From 6ddb7575f37d9d534f014cbd105b2f07660d59c6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 2 May 2019 18:54:22 +0200 Subject: Remove reference to archived kinfit package from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_D.html | 6 ++--- docs/articles/FOCUS_L.html | 42 ++++++++++++++--------------- docs/articles/mkin.html | 13 +++------ docs/articles/web_only/benchmarks.html | 22 +++++++-------- docs/articles/web_only/compiled_models.html | 10 +++---- 5 files changed, 43 insertions(+), 50 deletions(-) (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 4b82dd03..3ce94de7 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -168,8 +168,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 17:42:41 2019 
-## Date of summary: Thu May  2 17:42:41 2019 
+## Date of fit:     Thu May  2 18:49:13 2019 
+## Date of summary: Thu May  2 18:49:14 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 396 model solutions performed in 1.055 s
+## Fitted using 396 model solutions performed in 0.999 s
 ## 
 ## Error model:
 ## Constant variance 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 05980b97..42f2dc60 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -114,15 +114,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 17:42:43 2019 
-## Date of summary: Thu May  2 17:42:43 2019 
+## Date of fit:     Thu May  2 18:49:16 2019 
+## Date of summary: Thu May  2 18:49:16 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.286 s
+## Fitted using 133 model solutions performed in 0.278 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -215,8 +215,8 @@
 ## finite result is doubtful
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 17:42:45 2019 
-## Date of summary: Thu May  2 17:42:45 2019 
+## Date of fit:     Thu May  2 18:49:17 2019 
+## Date of summary: Thu May  2 18:49:17 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -228,7 +228,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 599 model solutions performed in 1.253 s
+## Fitted using 599 model solutions performed in 1.26 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -319,15 +319,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 17:42:46 2019 
-## Date of summary: Thu May  2 17:42:46 2019 
+## Date of fit:     Thu May  2 18:49:18 2019 
+## Date of summary: Thu May  2 18:49:18 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 240 model solutions performed in 0.485 s
+## Fitted using 240 model solutions performed in 0.486 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -394,8 +394,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 17:42:47 2019 
-## Date of summary: Thu May  2 17:42:47 2019 
+## Date of fit:     Thu May  2 18:49:20 2019 
+## Date of summary: Thu May  2 18:49:20 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,7 +404,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 587 model solutions performed in 1.22 s
+## Fitted using 587 model solutions performed in 1.223 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -493,8 +493,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 17:42:49 2019 
-## Date of summary: Thu May  2 17:42:49 2019 
+## Date of fit:     Thu May  2 18:49:21 2019 
+## Date of summary: Thu May  2 18:49:22 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,7 +503,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 372 model solutions performed in 0.769 s
+## Fitted using 372 model solutions performed in 0.768 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -598,15 +598,15 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 17:42:50 2019 
-## Date of summary: Thu May  2 17:42:50 2019 
+## Date of fit:     Thu May  2 18:49:22 2019 
+## Date of summary: Thu May  2 18:49:23 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 146 model solutions performed in 0.293 s
+## Fitted using 146 model solutions performed in 0.294 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -662,15 +662,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 17:42:50 2019 
-## Date of summary: Thu May  2 17:42:50 2019 
+## Date of fit:     Thu May  2 18:49:23 2019 
+## Date of summary: Thu May  2 18:49:23 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 0.454 s
 ## 
 ## Error model:
 ## Constant variance 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index bf52f364..132e0c14 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -136,10 +136,9 @@
 

 Background

 
Many approaches are possible regarding the evaluation of chemical degradation data.

-
The now deprecated kinfit package (Ranke 2015) in R (R Development Core Team 2016) implements the approach recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe (FOCUS Work Group on Degradation Kinetics 2006, 2014) for simple data series for one parent compound in one compartment.

-
The mkin package (Ranke 2016) extends this approach to data series with transformation products, commonly termed metabolites, and to more than one compartment. It is also possible to include back reactions, so equilibrium reactions and equilibrium partitioning can be specified, although this oftentimes leads to an overparameterisation of the model.

+
The mkin package (Ranke 2016) implements the approach recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe (FOCUS Work Group on Degradation Kinetics 2006, 2014) implements this approach for simple decline data series, data series with transformation products, commonly termed metabolites, data series for more than one compartment. It is also possible to include back reactions, so equilibrium reactions and equilibrium partitioning can be specified, although this oftentimes leads to an overparameterisation of the model.

