From 6653ff2507f45eae909f491a9af3f1eb5358a600 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Mar 2018 14:32:46 +0100 Subject: Static documentation rebuilt using current pkgdown::build_site() --- docs/articles/FOCUS_L.html | 127 ++++++++++++++++++++++----------------------- 1 file changed, 62 insertions(+), 65 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 42ec2df1..5de06ad5 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -8,8 +8,11 @@ Example evaluation of FOCUS Laboratory Data L1 to L3 • mkin - - + + + + @@ -77,7 +80,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2018-01-16

+

2018-03-01

@@ -88,27 +91,27 @@ Laboratory Data L1

The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:

library("mkin", quietly = TRUE)
-FOCUS_2006_L1 = data.frame(
+FOCUS_2006_L1 = data.frame(
   t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
   parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
              72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
              27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
-FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
+FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

Here we use the assumptions of simple first order (SFO), the case of declining rate constant over time (FOMC) and the case of two different phases of the kinetics (DFOP). For a more detailed discussion of the models, please see the FOCUS kinetics report.

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

-
## mkin version:    0.9.47.1 
+
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Tue Jan 16 06:11:06 2018 
-## Date of summary: Tue Jan 16 06:11:06 2018 
+## Date of fit:     Thu Mar  1 14:31:57 2018 
+## Date of summary: Thu Mar  1 14:31:57 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 0.245 s
+## Fitted with method Port using 37 model solutions performed in 0.24 s
 ## 
 ## Weighting: none
 ## 
@@ -185,28 +188,21 @@ FOCUS_2006_L1_mkin <- 
mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")

For comparison, the FOMC model is fitted as well, and the \(\chi^2\) error level is checked.

-
m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
-
## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge.
-## Convergence code is 1
-
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")
+
m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
+plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

summary(m.L1.FOMC, data = FALSE)
-
## mkin version:    0.9.47.1 
+
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Tue Jan 16 06:11:07 2018 
-## Date of summary: Tue Jan 16 06:11:07 2018 
-## 
-## 
-## Warning: Optimisation by method Port did not converge.
-## Convergence code is 1 
-## 
+## Date of fit:     Thu Mar  1 14:31:59 2018 
+## Date of summary: Thu Mar  1 14:32:00 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 155 model solutions performed in 0.424 s
+## Fitted with method Port using 611 model solutions performed in 1.375 s
 ## 
 ## Weighting: none
 ## 
@@ -226,16 +222,16 @@ FOCUS_2006_L1_mkin <-   
 Laboratory Data L2
 
The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:

-
FOCUS_2006_L2 = data.frame(
+
FOCUS_2006_L2 = data.frame(
   t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
   parent = c(96.1, 91.8, 41.4, 38.7,
              19.3, 22.3, 4.6, 4.6,
              2.6, 1.2, 0.3, 0.6))
-FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)

+FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)

 

 

 SFO fit for L2

 
Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument show_residuals to the plot command.

-
m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
+
m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
 plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - SFO")

 

@@ -286,22 +282,22 @@ FOCUS_2006_L2_mkin <- 
 FOMC fit for L2
 
For comparison, the FOMC model is fitted as well, and the \(\chi^2\) error level is checked.

-
m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
+
m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
 plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

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

-
## mkin version:    0.9.47.1 
+
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Tue Jan 16 06:11:08 2018 
-## Date of summary: Tue Jan 16 06:11:08 2018 
+## Date of fit:     Thu Mar  1 14:32:00 2018 
+## Date of summary: Thu Mar  1 14:32:00 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 0.158 s
 ## 
 ## Weighting: none
 ## 
@@ -357,15 +353,15 @@ FOCUS_2006_L2_mkin <- 
 DFOP fit for L2
 
Fitting the four parameter DFOP model further reduces the \(\chi^2\) error level.

-
m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
+
m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
 plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

 

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

-
## mkin version:    0.9.47.1 
+
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Tue Jan 16 06:11:09 2018 
-## Date of summary: Tue Jan 16 06:11:09 2018 
+## Date of fit:     Thu Mar  1 14:32:01 2018 
+## Date of summary: Thu Mar  1 14:32:01 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -374,7 +370,7 @@ FOCUS_2006_L2_mkin <-  
 Laboratory Data L3
 
The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.

-
FOCUS_2006_L3 = data.frame(
+
FOCUS_2006_L3 = data.frame(
   t = c(0, 3, 7, 14, 30, 60, 91, 120),
   parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
-FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)

+FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)

 

 

 Fit multiple models

 
As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function mmkin. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.

 
# Only use one core here, not to offend the CRAN checks
 mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
-               list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
+               list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
 plot(mm.L3)

 

 
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.

@@ -454,10 +450,10 @@ mm.L3 <- 
summary(mm.L3[["DFOP", 1]])

-
## mkin version:    0.9.47.1 
+
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Tue Jan 16 06:11:10 2018 
-## Date of summary: Tue Jan 16 06:11:10 2018 
+## Date of fit:     Thu Mar  1 14:32:02 2018 
+## Date of summary: Thu Mar  1 14:32:02 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -542,30 +538,30 @@ mm.L3 <- 
 Laboratory Data L4
 
The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:

-
FOCUS_2006_L4 = data.frame(
+
FOCUS_2006_L4 = data.frame(
   t = c(0, 3, 7, 14, 30, 60, 91, 120),
   parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
-FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)

+FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)

 
Fits of the SFO and FOMC models, plots and summaries are produced below:

 
# Only use one core here, not to offend the CRAN checks
 mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
-               list("FOCUS L4" = FOCUS_2006_L4_mkin),
+               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)

-
## mkin version:    0.9.47.1 
+
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Tue Jan 16 06:11:10 2018 
-## Date of summary: Tue Jan 16 06:11:10 2018 
+## Date of fit:     Thu Mar  1 14:32:03 2018 
+## Date of summary: Thu Mar  1 14:32:03 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 0.094 s
+## Fitted with method Port using 46 model solutions performed in 0.089 s
 ## 
 ## Weighting: none
 ## 
@@ -615,17 +611,17 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version:    0.9.47.1 
+
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Tue Jan 16 06:11:10 2018 
-## Date of summary: Tue Jan 16 06:11:10 2018 
+## Date of fit:     Thu Mar  1 14:32:03 2018 
+## Date of summary: Thu Mar  1 14:32:03 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 0.139 s
+## Fitted with method Port using 66 model solutions performed in 0.134 s
 ## 
 ## Weighting: none
 ## 
@@ -690,7 +686,8 @@ mm.L4 <- 
         

-      
Contents

+      

+Contents

       

 
       
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