From 798195d367111e592e5247309b90fac29ed7ddfd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 3 Jul 2019 16:45:09 +0200 Subject: Update DESCRIPTION, improve NEWS Static documentation rebuilt by pkgdown --- DESCRIPTION | 2 +- NEWS.md | 16 +++++----- docs/articles/FOCUS_D.html | 8 ++--- docs/articles/FOCUS_L.html | 44 ++++++++++++++-------------- docs/articles/mkin.html | 2 +- docs/articles/twa.html | 4 +-- 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 | 20 ++++++------- docs/reference/index.html | 2 +- docs/reference/mkinfit.html | 30 +++++++++---------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +-- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 4 +-- vignettes/mkin_benchmarks.rda | Bin 876 -> 877 bytes 18 files changed, 91 insertions(+), 91 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 03a1c9dd..eab410b5 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: 2019-06-04 +Date: 2019-07-03 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 0a2b3300..37964fd9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ -# mkin 0.9.49.5 (2019-06-04) +# mkin 0.9.49.5 (2019-07-03) -- 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 tries direct minimization and a three step procedure, and returns the model with the highest likelihood. +- 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. - The argument 'reweight.method' to mkinfit and mmkin is now obsolete, use 'error_model' and 'error_model_algorithm' instead @@ -8,19 +8,19 @@ - New function 'mkinerrplot'. This function is also used for residual plots in 'plot.mmkin' if the argument 'resplot = "errmod"' is given, and in 'plot.mkinfit' if 'show_errplot' is set to TRUE. -- Remove dependency on FME, only use nlminb for optimisation +- 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 +- 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 benchmark vignette to document the impact on performance. For very simple fits, the new code is a bit slower, presumably because of the time it takes to calculate the hessian matrices with and without parameter transformation +- Add a simple benchmark vignette to document the impact on performance. -- The code for manual weighting was removed +- The code for manual weighting was removed. This functionality might get added again at a later time. -- The fitting time reported in the summary now includes the calculation of the hessians +- 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 via mmkin this could easily go unnoticed. +- 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. # mkin 0.9.48.1 (2019-03-04) diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index be1f40f5..88a3fa6a 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

-

2019-06-05

+

2019-07-03

@@ -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 Jun  5 15:10:49 2019 
-## Date of summary: Wed Jun  5 15:10:50 2019 
+## Date of fit:     Wed Jul  3 16:39:00 2019 
+## Date of summary: Wed Jul  3 16:39:00 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 0.984 s
+## Fitted using 389 model solutions performed in 0.977 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 4388edd2..1b54252f 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

             
-            
2019-06-05

+            
2019-07-03

       
       
       
@@ -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 Jun  5 15:10:52 2019 
-## Date of summary: Wed Jun  5 15:10:52 2019 
+## Date of fit:     Wed Jul  3 16:39:02 2019 
+## Date of summary: Wed Jul  3 16:39:02 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.277 s
+## Fitted using 133 model solutions performed in 0.279 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 Jun  5 15:10:54 2019 
-## Date of summary: Wed Jun  5 15:10:54 2019 
+## Date of fit:     Wed Jul  3 16:39:04 2019 
+## Date of summary: Wed Jul  3 16:39:04 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -229,7 +229,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.877 s
+## Fitted using 899 model solutions performed in 1.874 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 Jun  5 15:10:55 2019 
-## Date of summary: Wed Jun  5 15:10:55 2019 
+## Date of fit:     Wed Jul  3 16:39:05 2019 
+## Date of summary: Wed Jul  3 16:39:05 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 0.492 s
+## Fitted using 239 model solutions performed in 0.485 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 Jun  5 15:10:56 2019 
-## Date of summary: Wed Jun  5 15:10:56 2019 
+## Date of fit:     Wed Jul  3 16:39:07 2019 
+## Date of summary: Wed Jul  3 16:39:07 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -407,7 +407,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.183 s
+## Fitted using 572 model solutions performed in 1.19 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -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 Jun  5 15:10:58 2019 
-## Date of summary: Wed Jun  5 15:10:58 2019 
+## Date of fit:     Wed Jul  3 16:39:08 2019 
+## Date of summary: Wed Jul  3 16:39:09 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 0.773 s
+## Fitted using 373 model solutions performed in 0.772 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -603,15 +603,15 @@
 
