From 4a2809943b4bcb234f1eb979619c8cd27341c124 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 22 Jun 2015 22:18:44 +0200 Subject: Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge --- vignettes/FOCUS_D.html | 13 ++++----- vignettes/FOCUS_L.html | 60 ++++++++++++++++++++--------------------- vignettes/FOCUS_Z.pdf | Bin 224268 -> 224263 bytes vignettes/compiled_models.html | 34 +++++++++++------------ vignettes/mkin.pdf | Bin 160260 -> 160260 bytes 5 files changed, 52 insertions(+), 55 deletions(-) diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 53711e88..58399198 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -69,11 +69,8 @@ img {

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")
-
## Loading required package: minpack.lm
-## Loading required package: rootSolve
-## Loading required package: inline
-
print(FOCUS_2006_D)
+
library("mkin")
+print(FOCUS_2006_D)
##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -140,8 +137,8 @@ img {
 
summary(fit)

 
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 18:45:34 2015 
-## Date of summary: Mon Jun 22 18:45:34 2015 
+## Date of fit:     Mon Jun 22 22:17:05 2015 
+## Date of summary: Mon Jun 22 22:17:05 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -149,7 +146,7 @@ img {
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.609 s
+## Fitted with method Port using 153 model solutions performed in 0.744 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 488d5dc8..276c7c35 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -93,15 +93,15 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

 summary(m.L1.SFO)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:34 2015 
-## Date of summary: Mon Jun 22 20:44:34 2015 
+## Date of fit:     Mon Jun 22 22:17:06 2015 
+## Date of summary: Mon Jun 22 22:17:06 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.093 s
+## Fitted with method Port using 37 model solutions performed in 0.09 s
 ## 
 ## Weighting: none
 ## 
@@ -183,8 +183,8 @@ summary(m.L1.SFO)
summary(m.L1.FOMC, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:35 2015 
-## Date of summary: Mon Jun 22 20:44:35 2015 
+## Date of fit:     Mon Jun 22 22:17:07 2015 
+## Date of summary: Mon Jun 22 22:17:07 2015 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -196,7 +196,7 @@ summary(m.L1.SFO)
## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.48 s +## Fitted with method Port using 188 model solutions performed in 0.476 s ## ## Weighting: none ## @@ -263,15 +263,15 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2) summary(m.L2.SFO) 
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:35 2015 
-## Date of summary: Mon Jun 22 20:44:35 2015 
+## Date of fit:     Mon Jun 22 22:17:07 2015 
+## Date of summary: Mon Jun 22 22:17:07 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.104 s
+## Fitted with method Port using 41 model solutions performed in 0.099 s
 ## 
 ## Weighting: none
 ## 
@@ -351,15 +351,15 @@ mkinresplot(m.L2.FOMC)
summary(m.L2.FOMC, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:36 2015 
-## Date of summary: Mon Jun 22 20:44:36 2015 
+## Date of fit:     Mon Jun 22 22:17:07 2015 
+## Date of summary: Mon Jun 22 22:17:07 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.203 s
+## Fitted with method Port using 81 model solutions performed in 0.237 s
 ## 
 ## Weighting: none
 ## 
@@ -423,8 +423,8 @@ plot(m.L2.DFOP)
summary(m.L2.DFOP, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:38 2015 
-## Date of summary: Mon Jun 22 20:44:38 2015 
+## Date of fit:     Mon Jun 22 22:17:10 2015 
+## Date of summary: Mon Jun 22 22:17:10 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +433,7 @@ plot(m.L2.DFOP)
## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.926 s +## Fitted with method Port using 336 model solutions performed in 0.841 s ## ## Weighting: none ## @@ -500,15 +500,15 @@ plot(m.L3.SFO) 
summary(m.L3.SFO)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:38 2015 
-## Date of summary: Mon Jun 22 20:44:38 2015 
+## Date of fit:     Mon Jun 22 22:17:10 2015 
+## Date of summary: Mon Jun 22 22:17:10 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.132 s
+## Fitted with method Port using 43 model solutions performed in 0.11 s
 ## 
 ## Weighting: none
 ## 
@@ -576,15 +576,15 @@ plot(m.L3.FOMC)
summary(m.L3.FOMC, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:39 2015 
-## Date of summary: Mon Jun 22 20:44:39 2015 
+## Date of fit:     Mon Jun 22 22:17:10 2015 
+## Date of summary: Mon Jun 22 22:17:10 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.221 s
+## Fitted with method Port using 83 model solutions performed in 0.2 s
 ## 
 ## Weighting: none
 ## 
@@ -642,8 +642,8 @@ plot(m.L3.DFOP)
summary(m.L3.DFOP, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:39 2015 
-## Date of summary: Mon Jun 22 20:44:39 2015 
+## Date of fit:     Mon Jun 22 22:17:11 2015 
+## Date of summary: Mon Jun 22 22:17:11 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +652,7 @@ plot(m.L3.DFOP)
## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.372 s +## Fitted with method Port using 137 model solutions performed in 0.423 s ## ## Weighting: none ## @@ -724,15 +724,15 @@ plot(m.L4.SFO) 
summary(m.L4.SFO, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:40 2015 
-## Date of summary: Mon Jun 22 20:44:40 2015 
+## Date of fit:     Mon Jun 22 22:17:11 2015 
+## Date of summary: Mon Jun 22 22:17:11 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.115 s
+## Fitted with method Port using 46 model solutions performed in 0.113 s
 ## 
 ## Weighting: none
 ## 
@@ -789,15 +789,15 @@ plot(m.L4.FOMC)
summary(m.L4.FOMC, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 20:44:40 2015 
-## Date of summary: Mon Jun 22 20:44:40 2015 
+## Date of fit:     Mon Jun 22 22:17:12 2015 
+## Date of summary: Mon Jun 22 22:17:12 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.169 s
+## Fitted with method Port using 66 model solutions performed in 0.179 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index d75b1288..94084bca 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index ed61b47a..0b77f1c2 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -98,19 +98,19 @@ mb.1 <- microbenchmark(
 smb.1 <- summary(mb.1)[-1]
 rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled")
 print(smb.1)
-
##                             min        lq      mean    median        uq
-## deSolve, not compiled 6585.7039 6651.4937 6685.6248 6717.2836 6735.5853
-## Eigenvalue based       971.2893  981.5618  998.2746  991.8344 1011.7673
-## deSolve, compiled      760.5522  765.4274  780.3243  770.3026  790.2103
-##                             max neval
-## deSolve, not compiled 6753.8871     3
-## Eigenvalue based      1031.7003     3
-## deSolve, compiled      810.1179     3
-

