0.486 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -397,8 +397,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed Jul  3 16:39:07 2019 
-## Date of summary: Wed Jul  3 16:39:07 2019 
+## Date of fit:     Thu Jul  4 08:04:30 2019 
+## Date of summary: Thu Jul  4 08:04:30 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -497,8 +497,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed Jul  3 16:39:08 2019 
-## Date of summary: Wed Jul  3 16:39:09 2019 
+## Date of fit:     Thu Jul  4 08:04:32 2019 
+## Date of summary: Thu Jul  4 08:04:32 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -507,7 +507,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.772 s
+## Fitted using 373 model solutions performed in 0.773 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -603,8 +603,8 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed Jul  3 16:39:09 2019 
-## Date of summary: Wed Jul  3 16:39:10 2019 
+## Date of fit:     Thu Jul  4 08:04:33 2019 
+## Date of summary: Thu Jul  4 08:04:33 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -668,15 +668,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed Jul  3 16:39:10 2019 
-## Date of summary: Wed Jul  3 16:39:10 2019 
+## Date of fit:     Thu Jul  4 08:04:33 2019 
+## Date of summary: Thu Jul  4 08:04:33 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.452 s
+## Fitted using 224 model solutions performed in 0.453 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index df694259..8ad4a8e9 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -88,7 +88,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2019-07-03

+            
2019-07-04

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 34b85796..98e5efdf 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -88,7 +88,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2019-07-03

+            
2019-07-04

       
       
       
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index b82e1e01..4a856b71 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -88,7 +88,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2019-07-03

+            
2019-07-04

       
       
       
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index c1922b64..3f6ff8b9 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -88,7 +88,7 @@
       
Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

                         
Johannes Ranke

             
-            
2019-07-03

+            
2019-07-04

       
       
       
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index c68db93b..005834cc 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -88,7 +88,7 @@
       
Benchmark timings for mkin on various systems

                         
Johannes Ranke

             
-            
2019-07-03

+            
2019-07-04

       
       
       
@@ -202,77 +202,77 @@
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.820
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.843
 ##                                                                         t2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.917
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.863
 ##                                                                        t3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.415
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.417
 ##                                                                         t4
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.588
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.484
 ##                                                                         t5
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1  9.495
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  6.395
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.675
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.386
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  6.002
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.317
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.307
 ##                                                                        t6
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.556
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.538
 ##                                                                        t7
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.213
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.196
 ##                                                                        t8
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.851
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.853
 ##                                                                         t9
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.763
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.645
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.643
 ##                                                                       t10
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.734
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.733
 ##                                                                        t11
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.489

+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.511

 
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")

 
   
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index b30488a0..3fc54cfa 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -88,7 +88,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2019-07-03

+            
2019-07-04

       
       
       
@@ -163,9 +163,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.043    1.000     3.042        0
-## 1 deSolve, not compiled            3  28.630    9.408    28.616        0
-## 2      Eigenvalue based            3   4.291    1.410     4.289        0
+## 3     deSolve, compiled            3   3.061    1.000     3.059        0
+## 1 deSolve, not compiled            3  28.502    9.311    28.487        0
+## 2      Eigenvalue based            3   4.321    1.412     4.318        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -214,8 +214,8 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.800    1.000     4.795    0.002
-## 1 deSolve, not compiled            3  53.371   11.119    53.346    0.000
+## 2     deSolve, compiled            3   4.818    1.000     4.814        0
+## 1 deSolve, not compiled            3  53.275   11.057    53.249        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/news/index.html b/docs/news/index.html
index f8504768..0b82cbcc 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -122,9 +122,9 @@
       
     
 
-    

+    

 

-mkin 0.9.49.5 (2019-07-03) Unreleased 
+mkin 0.9.49.5 (2019-07-04) Unreleased 
 

 
    
 
  • Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.
    • 
@@ -134,10 +134,11 @@
 
  • Remove dependency on FME, only use nlminb for optimisation (‘Port’ algorithm). I cannot remember cases where one of the other optimisation algorithms was preferable, except that I sometime used Levenberg-Marquardt for speed in cases where I did not expect to get trapped in a local minimum.
    • 
 
  • Use the numDeriv package to calculate hessians. This results in slightly different confidence intervals, takes a bit longer, but is apparently more robust
    • 
 
  • Add a simple benchmark vignette to document the impact on performance.
    • 
-
  • The code for manual weighting was removed. This functionality might get added again at a later time.
    • 
+
  • The code for manual weighting was removed. This functionality might get added again at a later time. For the time being, please use an earlier version, e.g. 0.9.48.1 if you want to do manual weighting.
    • 
 
  • The fitting time reported in the summary now includes the time used for calculation of the hessians
    • 
 
  • Adapt tests
    • 
 
  • Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting in parallel via mmkin this could go unnoticed.
    • 
+
  • Add example datasets obtained from risk assessment reports published by the European Food Safety Agency.
    • 
 

 

     

@@ -698,7 +699,7 @@
     

       
Contents

       
    
