From b2aa7f7d6180edda1ac1ba4d8c3c3d364cbd3754 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 23 Jun 2015 12:24:10 +0200 Subject: Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge --- Rplots.pdf | Bin 0 -> 4805 bytes vignettes/FOCUS_D.html | 6 ++--- vignettes/FOCUS_L.html | 58 ++++++++++++++++++++--------------------- vignettes/FOCUS_Z.pdf | Bin 225020 -> 224997 bytes vignettes/compiled_models.html | 30 ++++++++++----------- vignettes/mkin.pdf | Bin 160260 -> 160260 bytes 6 files changed, 47 insertions(+), 47 deletions(-) create mode 100644 Rplots.pdf diff --git a/Rplots.pdf b/Rplots.pdf new file mode 100644 index 00000000..9af1946c Binary files /dev/null and b/Rplots.pdf differ diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 099004ad..45104f6a 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 11:42:55 2015 
-## Date of summary: Tue Jun 23 11:42:55 2015 
+## Date of fit:     Tue Jun 23 12:22:01 2015 
+## Date of summary: Tue Jun 23 12:22:01 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 0.719 s +## Fitted with method Port using 153 model solutions performed in 0.689 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index ec4203b7..715b6a20 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 11:42:56 2015 
-## Date of summary: Tue Jun 23 11:42:56 2015 
+## Date of fit:     Tue Jun 23 12:22:02 2015 
+## Date of summary: Tue Jun 23 12:22:02 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.096 s
+## Fitted with method Port using 37 model solutions performed in 0.098 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 11:42:57 2015 
-## Date of summary: Tue Jun 23 11:42:57 2015 
+## Date of fit:     Tue Jun 23 12:22:03 2015 
+## Date of summary: Tue Jun 23 12:22:03 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 0.466 s +## Fitted with method Port using 188 model solutions performed in 0.53 s ## ## Weighting: none ## @@ -263,8 +263,8 @@ 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 11:42:57 2015 
-## Date of summary: Tue Jun 23 11:42:57 2015 
+## Date of fit:     Tue Jun 23 12:22:03 2015 
+## Date of summary: Tue Jun 23 12:22:03 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
@@ -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 11:42:57 2015 
-## Date of summary: Tue Jun 23 11:42:57 2015 
+## Date of fit:     Tue Jun 23 12:22:04 2015 
+## Date of summary: Tue Jun 23 12:22:04 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 0.214 s
+## Fitted with method Port using 81 model solutions performed in 0.205 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 11:43:00 2015 
-## Date of summary: Tue Jun 23 11:43:00 2015 
+## Date of fit:     Tue Jun 23 12:22:06 2015 
+## Date of summary: Tue Jun 23 12:22:06 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 0.917 s +## Fitted with method Port using 336 model solutions performed in 0.913 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 11:43:00 2015 
-## Date of summary: Tue Jun 23 11:43:00 2015 
+## Date of fit:     Tue Jun 23 12:22:06 2015 
+## Date of summary: Tue Jun 23 12:22:06 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.108 s
+## Fitted with method Port using 43 model solutions performed in 0.107 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 11:43:00 2015 
-## Date of summary: Tue Jun 23 11:43:00 2015 
+## Date of fit:     Tue Jun 23 12:22:07 2015 
+## Date of summary: Tue Jun 23 12:22:07 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 0.207 s
+## Fitted with method Port using 83 model solutions performed in 0.214 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 11:43:01 2015 
-## Date of summary: Tue Jun 23 11:43:01 2015 
+## Date of fit:     Tue Jun 23 12:22:07 2015 
+## Date of summary: Tue Jun 23 12:22:07 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 0.349 s +## Fitted with method Port using 137 model solutions performed in 0.356 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 11:43:01 2015 
-## Date of summary: Tue Jun 23 11:43:01 2015 
+## Date of fit:     Tue Jun 23 12:22:08 2015 
+## Date of summary: Tue Jun 23 12:22:08 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.114 s
+## Fitted with method Port using 46 model solutions performed in 0.117 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 11:43:02 2015 
-## Date of summary: Tue Jun 23 11:43:02 2015 
+## Date of fit:     Tue Jun 23 12:22:08 2015 
+## Date of summary: Tue Jun 23 12:22:08 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 0.166 s
+## Fitted with method Port using 66 model solutions performed in 0.177 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 1ac6002b..5ed80680 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 814f3a52..2fbef8ae 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 6650.2684 6684.4530 6774.1607 6718.6377 6836.1068
-## Eigenvalue based       903.5520  916.8598  927.3873  930.1676  939.3049
-## deSolve, compiled      751.1205  752.5239  756.1227  753.9273  758.6238
+## 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
 ##                             max neval
-## deSolve, not compiled 6953.5760     3
-## Eigenvalue based       948.4423     3
-## deSolve, compiled      763.3202     3
-

We see that using the compiled model is by a factor of 8.9 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 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:

smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 8.911519
-## Eigenvalue based      1.233763
+## deSolve, not compiled 7.838551
+## Eigenvalue based      1.109205
 ## deSolve, compiled     1.000000
@@ -127,15 +127,15 @@ print(smb.1) 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 14.32061 14.336413 14.380847 14.352216 14.410966
-## deSolve, compiled      1.34366  1.344778  1.371116  1.345897  1.384844
+
##                             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
 ##                             max neval
-## deSolve, not compiled 14.469716     3
-## deSolve, compiled      1.423791     3

+## deSolve, not compiled 14.436224     3
+## deSolve, compiled      1.394235     3
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 10.66368
+## 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!

This vignette was built with mkin 0.9.37 on

diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf index 7534bc6d..79b6a5ab 100644 Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ -- cgit v1.2.1