From 4ff86dfb0f9180f2aa099908fa6ecba630483553 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 4 Nov 2016 17:14:02 +0100 Subject: Static documentation rebuilt by pkgdown::build_site() To also include the pkgdown articles --- docs/articles/FOCUS_L.html | 42 ++++++++++----------- docs/articles/compiled_models.html | 26 ++++++------- .../figure-html/benchmark_FOMC_SFO-1.png | Bin 9973 -> 10652 bytes .../figure-html/benchmark_SFO_SFO-1.png | Bin 12199 -> 11994 bytes docs/articles/mkin_cache/html/__packages | 9 ++++- ...-chunk-2_60bc93a2c97228ef4815e972498edefa.RData | Bin 0 -> 3274 bytes ...ed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb | Bin 0 -> 20269 bytes ...ed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx | Bin 0 -> 226 bytes .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 112161 -> 45379 bytes 9 files changed, 41 insertions(+), 36 deletions(-) create mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData create mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb create mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 2244a359..4c3e5c9b 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -63,15 +63,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO) 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov  4 16:56:21 2016 
-## Date of summary: Fri Nov  4 16:56:21 2016 
+## Date of fit:     Fri Nov  4 17:13:56 2016 
+## Date of summary: Fri Nov  4 17:13:56 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.089 s
 ## 
 ## Weighting: none
 ## 
@@ -156,8 +156,8 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov  4 16:56:21 2016 
-## Date of summary: Fri Nov  4 16:56:21 2016 
+## Date of fit:     Fri Nov  4 17:13:57 2016 
+## Date of summary: Fri Nov  4 17:13:57 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -169,7 +169,7 @@ FOCUS_2006_L1_mkin <-  
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov  4 16:56:22 2016 
-## Date of summary: Fri Nov  4 16:56:22 2016 
+## Date of fit:     Fri Nov  4 17:13:58 2016 
+## Date of summary: Fri Nov  4 17:13:58 2016 
 ## 
 ## 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 0.199 s
+## Fitted with method Port using 81 model solutions performed in 0.194 s
 ## 
 ## Weighting: none
 ## 
@@ -323,8 +323,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov  4 16:56:23 2016 
-## Date of summary: Fri Nov  4 16:56:23 2016 
+## Date of fit:     Fri Nov  4 17:13:59 2016 
+## Date of summary: Fri Nov  4 17:13:59 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -333,7 +333,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov  4 16:56:24 2016 
-## Date of summary: Fri Nov  4 16:56:25 2016 
+## Date of fit:     Fri Nov  4 17:14:00 2016 
+## Date of summary: Fri Nov  4 17:14:00 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -422,7 +422,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov  4 16:56:25 2016 
-## Date of summary: Fri Nov  4 16:56:25 2016 
+## Date of fit:     Fri Nov  4 17:14:01 2016 
+## Date of summary: Fri Nov  4 17:14:01 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.109 s
+## Fitted with method Port using 46 model solutions performed in 0.114 s
 ## 
 ## Weighting: none
 ## 
@@ -572,15 +572,15 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov  4 16:56:25 2016 
-## Date of summary: Fri Nov  4 16:56:25 2016 
+## Date of fit:     Fri Nov  4 17:14:01 2016 
+## Date of summary: Fri Nov  4 17:14:01 2016 
 ## 
 ## 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 0.16 s
+## Fitted with method Port using 66 model solutions performed in 0.162 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index e1572b17..153841ae 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -78,21 +78,21 @@ mb.1 <- micr
 print(mb.1)

 
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069
-##       Eigenvalue based  925.7797  935.9924  939.8725  946.2051  946.9189
-##      deSolve, compiled  740.2821  750.0017  767.8440  759.7212  781.6249
+##  deSolve, not compiled 6282.2220 6293.7637 6323.0479 6305.3053 6343.4608
+##       Eigenvalue based  873.2553  886.5949  903.6178  899.9345  918.7990
+##      deSolve, compiled  737.7899  738.8794  752.3343  739.9689  759.6065
 ##        max neval cld
-##  6671.1797     3   b
-##   947.6327     3  a 
-##   803.5287     3  a

+##  6381.6162     3   c
+##   937.6634     3  b 
+##   779.2441     3 a

 
autoplot(mb.1)

 

 
We see that using the compiled model is by a factor of 8.5 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:

 
rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]

 
##                         median
-## deSolve, not compiled 8.464993
-## Eigenvalue based      1.245464
+## deSolve, not compiled 8.521041
+## Eigenvalue based      1.216179
 ## deSolve, compiled     1.000000

 
 

@@ -114,18 +114,18 @@ smb.1["median"]/smbprint(mb.2)

 
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.619556 13.761382 13.825679 13.903207 13.928741
-##      deSolve, compiled  1.316871  1.322577  1.358847  1.328283  1.379834
+##  deSolve, not compiled 13.644880 13.648332 13.835874 13.651784 13.931372
+##      deSolve, compiled  1.422381  1.448574  1.495091  1.474767  1.531446
 ##        max neval cld
-##  13.954275     3   b
-##   1.431386     3  a

+##  14.210959     3   b
+##   1.588125     3  a

 
smb.2["median"]/smb.2["deSolve, compiled", "median"]

 
##   median
 ## 1     NA
 ## 2     NA

 
autoplot(mb.2)

 

-
Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code!

+
Here we get a performance benefit of a factor of 9.3 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.44.9000 on

 
## R version 3.3.2 (2016-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
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diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index c8b1e877..03ece635 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -1,8 +1,13 @@
 base
+datasets
+utils
+grDevices
+graphics
+stats
 knitr
 minpack.lm
 rootSolve
+methods
 inline
+parallel
 mkin
-microbenchmark
-ggplot2
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