From 95178837d3f91e84837628446b5fd468179af2b9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 4 Jun 2019 15:09:28 +0200 Subject: Additional algorithm "d_c", more tests, docs The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets. --- docs/articles/FOCUS_L.html | 60 +++++++++++++++++++++++----------------------- 1 file changed, 30 insertions(+), 30 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 6771bf63..75b2cf10 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -30,7 +30,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -88,7 +88,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2019-05-08

+

2019-06-04

@@ -112,17 +112,17 @@

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:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:29 2019 
-## Date of summary: Wed May  8 20:52:29 2019 
+## Date of fit:     Tue Jun  4 15:03:20 2019 
+## Date of summary: Tue Jun  4 15:03:20 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.276 s
+## Fitted using 133 model solutions performed in 0.28 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -213,10 +213,10 @@
 
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt

 
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:31 2019 
-## Date of summary: Wed May  8 20:52:31 2019 
+## Date of fit:     Tue Jun  4 15:03:22 2019 
+## Date of summary: Tue Jun  4 15:03:22 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -317,17 +317,17 @@
      main = "FOCUS L2 - FOMC")

 

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

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:32 2019 
-## Date of summary: Wed May  8 20:52:32 2019 
+## Date of fit:     Tue Jun  4 15:03:23 2019 
+## Date of summary: Tue Jun  4 15:03:23 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 0.483 s
+## Fitted using 239 model solutions performed in 0.484 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -392,10 +392,10 @@
      main = "FOCUS L2 - DFOP")

 

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

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:33 2019 
-## Date of summary: Wed May  8 20:52:33 2019 
+## Date of fit:     Tue Jun  4 15:03:25 2019 
+## Date of summary: Tue Jun  4 15:03:25 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,7 +404,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.185 s
+## Fitted using 572 model solutions performed in 1.193 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -491,10 +491,10 @@
 
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:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:35 2019 
-## Date of summary: Wed May  8 20:52:35 2019 
+## Date of fit:     Tue Jun  4 15:03:26 2019 
+## Date of summary: Tue Jun  4 15:03:27 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,7 +503,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.768 s
+## Fitted using 373 model solutions performed in 0.767 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -596,17 +596,17 @@
 

 
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:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:36 2019 
-## Date of summary: Wed May  8 20:52:37 2019 
+## Date of fit:     Tue Jun  4 15:03:27 2019 
+## Date of summary: Tue Jun  4 15:03:28 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.289 s
+## Fitted using 142 model solutions performed in 0.288 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -660,17 +660,17 @@
 ##        DT50 DT90
 ## parent  106  352

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

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:36 2019 
-## Date of summary: Wed May  8 20:52:37 2019 
+## Date of fit:     Tue Jun  4 15:03:28 2019 
+## Date of summary: Tue Jun  4 15:03:28 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 0.45 s
+## Fitted using 224 model solutions performed in 0.449 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -769,7 +769,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
 
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