From d5ff53448c61134c46cc4df9ea88fd86fa376d66 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 17 Feb 2023 14:44:29 +0100 Subject: Finish adapting to upcoming deSolve --- vignettes/FOCUS_L.html | 64 +++++++++++++++++++++++++------------------------- 1 file changed, 32 insertions(+), 32 deletions(-) (limited to 'vignettes/FOCUS_L.html') diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 98fe86c1..190ab65b 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -1534,7 +1534,7 @@ div.tocify {

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

Last change 18 May 2022 (rebuilt 2023-01-05)

+

Last change 18 May 2022 (rebuilt 2023-02-17)

@@ -1561,10 +1561,10 @@ 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 used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:14 2023 
-## Date of summary: Thu Jan  5 14:50:14 2023 
+## Date of fit:     Fri Feb 17 10:41:53 2023 
+## Date of summary: Fri Feb 17 10:41:53 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -1648,7 +1648,7 @@ summary(m.L1.SFO)

 
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")

 

@@ -1658,23 +1658,23 @@ checked.

 
## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge:
 ## false convergence (8)

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

-

+

 
summary(m.L1.FOMC, data = FALSE)

 
## Warning in sqrt(diag(covar)): NaNs produced

 
## Warning in sqrt(1/diag(V)): NaNs produced

 
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful

-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:15 2023 
-## Date of summary: Thu Jan  5 14:50:15 2023 
+## Date of fit:     Fri Feb 17 10:41:53 2023 
+## Date of summary: Fri Feb 17 10:41:53 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 369 model solutions performed in 0.025 s
+## Fitted using 369 model solutions performed in 0.026 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1785,7 +1785,7 @@ residual plot can be obtained simply by adding the argument
 
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
@@ -1810,10 +1810,10 @@ plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

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

-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:15 2023 
-## Date of summary: Thu Jan  5 14:50:15 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -1889,12 +1889,12 @@ order to explain the data.

 
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 used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:15 2023 
-## Date of summary: Thu Jan  5 14:50:15 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1988,7 +1988,7 @@ only the L3 dataset prepared above.

 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
@@ -2004,10 +2004,10 @@ as a row index and datasets as a column index.

 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 used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:15 2023 
-## Date of summary: Thu Jan  5 14:50:15 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2016,7 +2016,7 @@ summary and plot functions working on mkinfit objects.

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.024 s
+## Fitted using 376 model solutions performed in 0.023 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2091,7 +2091,7 @@ summary and plot functions working on mkinfit objects.

 ##    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
@@ -2119,24 +2119,24 @@ 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 used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:16 2023 
-## Date of summary: Thu Jan  5 14:50:16 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.01 s
+## Fitted using 142 model solutions performed in 0.009 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2190,10 +2190,10 @@ negligible.

 ##        DT50 DT90
 ## parent  106  352

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

-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:16 2023 
-## Date of summary: Thu Jan  5 14:50:16 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
-- 
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