From 7c62da1269e8910a210ba1917d4dc62d186d5606 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Oct 2016 09:40:35 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/articles/FOCUS_L.html | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 353f1484..5d586799 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -138,16 +138,16 @@ FOCUS_2006_L1_mkin <- 
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 \(\chi^2\) 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")
-

+

summary(m.L1.FOMC, data = FALSE)
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
@@ -233,7 +233,7 @@ FOCUS_2006_L2_mkin <- 
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.

 
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.

@@ -244,7 +244,7 @@ FOCUS_2006_L2_mkin <- 
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:    0.9.44.9000 
 ## R version:       3.3.1 
@@ -314,7 +314,7 @@ FOCUS_2006_L2_mkin <- 
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:    0.9.44.9000 
 ## R version:       3.3.1 
@@ -397,7 +397,7 @@ FOCUS_2006_L3_mkin <-  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.

 
 

@@ -484,7 +484,7 @@ mm.L3 <- 
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.

 
@@ -502,7 +502,7 @@ 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)

 
## mkin version:    0.9.44.9000 
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