From 1c7b39f3c542de75a1ba685fec3c154bef8a3301 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 18:30:21 +0200 Subject: Static documentation rebuilt by pkgdown to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly --- docs/articles/FOCUS_D.html | 6 ++-- docs/articles/FOCUS_L.html | 42 ++++++++++++++-------------- docs/articles/twa.html | 2 +- docs/articles/web_only/benchmarks.html | 20 ++++++------- docs/articles/web_only/compiled_models.html | 10 +++---- docs/reference/mkinfit.html | 28 +++++++++---------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 ++-- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 6 ++-- vignettes/mkin_benchmarks.rda | Bin 885 -> 880 bytes vignettes/twa.Rmd | 8 ++---- vignettes/twa.html | 2 +- 13 files changed, 67 insertions(+), 69 deletions(-) diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index c22eb2c3..53164ffd 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -170,8 +170,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:05 2019 
-## Date of summary: Wed Sep 18 17:55:06 2019 
+## Date of fit:     Wed Sep 18 18:24:07 2019 
+## Date of summary: Wed Sep 18 18:24:08 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +179,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 1.003 s
+## Fitted using 389 model solutions performed in 1.014 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 428ca84f..50c83db6 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -116,15 +116,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:08 2019 
-## Date of summary: Wed Sep 18 17:55:08 2019 
+## Date of fit:     Wed Sep 18 18:24:09 2019 
+## Date of summary: Wed Sep 18 18:24:09 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.293 s
+## Fitted using 133 model solutions performed in 0.287 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -218,8 +218,8 @@
 ## finite result is doubtful
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:10 2019 
-## Date of summary: Wed Sep 18 17:55:10 2019 
+## Date of fit:     Wed Sep 18 18:24:12 2019 
+## Date of summary: Wed Sep 18 18:24:12 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -231,7 +231,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.914 s
+## Fitted using 899 model solutions performed in 1.954 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -323,15 +323,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:11 2019 
-## Date of summary: Wed Sep 18 17:55:11 2019 
+## Date of fit:     Wed Sep 18 18:24:13 2019 
+## Date of summary: Wed Sep 18 18:24:13 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 0.511 s
+## Fitted using 239 model solutions performed in 0.497 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -399,8 +399,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:12 2019 
-## Date of summary: Wed Sep 18 17:55:12 2019 
+## Date of fit:     Wed Sep 18 18:24:14 2019 
+## Date of summary: Wed Sep 18 18:24:14 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -409,7 +409,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.217 s
+## Fitted using 572 model solutions performed in 1.215 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -499,8 +499,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:14 2019 
-## Date of summary: Wed Sep 18 17:55:14 2019 
+## Date of fit:     Wed Sep 18 18:24:16 2019 
+## Date of summary: Wed Sep 18 18:24:16 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -509,7 +509,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.803 s
+## Fitted using 373 model solutions performed in 0.778 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -605,15 +605,15 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:15 2019 
-## Date of summary: Wed Sep 18 17:55:15 2019 
+## Date of fit:     Wed Sep 18 18:24:17 2019 
+## Date of summary: Wed Sep 18 18:24:17 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.301 s
+## Fitted using 142 model solutions performed in 0.293 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -670,15 +670,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:15 2019 
-## Date of summary: Wed Sep 18 17:55:15 2019 
+## Date of fit:     Wed Sep 18 18:24:17 2019 
+## Date of summary: Wed Sep 18 18:24:17 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 0.458 s
+## Fitted using 224 model solutions performed in 0.46 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 799349d9..2d44a89d 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -130,7 +130,7 @@
 
\[f_\textrm{twa} = \frac{1}{t} \left(
   \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
   \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) \]

-
Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the ‘max_twa_parent’ function. If the same is needed for metabolites, the function ‘max_twa’ from the ‘pfm’ package can be used.

+
Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the max_twa_parent() function. If the same is needed for metabolites, the function pfm::max_twa() from the ‘pfm’ package can be used.

 

 

 
FOCUS Work Group on Degradation Kinetics. 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.

diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 144c4c29..d46e738a 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -204,70 +204,70 @@
 ## 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 0.9.49.6 5.940
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.970
 ##                                                                         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 0.9.49.6 36.631
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.524
 ##                                                                        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 0.9.49.6 4.507
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.607
 ##                                                                         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 0.9.49.6 31.282
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.617
 ##                                                                         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 0.9.49.6 10.727
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.543
 ##                                                                        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 0.9.49.6 2.634
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.579
 ##                                                                        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 0.9.49.6 4.295
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.341
 ##                                                                        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 0.9.49.6  8.13
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.101
 ##                                                                         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 0.9.49.6 16.064
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.211
 ##                                                                       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 0.9.49.6 8.034
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.041
 ##                                                                        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
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 6594c3e6..1876e2b3 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -165,9 +165,9 @@
 ## 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   3.143    1.000     3.141        0
-## 1 deSolve, not compiled            3  28.853    9.180    28.839        0
-## 2      Eigenvalue based            3   4.427    1.409     4.425        0
+## 3     deSolve, compiled            3   3.129    1.000     3.127        0
+## 1 deSolve, not compiled            3  28.841    9.217    28.827        0
+## 2      Eigenvalue based            3   4.433    1.417     4.430        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -216,8 +216,8 @@
 ## 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   4.956    1.000     4.952        0
-## 1 deSolve, not compiled            3  53.338   10.762    53.312        0
+## 2     deSolve, compiled            3   4.860    1.000     4.857        0
+## 1 deSolve, not compiled            3  53.877   11.086    53.850        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 954086b5..dc052f2a 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -408,15 +408,15 @@ 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:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 17:53:04 2019 
-#> Date of summary: Wed Sep 18 17:53:04 2019 
+#> Date of fit:     Wed Sep 18 18:22:06 2019 
+#> Date of summary: Wed Sep 18 18:22:06 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 0.467 s
+#> Fitted using 222 model solutions performed in 0.459 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -490,7 +490,7 @@ 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 
-#>       1.524       0.000       1.527 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.494       0.000       1.496 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -563,7 +563,7 @@ 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 
-#>       1.115       0.000       1.116 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.056       0.000       1.057 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -599,8 +599,8 @@ 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:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 17:53:19 2019 
-#> Date of summary: Wed Sep 18 17:53:19 2019 
+#> Date of fit:     Wed Sep 18 18:22:22 2019 
+#> Date of summary: Wed Sep 18 18:22:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -608,7 +608,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.167 s
+#> Fitted using 421 model solutions performed in 1.15 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -718,8 +718,8 @@ 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:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 17:53:22 2019 
-#> Date of summary: Wed Sep 18 17:53:22 2019 
+#> Date of fit:     Wed Sep 18 18:22:24 2019 
+#> Date of summary: Wed Sep 18 18:22:24 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -727,7 +727,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.583 s
+#> Fitted using 979 model solutions performed in 2.553 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -850,8 +850,8 @@ 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:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 17:53:31 2019 
-#> Date of summary: Wed Sep 18 17:53:31 2019 
+#> Date of fit:     Wed Sep 18 18:22:34 2019 
+#> Date of summary: Wed Sep 18 18:22:34 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -859,7 +859,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.35 s
+#> Fitted using 2289 model solutions performed in 9.369 s
 #> 
 #> Error model: Two-component variance function 
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 4c73a0db..a5cdd04d 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -239,7 +239,7 @@ 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 file195c26c6bf0a.c 2> file195c26c6bf0a.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file310b6c1fede0.c 2> file310b6c1fede0.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index f2c6f87f..97d3ca3a 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -332,17 +332,17 @@
                 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       0.003 
  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 
-#>       0.001       0.000       0.001 
  system.time(
+#>       0.001       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
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.022       0.000       0.022 

+#>       0.021       0.000       0.022 

   # \dontrun{
     # 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
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index eac99579..81ebde7c 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -199,8 +199,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.013       0.027       5.014 
time_1
#>        User      System verstrichen 
-#>      19.047       0.000      19.057 

+#>       0.013       0.039       5.128 
time_1
#>        User      System verstrichen 
+#>      18.942       0.000      18.951 

 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 cc2ac55a..c5d58911 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -215,15 +215,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 17:54:50 2019 
-#> Date of summary: Wed Sep 18 17:54:50 2019 
+#> Date of fit:     Wed Sep 18 18:23:52 2019 
+#> Date of summary: Wed Sep 18 18:23:52 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.27 s
+#> Fitted using 131 model solutions performed in 0.268 s
 #> 
 #> Error model: Constant variance 
 #> 
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
index 764c874c..aa794a02 100644
Binary files a/vignettes/mkin_benchmarks.rda and b/vignettes/mkin_benchmarks.rda differ
diff --git a/vignettes/twa.Rmd b/vignettes/twa.Rmd
index 6ebb7b89..6f283eb2 100644
--- a/vignettes/twa.Rmd
+++ b/vignettes/twa.Rmd
@@ -74,8 +74,6 @@ $$f_\textrm{twa} = \frac{1}{t} \left(
 
 Note that a method for calculating maximum moving window time weighted average
 concentrations for a model fitted by 'mkinfit' or from parent decline model
-parameters is included in the
-['max_twa_parent'](https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html)
-function.
-If the same is needed for metabolites, the function 
-['max_twa'](https://pkgdown.jrwb.de/pfm/reference/max_twa.html) from the 'pfm' package can be used.
+parameters is included in the `max_twa_parent()` function. If the same is
+needed for metabolites, the function `pfm::max_twa()` from the 'pfm' package
+can be used.
diff --git a/vignettes/twa.html b/vignettes/twa.html
index 0db7eeff..41989b5d 100644
--- a/vignettes/twa.html
+++ b/vignettes/twa.html
@@ -252,7 +252,7 @@ code > span.fu { color: #900; font-weight: bold; }  code > span.er { color: #a61
 
\[f_\textrm{twa} = \frac{1}{t} \left(
   \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
   \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) \]

-
Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the ‘max_twa_parent’ function. If the same is needed for metabolites, the function ‘max_twa’ from the ‘pfm’ package can be used.

+
Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the max_twa_parent() function. If the same is needed for metabolites, the function pfm::max_twa() from the ‘pfm’ package can be used.

 

 

 
FOCUS Work Group on Degradation Kinetics. 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.

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