From 6653ff2507f45eae909f491a9af3f1eb5358a600 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Mar 2018 14:32:46 +0100 Subject: Static documentation rebuilt using current pkgdown::build_site() --- docs/articles/FOCUS_D.html | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) (limited to 'docs/articles/FOCUS_D.html') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index d9dd8ad5..af04f755 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -8,8 +8,11 @@ Example evaluation of FOCUS Example Dataset D • mkin - - + + + + @@ -77,7 +80,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-01-16

+

2018-03-01

@@ -85,7 +88,7 @@

This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using mkin. After loading the library we look a the data. We have observed concentrations in the column named value at the times specified in column time for the two observed variables named parent and m1.

library("mkin", quietly = TRUE)
-print(FOCUS_2006_D)
+print(FOCUS_2006_D)
##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -135,13 +138,13 @@
 
The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector $diffs of the mkinmod object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.

 
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))

 
## Successfully compiled differential equation model from auto-generated C code.

-
print(SFO_SFO$diffs)

+
print(SFO_SFO$diffs)

 
##                                                       parent 
 ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" 
 ##                                                           m1 
 ##             "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"

 
We do the fitting without progress report (quiet = TRUE).

-
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

+
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

 
A plot of the fit including a residual plot for both observed variables is obtained using the plot_sep method for mkinfit objects, which shows separate graphs for all compounds and their residuals.

 
plot_sep(fit, lpos = c("topright", "bottomright"))

 

@@ -150,10 +153,10 @@
 

 
A comprehensive report of the results is obtained using the summary method for mkinfit objects.

 
summary(fit)

-
## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:01 2017 
-## Date of summary: Thu Sep 14 12:15:02 2017 
+
## mkin version:    0.9.46.3 
+## R version:       3.4.3 
+## Date of fit:     Thu Mar  1 14:17:55 2018 
+## Date of summary: Thu Mar  1 14:17:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -161,7 +164,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 1.14 s
+## Fitted with method Port using 153 model solutions performed in 0.993 s
 ## 
 ## Weighting: none
 ## 
@@ -286,7 +289,7 @@
 
 
 

-  
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+  
Site built with pkgdown.

 

 
       
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