From 0b677308e3ffbf742880f05cc54da469f3ecc854 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 9 Mar 2018 23:14:39 +0100 Subject: Another rebuild of the static docs Now with rbenchmark installed, to get results for the compiled_models vignette --- docs/articles/FOCUS_D.html | 13 +++--- docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 96321 -> 98934 bytes .../FOCUS_D_files/figure-html/plot_2-1.png | Bin 14047 -> 14308 bytes docs/articles/FOCUS_L.html | 47 ++++++++++----------- .../figure-html/unnamed-chunk-10-1.png | Bin 28683 -> 29157 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 52097 -> 54520 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 21427 -> 21712 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 36600 -> 38347 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 23247 -> 23493 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 14668 -> 14866 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 23624 -> 23973 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 27537 -> 27988 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 27959 -> 28412 bytes docs/articles/FOCUS_Z.html | 7 +-- .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 83846 -> 85456 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 123289 -> 128546 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 122641 -> 128162 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 96633 -> 101891 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 22186 -> 22697 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 84217 -> 86036 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 83907 -> 85658 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 96969 -> 101516 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 123363 -> 129164 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 123396 -> 128994 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 103846 -> 108244 bytes docs/articles/compiled_models.html | 37 +++++++++------- docs/articles/index.html | 1 - docs/articles/mkin.html | 7 +-- .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 110404 -> 114757 bytes docs/articles/twa.html | 7 +-- 30 files changed, 54 insertions(+), 65 deletions(-) (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index af04f755..d85246f8 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -9,10 +9,7 @@ - - - - @@ -80,7 +77,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-03-01

+

2018-03-09

@@ -155,8 +152,8 @@ 
summary(fit)
## 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 
+## Date of fit:     Fri Mar  9 23:09:48 2018 
+## Date of summary: Fri Mar  9 23:09:48 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -164,7 +161,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.993 s
+## Fitted with method Port using 153 model solutions performed in 0.99 s
 ## 
 ## Weighting: none
 ## 
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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 5de06ad5..196a0c4f 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
@@ -103,15 +100,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO)
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:31:57 2018 
-## Date of summary: Thu Mar  1 14:31:57 2018 
+## Date of fit:     Fri Mar  9 23:09:50 2018 
+## Date of summary: Fri Mar  9 23:09:50 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.24 s
+## Fitted with method Port using 37 model solutions performed in 0.264 s
 ## 
 ## Weighting: none
 ## 
@@ -194,15 +191,15 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:31:59 2018 
-## Date of summary: Thu Mar  1 14:32:00 2018 
+## Date of fit:     Fri Mar  9 23:09:52 2018 
+## Date of summary: Fri Mar  9 23:09:52 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.375 s
+## Fitted with method Port using 611 model solutions performed in 1.451 s
 ## 
 ## Weighting: none
 ## 
@@ -289,15 +286,15 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:00 2018 
-## Date of summary: Thu Mar  1 14:32:00 2018 
+## Date of fit:     Fri Mar  9 23:09:53 2018 
+## Date of summary: Fri Mar  9 23:09:53 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.158 s
+## Fitted with method Port using 81 model solutions performed in 0.175 s
 ## 
 ## Weighting: none
 ## 
@@ -360,8 +357,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:01 2018 
-## Date of summary: Thu Mar  1 14:32:01 2018 
+## Date of fit:     Fri Mar  9 23:09:54 2018 
+## Date of summary: Fri Mar  9 23:09:54 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -370,7 +367,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:02 2018 
-## Date of summary: Thu Mar  1 14:32:02 2018 
+## Date of fit:     Fri Mar  9 23:09:55 2018 
+## Date of summary: Fri Mar  9 23:09:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -462,7 +459,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:03 2018 
-## Date of summary: Thu Mar  1 14:32:03 2018 
+## Date of fit:     Fri Mar  9 23:09:55 2018 
+## Date of summary: Fri Mar  9 23:09:56 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.089 s
+## Fitted with method Port using 46 model solutions performed in 0.09 s
 ## 
 ## Weighting: none
 ## 
@@ -613,8 +610,8 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:03 2018 
-## Date of summary: Thu Mar  1 14:32:03 2018 
+## Date of fit:     Fri Mar  9 23:09:56 2018 
+## Date of summary: Fri Mar  9 23:09:56 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
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index 52a1db77..606121ff 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
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diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 9f0b5708..915e5474 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
@@ -101,7 +98,7 @@ SFO_SFO <- 
if (require(rbenchmark)) {
-  b.1 <- benchmark(
+  b.1 <- benchmark(
     "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                       solution_type = "deSolve",
                                       use_compiled = FALSE, quiet = TRUE),
@@ -117,10 +114,15 @@ SFO_SFO <- print("R package benchmark is not available")
 }

 
## Lade nötiges Paket: rbenchmark

-
## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'

-
## [1] "R package benchmark is not available"

-
We see that using the compiled model is by a factor of around NA 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.

+
##                    test replications elapsed relative user.self sys.self
+## 3     deSolve, compiled            3   2.044    1.000     2.042        0
+## 1 deSolve, not compiled            3  14.198    6.946    14.185        0
+## 2      Eigenvalue based            3   2.751    1.346     2.747        0
+##   user.child sys.child
+## 3          0         0
+## 1          0         0
+## 2          0         0

+
We see that using the compiled model is by a factor of around 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.

 
 

 

@@ -131,7 +133,7 @@ SFO_SFO <- parent = mkinsub("FOMC", "m1"),
     m1 = mkinsub( "SFO"))
 
-  b.2 <- benchmark(
+  b.2 <- benchmark(
     "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
                                       use_compiled = FALSE, quiet = TRUE),
     "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
@@ -142,11 +144,14 @@ SFO_SFO <-  NA
   print("R package benchmark is not available")
 }

-
## Lade nötiges Paket: rbenchmark

-
## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'

-
## [1] "R package benchmark is not available"

-
Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!

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

+
##                    test replications elapsed relative user.self sys.self
+## 2     deSolve, compiled            3   3.695    1.000     3.692        0
+## 1 deSolve, not compiled            3  31.143    8.428    31.114        0
+##   user.child sys.child
+## 2          0         0
+## 1          0         0

+
Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.46.3 on

 
## R version 3.4.3 (2017-11-30)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
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index 2b16580a..c0c5864b 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -27,7 +27,6 @@
 
   
   
-
 
 
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index a91da0a4..f668b500 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
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index 400b1383..e5b68cfe 100644
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+++ b/docs/articles/twa.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
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