From d0a358a8f4fd03c95536409523e492eb15726f44 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Mar 2019 10:12:43 +0100 Subject: Review tests and examples based on winbuilder results Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_L.html | 154 ++++++++++++++++++++++----------------------- 1 file changed, 77 insertions(+), 77 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index aeded526..7157f973 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

-

2019-02-26

+

2019-03-04

@@ -101,28 +101,28 @@

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(
-  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)
+
library("mkin", quietly = TRUE)
+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)

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)
-summary(m.L1.SFO)
+
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
+summary(m.L1.SFO)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Tue Feb 26 21:09:17 2019 
-## Date of summary: Tue Feb 26 21:09:17 2019 
+## Date of fit:     Mon Mar  4 10:09:35 2019 
+## Date of summary: Mon Mar  4 10:09:35 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 0.096 s
+## Fitted with method Port using 37 model solutions performed in 0.102 s
 ## 
 ## Weighting: none
 ## 
@@ -193,27 +193,27 @@
 ##    30   parent      2.9     5.251  -2.3513
 ##    30   parent      4.0     5.251  -1.2513

A plot of the fit is obtained with the plot function for mkinfit objects.

-
plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")
+
plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")

The residual plot can be easily obtained by

-
mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
+
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)
-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)
+
summary(m.L1.FOMC, data = FALSE)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Tue Feb 26 21:09:19 2019 
-## Date of summary: Tue Feb 26 21:09:19 2019 
+## Date of fit:     Mon Mar  4 10:09:36 2019 
+## Date of summary: Mon Mar  4 10:09:36 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 1.539 s
+## Fitted with method Port using 611 model solutions performed in 1.508 s
 ## 
 ## Weighting: none
 ## 
@@ -271,19 +271,19 @@
 

 Laboratory Data L2

 
The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:

-
+
 

 

 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)
-plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
-     main = "FOCUS L2 - SFO")

+
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")

 

 
The \(\chi^2\) error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.

 
In the FOCUS kinetics report, it is stated that there is no apparent systematic error observed from the residual plot up to the measured DT90 (approximately at day 5), and there is an underestimation beyond that point.

@@ -293,22 +293,22 @@
 

 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)
-plot(m.L2.FOMC, show_residuals = TRUE,
-     main = "FOCUS L2 - FOMC")

+
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)

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

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Tue Feb 26 21:09:19 2019 
-## Date of summary: Tue Feb 26 21:09:19 2019 
+## Date of fit:     Mon Mar  4 10:09:37 2019 
+## Date of summary: Mon Mar  4 10:09:37 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 0.199 s
+## Fitted with method Port using 81 model solutions performed in 0.196 s
 ## 
 ## Weighting: none
 ## 
@@ -364,15 +364,17 @@
 

 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)
-plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
-     main = "FOCUS L2 - DFOP")

+
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)

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

+
## Warning in summary.mkinfit(m.L2.DFOP, data = FALSE): Could not estimate
+## covariance matrix; singular system.

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Tue Feb 26 21:09:20 2019 
-## Date of summary: Tue Feb 26 21:09:20 2019 
+## Date of fit:     Mon Mar  4 10:09:38 2019 
+## Date of summary: Mon Mar  4 10:09:38 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -381,7 +383,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.844 s
+## Fitted with method Port using 336 model solutions performed in 0.841 s
 ## 
 ## Weighting: none
 ## 
@@ -409,10 +411,8 @@
 ## log_k2    -1.0880         NA    NA    NA
 ## g_ilr     -0.2821         NA    NA    NA
 ## 
-## Parameter correlation:

-
## Warning in print.summary.mkinfit(x): Could not estimate covariance matrix; singular system:

-
## Could not estimate covariance matrix; singular system:
-## 
+## Parameter correlation:
+## Could not estimate covariance matrix; singular system.
 ## Residual standard error: 1.732 on 8 degrees of freedom
 ## 
 ## Backtransformed parameters:
@@ -440,18 +440,18 @@
 

 Laboratory Data L3

 
The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.

-
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 = 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)

 

 

 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)
-plot(mm.L3)

+
# 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)
+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.

 

@@ -460,11 +460,11 @@
 Accessing mmkin objects
 
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]])

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

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Tue Feb 26 21:09:21 2019 
-## Date of summary: Tue Feb 26 21:09:22 2019 
+## Date of fit:     Mon Mar  4 10:09:39 2019 
+## Date of summary: Mon Mar  4 10:09:39 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -473,7 +473,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.344 s
+## Fitted with method Port using 137 model solutions performed in 0.343 s
 ## 
 ## Weighting: none
 ## 
@@ -539,7 +539,7 @@
 ##    60   parent     22.0     23.26 -1.25919
 ##    91   parent     15.0     15.18 -0.18181
 ##   120   parent     12.0     10.19  1.81395

-
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)

+
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)

 

 
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.

@@ -549,23 +549,23 @@
 

 Laboratory Data L4

 
The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:

-
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 = 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)

 
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),
-               quiet = TRUE)
-plot(mm.L4)

+
# 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),
+               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)

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

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Tue Feb 26 21:09:22 2019 
-## Date of summary: Tue Feb 26 21:09:22 2019 
+## Date of fit:     Mon Mar  4 10:09:40 2019 
+## Date of summary: Mon Mar  4 10:09:40 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -621,18 +621,18 @@
 ## Estimated disappearance times:
 ##        DT50 DT90
 ## parent  106  352

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

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

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Tue Feb 26 21:09:22 2019 
-## Date of summary: Tue Feb 26 21:09:22 2019 
+## Date of fit:     Mon Mar  4 10:09:40 2019 
+## Date of summary: Mon Mar  4 10:09:40 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 0.163 s
+## Fitted with method Port using 66 model solutions performed in 0.162 s
 ## 
 ## Weighting: none
 ## 
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