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 +++---- 5 files changed, 40 insertions(+), 40 deletions(-) (limited to 'docs/articles') 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

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