From 092c6fdc8b8bbadd3724b4023de60b7f1fe1500f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 21 Jul 2017 18:05:21 +0200 Subject: Fix another URL, vignette builder, rebuild --- vignettes/FOCUS_L.html | 90 +++++++++++++++++++++++++------------------------- 1 file changed, 45 insertions(+), 45 deletions(-) (limited to 'vignettes/FOCUS_L.html') diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index fd531133..180c0323 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -11,7 +11,7 @@ - + Example evaluation of FOCUS Laboratory Data L1 to L3 @@ -223,7 +223,7 @@ div.tocify {

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2017-05-05

+

2017-07-21

@@ -242,17 +242,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

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:    0.9.45 
-## R version:       3.4.0 
-## Date of fit:     Fri May  5 12:14:02 2017 
-## Date of summary: Fri May  5 12:14:02 2017 
+
## mkin version:    0.9.45.2 
+## R version:       3.4.1 
+## Date of fit:     Fri Jul 21 18:02:22 2017 
+## Date of summary: Fri Jul 21 18:02:22 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.263 s
+## Fitted with method Port using 37 model solutions performed in 0.258 s
 ## 
 ## Weighting: none
 ## 
@@ -324,21 +324,21 @@ summary(m.L1.SFO)

 ##    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")
-

+

The residual plot can be easily obtained by

mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
-

+

For comparison, the FOMC model is fitted as well, and the χ2 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")
-

+

summary(m.L1.FOMC, data = FALSE)
-
## mkin version:    0.9.45 
-## R version:       3.4.0 
-## Date of fit:     Fri May  5 12:14:03 2017 
-## Date of summary: Fri May  5 12:14:03 2017 
+
## mkin version:    0.9.45.2 
+## R version:       3.4.1 
+## Date of fit:     Fri Jul 21 18:02:23 2017 
+## Date of summary: Fri Jul 21 18:02:23 2017 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -350,7 +350,7 @@ summary(m.L1.SFO)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 155 model solutions performed in 0.439 s
+## Fitted with method Port using 155 model solutions performed in 0.445 s
 ## 
 ## Weighting: none
 ## 
@@ -419,7 +419,7 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
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 χ2 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.

We may add that it is difficult to judge the random nature of the residuals just from the three samplings at days 0, 1 and 3. Also, it is not clear a priori why a consistent underestimation after the approximate DT90 should be irrelevant. However, this can be rationalised by the fact that the FOCUS fate models generally only implement SFO kinetics.

@@ -430,19 +430,19 @@ plot(m.L2.SFO, show_residuals = TRUE, show_errmin = 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:    0.9.45 
-## R version:       3.4.0 
-## Date of fit:     Fri May  5 12:14:04 2017 
-## Date of summary: Fri May  5 12:14:04 2017 
+
## mkin version:    0.9.45.2 
+## R version:       3.4.1 
+## Date of fit:     Fri Jul 21 18:02:24 2017 
+## Date of summary: Fri Jul 21 18:02:24 2017 
 ## 
 ## 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 0.171 s
+## Fitted with method Port using 81 model solutions performed in 0.246 s
 ## 
 ## Weighting: none
 ## 
@@ -500,12 +500,12 @@ plot(m.L2.FOMC, show_residuals = 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:    0.9.45 
-## R version:       3.4.0 
-## Date of fit:     Fri May  5 12:14:05 2017 
-## Date of summary: Fri May  5 12:14:05 2017 
+
## mkin version:    0.9.45.2 
+## R version:       3.4.1 
+## Date of fit:     Fri Jul 21 18:02:24 2017 
+## Date of summary: Fri Jul 21 18:02:24 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -583,7 +583,7 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)

 mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
                list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
 plot(mm.L3)

-

+

 
The χ2 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 χ2 test passes of 7%. Fitting the four parameter DFOP model further reduces the χ2 error level considerably.

 
 

@@ -591,10 +591,10 @@ plot(mm.L3)

 
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:    0.9.45 
-## R version:       3.4.0 
-## Date of fit:     Fri May  5 12:14:06 2017 
-## Date of summary: Fri May  5 12:14:06 2017 
+
## mkin version:    0.9.45.2 
+## R version:       3.4.1 
+## Date of fit:     Fri Jul 21 18:02:25 2017 
+## Date of summary: Fri Jul 21 18:02:25 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -603,7 +603,7 @@ plot(mm.L3)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.348 s
+## Fitted with method Port using 137 model solutions performed in 0.371 s
 ## 
 ## Weighting: none
 ## 
@@ -670,7 +670,7 @@ plot(mm.L3)

 ##    91   parent     15.0     15.18 -0.18181
 ##   120   parent     12.0     10.19  1.81395
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 χ2 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.

@@ -688,20 +688,20 @@ mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1, list("FOCUS L4" = FOCUS_2006_L4_mkin), quiet = TRUE) plot(mm.L4) -

+

The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test passes is slightly lower for the FOMC model. However, the difference appears negligible.

summary(mm.L4[["SFO", 1]], data = FALSE)
-
## mkin version:    0.9.45 
-## R version:       3.4.0 
-## Date of fit:     Fri May  5 12:14:06 2017 
-## Date of summary: Fri May  5 12:14:06 2017 
+
## mkin version:    0.9.45.2 
+## R version:       3.4.1 
+## Date of fit:     Fri Jul 21 18:02:26 2017 
+## Date of summary: Fri Jul 21 18:02:26 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.096 s
+## Fitted with method Port using 46 model solutions performed in 0.098 s
 ## 
 ## Weighting: none
 ## 
@@ -751,17 +751,17 @@ plot(mm.L4)

 ##        DT50 DT90
 ## parent  106  352
summary(mm.L4[["FOMC", 1]], data = FALSE)
-
## mkin version:    0.9.45 
-## R version:       3.4.0 
-## Date of fit:     Fri May  5 12:14:06 2017 
-## Date of summary: Fri May  5 12:14:06 2017 
+
## mkin version:    0.9.45.2 
+## R version:       3.4.1 
+## Date of fit:     Fri Jul 21 18:02:26 2017 
+## Date of summary: Fri Jul 21 18:02:26 2017 
 ## 
 ## 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 0.141 s
 ## 
 ## Weighting: none
 ## 
-- 
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