From b74b5603abb50a3a09f41811dc5d79ceca5a3bc8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 23 Jun 2015 13:16:47 +0200 Subject: Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge --- Rplots.pdf | Bin 4805 -> 4805 bytes vignettes/FOCUS_D.html | 6 ++--- vignettes/FOCUS_L.html | 60 ++++++++++++++++++++--------------------- vignettes/FOCUS_Z.pdf | Bin 224997 -> 225008 bytes vignettes/compiled_models.html | 32 +++++++++++----------- vignettes/mkin.pdf | Bin 160260 -> 160260 bytes 6 files changed, 49 insertions(+), 49 deletions(-) diff --git a/Rplots.pdf b/Rplots.pdf index 9af1946c..a0b55668 100644 Binary files a/Rplots.pdf and b/Rplots.pdf differ diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 45104f6a..0ec2542c 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -137,8 +137,8 @@ print(FOCUS_2006_D) 
summary(fit)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 12:22:01 2015 
-## Date of summary: Tue Jun 23 12:22:01 2015 
+## Date of fit:     Tue Jun 23 13:14:52 2015 
+## Date of summary: Tue Jun 23 13:14:52 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -146,7 +146,7 @@ print(FOCUS_2006_D)
## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.689 s +## Fitted with method Port using 153 model solutions performed in 0.682 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 715b6a20..bb012d65 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:     Tue Jun 23 12:22:02 2015 
-## Date of summary: Tue Jun 23 12:22:02 2015 
+## Date of fit:     Tue Jun 23 13:14:53 2015 
+## Date of summary: Tue Jun 23 13:14:53 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.098 s
+## Fitted with method Port using 37 model solutions performed in 0.1 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:     Tue Jun 23 12:22:03 2015 
-## Date of summary: Tue Jun 23 12:22:03 2015 
+## Date of fit:     Tue Jun 23 13:14:54 2015 
+## Date of summary: Tue Jun 23 13:14:54 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 0.53 s +## Fitted with method Port using 188 model solutions performed in 0.539 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:     Tue Jun 23 12:22:03 2015 
-## Date of summary: Tue Jun 23 12:22:03 2015 
+## Date of fit:     Tue Jun 23 13:14:54 2015 
+## Date of summary: Tue Jun 23 13:14:54 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.108 s
+## Fitted with method Port using 41 model solutions performed in 0.109 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:     Tue Jun 23 12:22:04 2015 
-## Date of summary: Tue Jun 23 12:22:04 2015 
+## Date of fit:     Tue Jun 23 13:14:54 2015 
+## Date of summary: Tue Jun 23 13:14:54 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 0.205 s
+## Fitted with method Port using 81 model solutions performed in 0.228 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:     Tue Jun 23 12:22:06 2015 
-## Date of summary: Tue Jun 23 12:22:06 2015 
+## Date of fit:     Tue Jun 23 13:14:57 2015 
+## Date of summary: Tue Jun 23 13:14:57 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 0.913 s +## Fitted with method Port using 336 model solutions performed in 0.907 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:     Tue Jun 23 12:22:06 2015 
-## Date of summary: Tue Jun 23 12:22:06 2015 
+## Date of fit:     Tue Jun 23 13:14:57 2015 
+## Date of summary: Tue Jun 23 13:14:57 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.107 s
+## Fitted with method Port using 43 model solutions performed in 0.112 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:     Tue Jun 23 12:22:07 2015 
-## Date of summary: Tue Jun 23 12:22:07 2015 
+## Date of fit:     Tue Jun 23 13:14:58 2015 
+## Date of summary: Tue Jun 23 13:14:58 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 0.214 s
+## Fitted with method Port using 83 model solutions performed in 0.204 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:     Tue Jun 23 12:22:07 2015 
-## Date of summary: Tue Jun 23 12:22:07 2015 
+## Date of fit:     Tue Jun 23 13:14:58 2015 
+## Date of summary: Tue Jun 23 13:14:58 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 0.356 s +## Fitted with method Port using 137 model solutions performed in 0.359 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:     Tue Jun 23 12:22:08 2015 
-## Date of summary: Tue Jun 23 12:22:08 2015 
+## Date of fit:     Tue Jun 23 13:14:59 2015 
+## Date of summary: Tue Jun 23 13:14:59 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.117 s
+## Fitted with method Port using 46 model solutions performed in 0.12 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:     Tue Jun 23 12:22:08 2015 
-## Date of summary: Tue Jun 23 12:22:08 2015 
+## Date of fit:     Tue Jun 23 13:14:59 2015 
+## Date of summary: Tue Jun 23 13:14:59 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 0.177 s
+## Fitted with method Port using 66 model solutions performed in 0.163 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 5ed80680..43592d51 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 2fbef8ae..a415c735 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -99,18 +99,18 @@ 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 6760.8015 6766.0464 6785.8509 6771.2913 6798.3756
-## Eigenvalue based       930.9980  944.5895  973.5743  958.1810  994.8625
-## deSolve, compiled      758.2721  811.0584  836.3348  863.8448  875.3661
+## deSolve, not compiled 6958.1752 7034.5639 7074.0173 7110.9526 7131.9383
+## Eigenvalue based       978.8821  988.5741 1012.6283  998.2660 1029.5014
+## deSolve, compiled      756.0280  767.9740  800.3639  779.9199  822.5318
 ##                             max neval
-## deSolve, not compiled 6825.4600     3
-## Eigenvalue based      1031.5439     3
-## deSolve, compiled      886.8875     3
-

We see that using the compiled model is by a factor of 7.8 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:

+## deSolve, not compiled 7152.9240 3 +## Eigenvalue based 1060.7367 3 +## deSolve, compiled 865.1437 3 +

We see that using the compiled model is by a factor of 9.1 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 7.838551
-## Eigenvalue based      1.109205
+## deSolve, not compiled 9.117542
+## Eigenvalue based      1.279960
 ## deSolve, compiled     1.000000
@@ -128,16 +128,16 @@ 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 14.231863 14.287058 14.336780 14.342252 14.389238
-## deSolve, compiled      1.344761  1.345452  1.361713  1.346142  1.370189
+## deSolve, not compiled 14.586587 14.604167 14.614147 14.621747 14.627927
+## deSolve, compiled      1.428573  1.449463  1.459828  1.470352  1.475455
 ##                             max neval
-## deSolve, not compiled 14.436224     3
-## deSolve, compiled      1.394235     3
+## deSolve, not compiled 14.634107 3 +## deSolve, compiled 1.480558 3 
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 10.65434
-## deSolve, compiled      1.00000
-

Here we get a performance benefit of a factor of 10.7 using the version of the differential equation model compiled from C code using the inline package!

+## deSolve, not compiled 9.944383 +## deSolve, compiled 1.000000 +

Here we get a performance benefit of a factor of 9.9 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)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 79b6a5ab..fe600666 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
-- 
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