From ec574cff822a1238138c0aa69b3d1459bdc3dfa8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 Jun 2015 17:46:11 +0200 Subject: Use odeintr instead of ccSolve for compiling models --- vignettes/FOCUS_D.html | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'vignettes/FOCUS_D.html') diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 6573cc7a..9522e881 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -276,13 +276,13 @@ kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics

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 -the ccSolve package is installed and functional, the differential equation model +a compiler (g++) 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"))
-
## Compiling differential equation model from auto-generated C code...
+
## Compiling differential equation model from auto-generated C++ code...
 

 
 
print(SFO_SFO$diffs)
@@ -312,7 +312,7 @@ using the plot method for mkinfit objects.

 
mkinparplot(fit)
 

 
-
plot of chunk unnamed-chunk-6 

+
plot of chunk unnamed-chunk-6 

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

@@ -322,16 +322,16 @@ objects.

 
 
## mkin version:    0.9.36 
 ## R version:       3.2.0 
-## Date of fit:     Fri Jun  5 14:20:31 2015 
-## Date of summary: Fri Jun  5 14:20:31 2015 
+## Date of fit:     Fri Jun 19 16:21:21 2015 
+## Date of summary: Fri Jun 19 16:21:21 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
 ## d_m1 = + k_parent_m1 * parent - k_m1_sink * m1
 ## 
-## Model predictions using solution type deSolve 
+## Model predictions using solution type odeintr 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.621 s
+## Fitted with method Port using 153 model solutions performed in 0.562 s
 ## 
 ## Weighting: none
 ## 
@@ -370,7 +370,7 @@ objects.

 ## parent_0           1.00000            0.6075        -0.06625       -0.1701
 ## log_k_parent_sink  0.60752            1.0000        -0.08740       -0.6253
 ## log_k_parent_m1   -0.06625           -0.0874         1.00000        0.4716
-## log_k_m1_sink     -0.17006           -0.6253         0.47163        1.0000
+## log_k_m1_sink     -0.17006           -0.6253         0.47164        1.0000
 ## 
 ## Residual standard error: 3.211 on 36 degrees of freedom
 ## 
-- 
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