From 9abab1e2d4385039b01ad3dc0d9c5966bbe94fee Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 9 Aug 2023 17:59:42 +0200 Subject: Update static docs --- docs/articles/FOCUS_L.html | 104 ++++++++++++++++++++++----------------------- 1 file changed, 52 insertions(+), 52 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index dabb16f2..7b5acf17 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -33,7 +33,7 @@ mkin - 1.2.4 + 1.2.5 @@ -135,7 +135,7 @@ to L3 Ranke

Last change 18 May 2023 -(rebuilt 2023-05-19)

+(rebuilt 2023-08-09) Source: vignettes/FOCUS_L.rmd @@ -168,18 +168,18 @@ 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:    1.2.4 
-## R version used for fitting:       4.3.0 
-## Date of fit:     Fri May 19 09:20:25 2023 
-## Date of summary: Fri May 19 09:20:25 2023 
+summary(m.L1.SFO)
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.1 
+## Date of fit:     Wed Aug  9 17:55:39 2023 
+## Date of summary: Wed Aug  9 17:55:39 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.011 s
+## Fitted using 133 model solutions performed in 0.031 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -256,7 +256,7 @@ report.

 
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

@@ -268,25 +268,25 @@ objects.

 
## 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")

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

-summary(m.L1.FOMC, data = FALSE)
+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:    1.2.4 
-## R version used for fitting:       4.3.0 
-## Date of fit:     Fri May 19 09:20:25 2023 
-## Date of summary: Fri May 19 09:20:25 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.1 
+## Date of fit:     Wed Aug  9 17:55:39 2023 
+## Date of summary: Wed Aug  9 17:55:39 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 342 model solutions performed in 0.021 s
+## Fitted using 342 model solutions performed in 0.07 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -398,7 +398,7 @@ 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,
+plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - SFO")

 

 
The \(\chi^2\) error level of 14%
@@ -422,22 +422,22 @@ kinetics.

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

 

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

-
## mkin version used for fitting:    1.2.4 
-## R version used for fitting:       4.3.0 
-## Date of fit:     Fri May 19 09:20:25 2023 
-## Date of summary: Fri May 19 09:20:25 2023 
+summary(m.L2.FOMC, data = FALSE)

+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.1 
+## Date of fit:     Wed Aug  9 17:55:40 2023 
+## Date of summary: Wed Aug  9 17:55:40 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.013 s
+## Fitted using 239 model solutions performed in 0.044 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -506,15 +506,15 @@ the data.

 
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,
+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:    1.2.4 
-## R version used for fitting:       4.3.0 
-## Date of fit:     Fri May 19 09:20:25 2023 
-## Date of summary: Fri May 19 09:20:25 2023 
+summary(m.L2.DFOP, data = FALSE)

+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.1 
+## Date of fit:     Wed Aug  9 17:55:40 2023 
+## Date of summary: Wed Aug  9 17:55:40 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -523,7 +523,7 @@ the data.

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.038 s
+## Fitted using 581 model solutions performed in 0.119 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -611,7 +611,7 @@ 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)

+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
@@ -627,11 +627,11 @@ 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:    1.2.4 
-## R version used for fitting:       4.3.0 
-## Date of fit:     Fri May 19 09:20:26 2023 
-## Date of summary: Fri May 19 09:20:26 2023 
+summary(mm.L3[["DFOP", 1]])

+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.1 
+## Date of fit:     Wed Aug  9 17:55:41 2023 
+## Date of summary: Wed Aug  9 17:55:41 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -640,7 +640,7 @@ summary and plot functions working on mkinfit objects.

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.021 s
+## Fitted using 376 model solutions performed in 0.075 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -715,7 +715,7 @@ 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)

+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
@@ -746,7 +746,7 @@ below:

 mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
                list("FOCUS L4" = FOCUS_2006_L4_mkin),
                quiet = TRUE)
-plot(mm.L4)
+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 @@ -754,18 +754,18 @@ 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 used for fitting:    1.2.4 
-## R version used for fitting:       4.3.0 
-## Date of fit:     Fri May 19 09:20:26 2023 
-## Date of summary: Fri May 19 09:20:26 2023 
+summary(mm.L4[["SFO", 1]], data = FALSE)
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.1 
+## Date of fit:     Wed Aug  9 17:55:42 2023 
+## Date of summary: Wed Aug  9 17:55:42 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.008 s
+## Fitted using 142 model solutions performed in 0.027 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -819,18 +819,18 @@ appears negligible.

 ##        DT50 DT90
 ## parent  106  352
-summary(mm.L4[["FOMC", 1]], data = FALSE)
-
## mkin version used for fitting:    1.2.4 
-## R version used for fitting:       4.3.0 
-## Date of fit:     Fri May 19 09:20:26 2023 
-## Date of summary: Fri May 19 09:20:26 2023 
+summary(mm.L4[["FOMC", 1]], data = FALSE)
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.1 
+## Date of fit:     Wed Aug  9 17:55:42 2023 
+## Date of summary: Wed Aug  9 17:55:42 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.012 s
+## Fitted using 224 model solutions performed in 0.04 s
 ## 
 ## Error model: Constant variance 
 ## 
-- 
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