We see that using the compiled model is by a factor of 8.7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

+
##                            min        lq      mean    median        uq
+## deSolve, not compiled 6737.589 6818.2149 6911.3916 6898.8407 6998.2929
+## Eigenvalue based       945.433  968.8592  979.7477  992.2854  996.9051
+## deSolve, compiled      744.785  748.8107  770.7521  752.8364  783.7357
+##                            max neval
+## deSolve, not compiled 7097.745     3
+## Eigenvalue based      1001.525     3
+## deSolve, compiled      814.635     3
+

We see that using the compiled model is by a factor of 9.2 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 8.720318
-## Eigenvalue based      1.287591
+## deSolve, not compiled 9.163798
+## Eigenvalue based      1.318062
 ## deSolve, compiled     1.000000
@@ -128,15 +128,15 @@ smb.2 <- summary(mb.2)[-1] rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled") print(smb.2) 
##                             min        lq      mean    median        uq
-## deSolve, not compiled 14.271472 14.285039 14.303450 14.298607 14.319440
-## deSolve, compiled      1.350642  1.390549  1.412823  1.430456  1.443914
+## deSolve, not compiled 13.955273 13.961009 14.041563 13.966745 14.084708
+## deSolve, compiled      1.350567  1.371225  1.381397  1.391882  1.396812
 ##                             max neval
-## deSolve, not compiled 14.340272     3
-## deSolve, compiled      1.457372     3
+## deSolve, not compiled 14.202672 3 +## deSolve, compiled 1.401743 3 
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 9.995841
-## deSolve, compiled     1.000000
+## deSolve, not compiled 10.03443 +## deSolve, compiled 1.00000

Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code using the inline package!

This vignette was built with mkin 0.9.37 on

## R version 3.2.1 (2015-06-18)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index d7381e6f..f2178a99 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
-- 
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