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 --- 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 ++++---- 8 files changed, 49 insertions(+), 49 deletions(-) (limited to 'docs/articles') 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

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