From 8b7edd4eaf0d196e674a085f744d1a69260a6c91 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Nov 2023 06:02:05 +0100 Subject: Update pkgdown docs to bootstrap 5 with search --- docs/articles/FOCUS_L.html | 293 +++++++++++++++++++-------------------------- 1 file changed, 124 insertions(+), 169 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 7b5acf17..7aa90c4a 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -4,142 +4,104 @@ - + + Example evaluation of FOCUS Laboratory Data L1 to L3 • mkin - - - + + + - - + - + + -

Example evaluation of FOCUS Laboratory Data L1 -to L3

+ +

@@ -168,18 +130,18 @@ 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:    1.2.5 
-## 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 
+summary(m.L1.SFO)

## mkin version used for fitting:    1.2.6 
+## R version used for fitting:       4.3.2 
+## Date of fit:     Thu Nov 16 04:20:13 2023 
+## Date of summary: Thu Nov 16 04:20:13 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.031 s
+## Fitted using 133 model solutions performed in 0.011 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -256,7 +218,7 @@ 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 +230,25 @@ 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:    1.2.5 
-## 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 
+## mkin version used for fitting:    1.2.6 
+## R version used for fitting:       4.3.2 
+## Date of fit:     Thu Nov 16 04:20:13 2023 
+## Date of summary: Thu Nov 16 04:20:13 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 0.07 s
+## Fitted using 342 model solutions performed in 0.023 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -398,7 +360,7 @@ 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 +384,22 @@ 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:    1.2.5 
-## 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 
+summary(m.L2.FOMC, data = FALSE)


+## mkin version used for fitting:    1.2.6 
+## R version used for fitting:       4.3.2 
+## Date of fit:     Thu Nov 16 04:20:13 2023 
+## Date of summary: Thu Nov 16 04:20:14 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 0.044 s
+## Fitted using 239 model solutions performed in 0.014 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -506,15 +468,15 @@ 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:    1.2.5 
-## 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 
+summary(m.L2.DFOP, data = FALSE)


+## mkin version used for fitting:    1.2.6 
+## R version used for fitting:       4.3.2 
+## Date of fit:     Thu Nov 16 04:20:14 2023 
+## Date of summary: Thu Nov 16 04:20:14 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -523,7 +485,7 @@ the data.
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.119 s
+## Fitted using 581 model solutions performed in 0.041 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -611,7 +573,7 @@ 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 +589,11 @@ 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:    1.2.5 
-## 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 
+summary(mm.L3[["DFOP", 1]])

+## mkin version used for fitting:    1.2.6 
+## R version used for fitting:       4.3.2 
+## Date of fit:     Thu Nov 16 04:20:14 2023 
+## Date of summary: Thu Nov 16 04:20:14 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -640,7 +602,7 @@ summary and plot functions working on mkinfit objects.
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.075 s
+## Fitted using 376 model solutions performed in 0.024 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -715,7 +677,7 @@ 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 +708,7 @@ 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 +716,18 @@ 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:    1.2.5 
-## 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 
+summary(mm.L4[["SFO", 1]], data = FALSE)

+## mkin version used for fitting:    1.2.6 
+## R version used for fitting:       4.3.2 
+## Date of fit:     Thu Nov 16 04:20:14 2023 
+## Date of summary: Thu Nov 16 04:20:15 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.027 s
+## Fitted using 142 model solutions performed in 0.01 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -819,18 +781,18 @@ appears negligible.
 ##        DT50 DT90
 ## parent  106  352
 -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 
+summary(mm.L4[["FOMC", 1]], data = FALSE)

+## mkin version used for fitting:    1.2.6 
+## R version used for fitting:       4.3.2 
+## Date of fit:     Thu Nov 16 04:20:15 2023 
+## Date of summary: Thu Nov 16 04:20:15 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 0.04 s
+## Fitted using 224 model solutions performed in 0.014 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -900,34 +862,27 @@ Validierung von Modellierungssoftware als Alternative zu ModelMaker
 
 
 
-  
-
-  
-
-        Contents
-    
+  On this page
+    
 
 
-
 
 
-
-      
+    
   
 Developed by Johannes Ranke.
 
 
-
+
   
 Site built with pkgdown 2.0.7.
 
 
-      
+    
 
 
   
 
-
   
 
   
-- 
cgit v1.2.1

Example evaluations with (generalised) nonlinear least squares

Example evaluations with hierarchical models (nonlinear mixed-effects models)

Performance

Miscellaneous

Example evaluation of FOCUS Laboratory Data L1 -to L3

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

Last change 18 May 2023 -(rebuilt 2023-08-09)