From 39b2c2c762b03922a2648b1b226d0f308600cc87 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 6 Jun 2018 01:24:15 +0200 Subject: Static documentation rebuilt by pkgdown 1.1.0 --- docs/articles/FOCUS_L.html | 102 ++++++++++++++++++++++++--------------------- 1 file changed, 55 insertions(+), 47 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 08e144bd..fcd0719d 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -8,8 +8,8 @@ Example evaluation of FOCUS Laboratory Data L1 to L3 • mkin - - + + -
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Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

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2018-03-21

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2018-06-06

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Laboratory Data L1

@@ -101,17 +108,17 @@ FOCUS_2006_L1_mkin <- 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)
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## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:03 2018 
-## Date of summary: Wed Mar 21 18:16:03 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:52 2018 
+## Date of summary: Wed Jun  6 01:21:52 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.257 s
+## Fitted with method Port using 37 model solutions performed in 0.094 s
 ## 
 ## Weighting: none
 ## 
@@ -192,17 +199,17 @@ FOCUS_2006_L1_mkin <- plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

summary(m.L1.FOMC, data = FALSE)
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## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:05 2018 
-## Date of summary: Wed Mar 21 18:16:05 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:53 2018 
+## Date of summary: Wed Jun  6 01:21:53 2018 
 ## 
 ## 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 1.404 s
+## Fitted with method Port using 611 model solutions performed in 1.369 s
 ## 
 ## Weighting: none
 ## 
@@ -287,17 +294,17 @@ FOCUS_2006_L2_mkin <- main = "FOCUS L2 - FOMC")

summary(m.L2.FOMC, data = FALSE)
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## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:06 2018 
-## Date of summary: Wed Mar 21 18:16:06 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:54 2018 
+## Date of summary: Wed Jun  6 01:21:54 2018 
 ## 
 ## 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 0.168 s
+## Fitted with method Port using 81 model solutions performed in 0.173 s
 ## 
 ## Weighting: none
 ## 
@@ -358,10 +365,10 @@ FOCUS_2006_L2_mkin <- main = "FOCUS L2 - DFOP")

summary(m.L2.DFOP, data = FALSE)
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## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:06 2018 
-## Date of summary: Wed Mar 21 18:16:06 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:55 2018 
+## Date of summary: Wed Jun  6 01:21:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -370,7 +377,7 @@ FOCUS_2006_L2_mkin <- 2006_L3_mkin <-  mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
                list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
 plot(mm.L3)
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+

The \(\chi^2\) error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the \(\chi^2\) test passes of 7%. Fitting the four parameter DFOP model further reduces the \(\chi^2\) error level considerably.

@@ -450,10 +457,10 @@ mm.L3 <- 
summary(mm.L3[["DFOP", 1]])
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## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:07 2018 
-## Date of summary: Wed Mar 21 18:16:07 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:56 2018 
+## Date of summary: Wed Jun  6 01:21:56 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -462,7 +469,7 @@ mm.L3 <-  
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)
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+

Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the \(\chi^2\) error level criterion for laboratory data L3.

This is also an example where the standard t-test for the parameter g_ilr is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter g is quite narrow.

@@ -548,20 +555,20 @@ mm.L4 <- list("FOCUS L4" = FOCUS_2006_L4_mkin), quiet = TRUE) plot(mm.L4) -

+

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)
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## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:08 2018 
-## Date of summary: Wed Mar 21 18:16:08 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:56 2018 
+## Date of summary: Wed Jun  6 01:21:57 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.092 s
+## Fitted with method Port using 46 model solutions performed in 0.099 s
 ## 
 ## Weighting: none
 ## 
@@ -611,17 +618,17 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

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## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:08 2018 
-## Date of summary: Wed Mar 21 18:16:08 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:57 2018 
+## Date of summary: Wed Jun  6 01:21:57 2018 
 ## 
 ## 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 0.138 s
+## Fitted with method Port using 66 model solutions performed in 0.146 s
 ## 
 ## Weighting: none
 ## 
@@ -680,7 +687,6 @@ mm.L4 <-