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 Jun  5 15:10:59 2019 
-## Date of summary: Wed Jun  5 15:10:59 2019 
+## Date of fit:     Wed Jul  3 16:39:09 2019 
+## Date of summary: Wed Jul  3 16:39:10 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.288 s
+## Fitted using 142 model solutions performed in 0.29 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -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 Jun  5 15:10:59 2019 
-## Date of summary: Wed Jun  5 15:10:59 2019 
+## Date of fit:     Wed Jul  3 16:39:10 2019 
+## Date of summary: Wed Jul  3 16:39:10 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 0.453 s
+## Fitted using 224 model solutions performed in 0.452 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 5977d642..df694259 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -88,7 +88,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2019-06-05

+            
2019-07-03

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index f98026e7..34b85796 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

             
-            
2019-06-05

+            
2019-07-03

       
       
       
@@ -98,7 +98,7 @@
     
     
 
Since version 0.9.45.1 of the ‘mkin’ package, a function for calculating time weighted average concentrations for decline kinetics (i.e. only for the compound applied in the experiment) is included. Strictly speaking, they are maximum moving window time weighted average concentrations, i.e. the maximum time weighted average concentration that can be found when moving a time window of a specified width over the decline curve.

-
Time weighted average concentrations for the SFO, FOMC and the DFOMP model are calculated using the formulas given in the FOCUS kinetics guidance (FOCUS Work Group on Degradation Kinetics 2014, 251):

+
Time weighted average concentrations for the SFO, FOMC and the DFOP model are calculated using the formulas given in the FOCUS kinetics guidance (FOCUS Work Group on Degradation Kinetics 2014, 251):

 
SFO:

 
\[c_\textrm{twa} = c_0 \frac{\left( 1 - e^{- k t} \right)}{ k t} \]

 
FOMC:

diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 542deb14..b82e1e01 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

             
-            
2019-06-05

+            
2019-07-03

       
       
       
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 4cd16437..c1922b64 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

             
-            
2019-06-05

+            
2019-07-03

       
       
       
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 507bdb61..c68db93b 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

             
-            
2019-06-05

+            
2019-07-03

       
       
       
@@ -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 5.828
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.820
 ##                                                                         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 35.869
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.917
 ##                                                                        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 4.412
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.415
 ##                                                                         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 30.497
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.588
 ##                                                                         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 10.329
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.317
 ##                                                                        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 2.548
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.556
 ##                                                                        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 4.192
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.213
 ##                                                                        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 7.827
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.851
 ##                                                                         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 15.653
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.645
 ##                                                                       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 7.762
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.734
 ##                                                                        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 10.512

+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.489

 
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 5f0301fc..b30488a0 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

             
-            
2019-06-05

+            
2019-07-03

       
       
       
@@ -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   3.041    1.000     3.039        0
-## 1 deSolve, not compiled            3  28.429    9.349    28.415        0
-## 2      Eigenvalue based            3   4.291    1.411     4.288        0
+## 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
 ##   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   4.927    1.000     4.924        0
-## 1 deSolve, not compiled            3  53.138   10.785    53.108        0
+## 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
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/news/index.html b/docs/news/index.html
index df6d53db..f8504768 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -122,22 +122,22 @@
       
     
 
-    

+    

 

-mkin 0.9.49.5 (2019-06-04) Unreleased 
+mkin 0.9.49.5 (2019-07-03) 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 tries direct minimization and a three step procedure, and returns the model with the highest likelihood.
    • 
+
  • 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.
    • 
 
  • The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead
    • 
 
  • Add a test that checks if we get the best known AIC for parent only fits to 12 test datasets. Add these test datasets for this purpose.
    • 
 
