From d89e3d22eb9dc383897b09e9c5aa1b57f65cdbf0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 21 Feb 2019 14:34:45 +0100 Subject: Add the logistic model --- docs/articles/FOCUS_D.html | 10 ++--- docs/articles/FOCUS_L.html | 58 ++++++++++++++--------------- docs/articles/mkin.html | 2 +- docs/articles/twa.html | 2 +- docs/articles/web_only/FOCUS_Z.html | 2 +- docs/articles/web_only/compiled_models.html | 14 +++---- 6 files changed, 44 insertions(+), 44 deletions(-) (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 9acab53a..6a8500a0 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -85,7 +85,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2019-01-31

+

2019-02-21

@@ -161,10 +161,10 @@

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:37 2019 
-## Date of summary: Thu Jan 31 16:52:38 2019 
+## Date of fit:     Thu Feb 21 14:32:03 2019 
+## Date of summary: Thu Feb 21 14:32:04 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.695 s
+## Fitted with method Port using 153 model solutions performed in 0.735 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index e3ca9aff..265dd96c 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -85,7 +85,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2019-01-31

+            
2019-02-21

       
       
       
@@ -109,17 +109,17 @@
 
Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

 
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)

-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:39 2019 
-## Date of summary: Thu Jan 31 16:52:39 2019 
+## Date of fit:     Thu Feb 21 14:32:06 2019 
+## Date of summary: Thu Feb 21 14:32:06 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.094 s
+## Fitted with method Port using 37 model solutions performed in 0.097 s
 ## 
 ## Weighting: none
 ## 
@@ -200,17 +200,17 @@
 plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

 

 
summary(m.L1.FOMC, data = FALSE)

-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:41 2019 
-## Date of summary: Thu Jan 31 16:52:41 2019 
+## Date of fit:     Thu Feb 21 14:32:08 2019 
+## Date of summary: Thu Feb 21 14:32:08 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.49 s
+## Fitted with method Port using 611 model solutions performed in 1.547 s
 ## 
 ## Weighting: none
 ## 
@@ -295,17 +295,17 @@
      main = "FOCUS L2 - FOMC")

 

 
summary(m.L2.FOMC, data = FALSE)

-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:42 2019 
-## Date of summary: Thu Jan 31 16:52:42 2019 
+## Date of fit:     Thu Feb 21 14:32:08 2019 
+## Date of summary: Thu Feb 21 14:32:08 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.198 s
+## Fitted with method Port using 81 model solutions performed in 0.201 s
 ## 
 ## Weighting: none
 ## 
@@ -366,10 +366,10 @@
      main = "FOCUS L2 - DFOP")

 

 
summary(m.L2.DFOP, data = FALSE)

-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:43 2019 
-## Date of summary: Thu Jan 31 16:52:43 2019 
+## Date of fit:     Thu Feb 21 14:32:09 2019 
+## Date of summary: Thu Feb 21 14:32:09 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.839 s
+## Fitted with method Port using 336 model solutions performed in 0.86 s
 ## 
 ## Weighting: none
 ## 
@@ -458,10 +458,10 @@
 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

 
We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

 
summary(mm.L3[["DFOP", 1]])

-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:44 2019 
-## Date of summary: Thu Jan 31 16:52:44 2019 
+## Date of fit:     Thu Feb 21 14:32:10 2019 
+## Date of summary: Thu Feb 21 14:32:11 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.341 s
+## Fitted with method Port using 137 model solutions performed in 0.351 s
 ## 
 ## Weighting: none
 ## 
@@ -559,17 +559,17 @@
 

 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
summary(mm.L4[["SFO", 1]], data = FALSE)

-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:44 2019 
-## Date of summary: Thu Jan 31 16:52:45 2019 
+## Date of fit:     Thu Feb 21 14:32:11 2019 
+## Date of summary: Thu Feb 21 14:32:11 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.11 s
+## Fitted with method Port using 46 model solutions performed in 0.113 s
 ## 
 ## Weighting: none
 ## 
@@ -619,17 +619,17 @@
 ##        DT50 DT90
 ## parent  106  352

 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:45 2019 
-## Date of summary: Thu Jan 31 16:52:45 2019 
+## Date of fit:     Thu Feb 21 14:32:11 2019 
+## Date of summary: Thu Feb 21 14:32:11 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.162 s
+## Fitted with method Port using 66 model solutions performed in 0.168 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 488ca302..c5b0d9c1 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -85,7 +85,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2019-01-31

+            
2019-02-21

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index d50b23ba..8a1f82a8 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -85,7 +85,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2019-01-31

+            
2019-02-21

       
       
       
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 84bd971f..c55abdbc 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -85,7 +85,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2019-01-31

+            
2019-02-21

       
       
       
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 08bb9b44..3a37d114 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -85,7 +85,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2019-01-31

+            
2019-02-21

       
       
       
@@ -126,9 +126,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.353    1.000     2.352        0
-## 1 deSolve, not compiled            3  17.619    7.488    17.609        0
-## 2      Eigenvalue based            3   2.899    1.232     2.898        0
+## 3     deSolve, compiled            3   2.429    1.000     2.427        0
+## 1 deSolve, not compiled            3  17.826    7.339    17.815        0
+## 2      Eigenvalue based            3   2.968    1.222     2.967        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -157,13 +157,13 @@
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.180    1.000     4.177        0
-## 1 deSolve, not compiled            3  37.331    8.931    37.312        0
+## 2     deSolve, compiled            3   4.234    1.000     4.232        0
+## 1 deSolve, not compiled            3  37.807    8.929    37.785        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

 
Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!

-
This vignette was built with mkin 0.9.47.5 on

+
This vignette was built with mkin 0.9.47.6 on

 
## R version 3.5.2 (2018-12-20)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)

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