 
When the first mkin code was published in 2010, the most commonly used tools for fitting more complex kinetic degradation models to experimental data were KinGUI (Schäfer et al. 2007), a MATLAB based tool with a graphical user interface that was specifically tailored to the task and included some output as proposed by the FOCUS Kinetics Workgroup, and ModelMaker, a general purpose compartment based tool providing infrastructure for fitting dynamic simulation models based on differential equations to data.

-
The code was first uploaded to the BerliOS platform. When this was taken down, the version control history was imported into the R-Forge site, where the code is still mirrored today (see e.g. the initial commit on 11 May 2010).

+
The code was first uploaded to the BerliOS platform. When this was taken down, the version control history was imported into the R-Forge site (see e.g. the initial commit on 11 May 2010), where the code is still occasionally updated.

 
At that time, the R package FME (Flexible Modelling Environment) (Soetaert and Petzoldt 2010) was already available, and provided a good basis for developing a package specifically tailored to the task. The remaining challenge was to make it as easy as possible for the users (including the author of this vignette) to specify the system of differential equations and to include the output requested by the FOCUS guidance, such as the relative standard deviation that has to be assumed for the residuals, such that the \(\chi^2\) goodness-of-fit test as defined by the FOCUS kinetics workgroup would pass using an significance level \(\alpha\) of 0.05.

 
Also, mkin introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to mkin for the case of linear differential equations (i.e. where the FOMC or DFOP models were not used for the parent compound), greatly improving the optimization speed for these cases.

 
The possibility to specify back-reactions and a biphasic model (SFORB) for metabolites were present in mkin from the very beginning.

@@ -194,11 +193,8 @@
 

 
———. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

 

-

-
Ranke, J. 2015. ‘Kinfit‘: Routines for Fitting Simple Kinetic Models to Chemical Degradation Data. https://CRAN.R-project.org/package=kinfit.

-

 

-
———. 2016. ‘Mkin‘: Kinetic Evaluation of Chemical Degradation Data. https://CRAN.R-project.org/package=mkin.

+
Ranke, J. 2016. ‘Mkin‘: Kinetic Evaluation of Chemical Degradation Data. https://CRAN.R-project.org/package=mkin.

 

 

 
Ranke, J., and R. Lehmann. 2012. “Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.” In SETAC World 20-24 May. Berlin.

@@ -206,9 +202,6 @@
 

 
———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In XV Symposium on Pesticide Chemistry 2-4 September 2015. Piacenza. http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf.

 

-

-
R Development Core Team. 2016. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org.

-

 

 
Schäfer, D., B. Mikolasch, P. Rainbird, and B. Harvey. 2007. “KinGUI: A New Kinetic Software Tool for Evaluations According to FOCUS Degradation Kinetics.” In Proceedings of the Xiii Symposium Pesticide Chemistry, edited by Del Re A. A. M., Capri E., Fragoulis G., and Trevisan M., 916–23. Piacenza.

 

diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 0653517a..5f6312ce 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -198,67 +198,67 @@
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184
 ## 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 5.853
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.850
 ##                                                                         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 19.968
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.019
 ##                                                                        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 4.320
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.293
 ##                                                                         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 14.542
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 14.570
 ##                                                                        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 5.786
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.772
 ##                                                                        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 2.524
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.647
 ##                                                                        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 4.224
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.257
 ##                                                                        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 4.696
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.703
 ##                                                                         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  7.776
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.742
 ##                                                                       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 3.432
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.421
 ##                                                                        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  5.599

+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.614

 
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 3174a067..362bc72c 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -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   3.199    1.000     3.198        0
-## 1 deSolve, not compiled            3  28.591    8.937    28.578        0
-## 2      Eigenvalue based            3   4.405    1.377     4.403        0
+## 3     deSolve, compiled            3   3.174    1.000     3.172        0
+## 1 deSolve, not compiled            3  28.777    9.066    28.764        0
+## 2      Eigenvalue based            3   4.386    1.382     4.383        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   4.553    1.000     4.551        0
-## 1 deSolve, not compiled            3  49.844   10.948    49.822        0
+## 2     deSolve, compiled            3   4.561    1.000     4.559        0
+## 1 deSolve, not compiled            3  49.847   10.929    49.823        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

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