From a401a9225d212ed4dc64e96765f04aaaf17cc8c1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 13:23:23 +0200 Subject: Further corrections of the twa vignette Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_D.html | 6 ++--- docs/articles/FOCUS_L.html | 42 ++++++++++++++--------------- docs/articles/twa.html | 2 +- docs/articles/web_only/benchmarks.html | 22 +++++++-------- docs/articles/web_only/compiled_models.html | 10 +++---- 5 files changed, 41 insertions(+), 41 deletions(-) (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 70739ae6..b62afbf8 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 12:57:33 2019 
-## Date of summary: Wed Sep 18 12:57:33 2019 
+## Date of fit:     Wed Sep 18 13:17:00 2019 
+## Date of summary: Wed Sep 18 13:17:00 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 1.01 s
+## Fitted using 389 model solutions performed in 1.115 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 81659030..0d5667f5 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 12:57:35 2019 
-## Date of summary: Wed Sep 18 12:57:35 2019 
+## Date of fit:     Wed Sep 18 13:17:02 2019 
+## Date of summary: Wed Sep 18 13:17:02 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.287 s
+## Fitted using 133 model solutions performed in 0.297 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 12:57:37 2019 
-## Date of summary: Wed Sep 18 12:57:37 2019 
+## Date of fit:     Wed Sep 18 13:17:05 2019 
+## Date of summary: Wed Sep 18 13:17:05 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -231,7 +231,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.921 s
+## Fitted using 899 model solutions performed in 2.099 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 12:57:38 2019 
-## Date of summary: Wed Sep 18 12:57:38 2019 
+## Date of fit:     Wed Sep 18 13:17:06 2019 
+## Date of summary: Wed Sep 18 13:17:06 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 0.49 s
+## Fitted using 239 model solutions performed in 0.554 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 12:57:40 2019 
-## Date of summary: Wed Sep 18 12:57:40 2019 
+## Date of fit:     Wed Sep 18 13:17:07 2019 
+## Date of summary: Wed Sep 18 13:17:07 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 1.209 s
+## Fitted using 572 model solutions performed in 1.273 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 12:57:42 2019 
-## Date of summary: Wed Sep 18 12:57:42 2019 
+## Date of fit:     Wed Sep 18 13:17:09 2019 
+## Date of summary: Wed Sep 18 13:17:09 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 0.783 s
+## Fitted using 373 model solutions performed in 0.792 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 12:57:42 2019 
-## Date of summary: Wed Sep 18 12:57:43 2019 
+## Date of fit:     Wed Sep 18 13:17:10 2019 
+## Date of summary: Wed Sep 18 13:17:11 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 0.299 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 12:57:43 2019 
-## Date of summary: Wed Sep 18 12:57:43 2019 
+## Date of fit:     Wed Sep 18 13:17:10 2019 
+## Date of summary: Wed Sep 18 13:17:11 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 0.463 s
+## Fitted using 224 model solutions performed in 0.488 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index b15f1522..799349d9 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’ is include in the ‘mkin’ package (‘max_twa_parent’. If the same is needed for metabolites, the function ‘max_twa’ 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 ‘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 f1ed1f96..0c78d346 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -204,77 +204,77 @@
 ## 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 0.9.49.6 5.920
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 6.106
 ##                                                                         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 36.932
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 37.249
 ##                                                                        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 4.519
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.739
 ##                                                                         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 31.518
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.761
 ##                                                                         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 10.619
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.794
 ##                                                                        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  2.61
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.702
 ##                                                                        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 4.312
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.351
 ##                                                                        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  8.07
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.303
 ##                                                                         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 16.102
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.339
 ##                                                                       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 8.013
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  8.12
 ##                                                                        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 0.9.49.6 10.805

+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  11.22

 
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 89977591..99b05623 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   3.124    1.000     3.122        0
-## 1 deSolve, not compiled            3  28.822    9.226    28.807        0
-## 2      Eigenvalue based            3   4.416    1.414     4.413        0
+## 3     deSolve, compiled            3   3.153    1.000     3.152        0
+## 1 deSolve, not compiled            3  28.771    9.125    28.756        0
+## 2      Eigenvalue based            3   4.444    1.409     4.443        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   4.878    1.000     4.875        0
-## 1 deSolve, not compiled            3  53.602   10.989    53.568        0
+## 2     deSolve, compiled            3   4.978    1.000     4.975    0.000
+## 1 deSolve, not compiled            3  54.194   10.887    54.160    0.004
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

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