  • New function ‘mkinerrplot’. This function is also used for residual plots in ‘plot.mmkin’ if the argument ‘resplot = “errmod”’ is given, and in ‘plot.mkinfit’ if ‘show_errplot’ is set to TRUE.
    • 
-
  • Remove dependency on FME, only use nlminb for optimisation
    • 
-
  • Use the numDeriv package to calculate hessians
    • 
-
  • Add a benchmark vignette to document the impact on performance. For very simple fits, the new code is a bit slower, presumably because of the time it takes to calculate the hessian matrices with and without parameter transformation
    • 
-
  • The code for manual weighting was removed
    • 
-
  • The fitting time reported in the summary now includes the calculation of the hessians
    • 
+
  • 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 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 via mmkin this could easily go unnoticed.
    • 
+
  • 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.
    • 
 

 

     

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

       
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/index.html b/docs/reference/index.html
index c5ac0d72..b645ea5a 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -505,7 +505,7 @@
       
         
           
    Deprecated functions
    
-          
    Functions that have been superseeded
    
+          
    Functions that have been superseded
    
         
       
       
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 700b6805..3e20fc5d 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -334,7 +334,7 @@ Per default, parameters in the kinetic models are internally transformed in
 
    The algorithm "direct" will directly minimize the negative
     log-likelihood.
    
 
    The algorithm "twostep" will minimize the negative log-likelihood
-    after an initial unweighted leas squares optimisation step.
    
+    after an initial unweighted least squares optimisation step.
    
 
    The algorithm "threestep" starts with unweighted least squares,
     then optimizes only the error model using the degradation model
     parameters found, and then minimizes the negative log-likelihood
@@ -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 Jun  5 15:08:20 2019 
-#> Date of summary: Wed Jun  5 15:08:20 2019 
+#> Date of fit:     Wed Jul  3 16:36:58 2019 
+#> Date of summary: Wed Jul  3 16:36:58 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 0.469 s
+#> Fitted using 222 model solutions performed in 0.46 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 
-#>       1.579       0.000       1.581 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.497       0.000       1.499 
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 
-#>       1.159       0.000       1.160 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.079       0.000       1.079 
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 Jun  5 15:08:36 2019 
-#> Date of summary: Wed Jun  5 15:08:36 2019 
+#> Date of fit:     Wed Jul  3 16:37:14 2019 
+#> Date of summary: Wed Jul  3 16:37:14 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 1.181 s
+#> Fitted using 421 model solutions performed in 1.107 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 Jun  5 15:08:39 2019 
-#> Date of summary: Wed Jun  5 15:08:39 2019 
+#> Date of fit:     Wed Jul  3 16:37:17 2019 
+#> Date of summary: Wed Jul  3 16:37:17 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 2.672 s
+#> Fitted using 979 model solutions performed in 2.612 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 Jun  5 15:08:50 2019 
-#> Date of summary: Wed Jun  5 15:08:50 2019 
+#> Date of fit:     Wed Jul  3 16:37:26 2019 
+#> Date of summary: Wed Jul  3 16:37:26 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 10.959 s
+#> Fitted using 2289 model solutions performed in 9.522 s
 #> 
 #> Error model: Two-component variance function 
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index ddab656c..f1793541 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 file50a55c3108b2.c 2> file50a55c3108b2.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file24f24fd75f75.c 2> file24f24fd75f75.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 7e71ec27..9c4263b6 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -328,12 +328,12 @@
                 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 
-#>       0.004       0.000       0.004 
  system.time(
+#>       0.003       0.000       0.004 
  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
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.003       0.000       0.002 
  system.time(
+#>       0.002       0.000       0.002 
  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", use_compiled = FALSE)[201,]))
#>     time   parent       m1
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 61a029fc..7a34ac7d 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 
-#>       0.038       0.050       6.779 
time_1
#>        User      System verstrichen 
-#>      27.209       0.004      27.278 

+#>       0.036       0.048       5.130 
time_1
#>        User      System verstrichen 
+#>      19.222       0.000      19.233 

 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 68b36542..4f2c9ecb 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 Jun  5 15:10:34 2019 
-#> Date of summary: Wed Jun  5 15:10:34 2019 
+#> Date of fit:     Wed Jul  3 16:38:45 2019 
+#> Date of summary: Wed Jul  3 16:38:45 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
index 17cf86ce..4828db0d 100644
Binary files a/vignettes/mkin_benchmarks.rda and b/vignettes/mkin_benchmarks.rda differ
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