-        
  • 0.9.49.5
    • 
+        
  • 0.9.49.5
    • 
         
  • 0.9.48.1
    • 
         
  • 0.9.47.5
    • 
         
  • 0.9.47.3
    • 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 3e20fc5d..0983007e 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -399,15 +399,15 @@ Per default, parameters in the kinetic models are internally transformed in
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed Jul  3 16:36:58 2019 
-#> Date of summary: Wed Jul  3 16:36:58 2019 
+#> Date of fit:     Thu Jul  4 08:02:21 2019 
+#> Date of summary: Thu Jul  4 08:02:21 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.46 s
+#> Fitted using 222 model solutions performed in 0.464 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -481,7 +481,7 @@ Per default, parameters in the kinetic models are internally transformed in
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.497       0.000       1.499 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.507       0.004       1.511 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -553,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.079       0.000       1.079 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.078       0.000       1.078 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -585,8 +585,8 @@ Per default, parameters in the kinetic models are internally transformed in
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed Jul  3 16:37:14 2019 
-#> Date of summary: Wed Jul  3 16:37:14 2019 
+#> Date of fit:     Thu Jul  4 08:02:37 2019 
+#> Date of summary: Thu Jul  4 08:02:37 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -594,7 +594,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.107 s
+#> Fitted using 421 model solutions performed in 1.096 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -704,8 +704,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   120       m1    25.15  28.78984 -3.640e+00
 #>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed Jul  3 16:37:17 2019 
-#> Date of summary: Wed Jul  3 16:37:17 2019 
+#> Date of fit:     Thu Jul  4 08:02:40 2019 
+#> Date of summary: Thu Jul  4 08:02:40 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -713,7 +713,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.612 s
+#> Fitted using 979 model solutions performed in 2.574 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -836,8 +836,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   120       m1    25.15  28.80429 -3.654e+00
 #>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed Jul  3 16:37:26 2019 
-#> Date of summary: Wed Jul  3 16:37:26 2019 
+#> Date of fit:     Thu Jul  4 08:02:49 2019 
+#> Date of summary: Thu Jul  4 08:02:49 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -845,7 +845,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.522 s
+#> Fitted using 2289 model solutions performed in 9.379 s
 #> 
 #> Error model: Two-component variance function 
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index f1793541..39fe631b 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -234,7 +234,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file24f24fd75f75.c 2> file24f24fd75f75.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file6e9c38dae9ed.c 2> file6e9c38dae9ed.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 9c4263b6..ef847245 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -328,7 +328,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.003       0.000       0.004 
  system.time(
+#>       0.004       0.000       0.003 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
@@ -338,7 +338,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.022       0.000       0.022 

+#>       0.022       0.000       0.021 

   
    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
 #> Sum of squared residuals at call 3: 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 7a34ac7d..38c46b6e 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -194,8 +194,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.036       0.048       5.130 
time_1
#>        User      System verstrichen 
-#>      19.222       0.000      19.233 

+#>       0.055       0.032       5.069 
time_1
#>        User      System verstrichen 
+#>      19.260       0.000      19.271 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340481   0.2659519   0.7505684   0.2494316 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 4f2c9ecb..c4d2653d 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,8 +211,8 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed Jul  3 16:38:45 2019 
-#> Date of summary: Wed Jul  3 16:38:45 2019 
+#> Date of fit:     Thu Jul  4 08:04:08 2019 
+#> Date of summary: Thu Jul  4 08:04:08 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R
index 33e44bf8..fbae6286 100644
--- a/tests/testthat/test_error_models.R
+++ b/tests/testthat/test_error_models.R
@@ -91,14 +91,17 @@ test_that("Reweighting method 'tc' produces reasonable variance estimates", {
     sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
     n = 1, reps = 100, digits = 5, LOD = -Inf, seed = 123456)
 
-  # Per default (on my box) use all cores minus one
-  n_cores <- parallel::detectCores() - 1
+  # Per default (on my box where I set NOT_CRAN) use all cores minus one
+  if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+    n_cores <- parallel::detectCores() - 1
+  } else {
+    n_cores <- 1
+  }
 
-  # We are only allowed one core on travis
+  # We are only allowed one core on travis, but they also set NOT_CRAN=true
   if (Sys.getenv("TRAVIS") != "") n_cores = 1
 
-  # Also on Windows we would need to make a cluster first,
-  # and I do not know how this would work on winbuilder or CRAN, so
+  # On Windows we would need to make a cluster first
   if (Sys.info()["sysname"] == "Windows") n_cores = 1
 
   # Unweighted fits
diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R
index 096287aa..8cb1895b 100644
--- a/tests/testthat/test_nafta.R
+++ b/tests/testthat/test_nafta.R
@@ -39,7 +39,9 @@ test_that("Test data from Appendix B are correctly evaluated", {
   expect_known_output(print(res), "NAFTA_SOP_Appendix_B.txt")
 
   plot_nafta <- function() plot(res)
-  vdiffr::expect_doppelganger("NAFTA SOP Appendix B", plot_nafta)
+  if(requireNamespace("vdiffr", quietly = TRUE)) {
+    vdiffr::expect_doppelganger("NAFTA SOP Appendix B", plot_nafta)
+  }
 })
 
 test_that("Test data from Appendix D are correctly evaluated", {
@@ -61,5 +63,7 @@ test_that("Test data from Appendix D are correctly evaluated", {
   expect_known_output(print(res), "NAFTA_SOP_Appendix_D.txt")
 
   plot_nafta <- function() plot(res)
-  vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta)
+  if(requireNamespace("vdiffr", quietly = TRUE)) {
+    vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta)
+  }
 })
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
index 4828db0d..521ccb7d 100644
Binary files a/vignettes/mkin_benchmarks.rda and b/vignettes/mkin_benchmarks.rda differ
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