From c6086d1dd97ad2d6420625de7b8009b1b0f85d06 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2016 15:01:53 +0100 Subject: Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE) Using branch 'jranke' on jranke/pkgdown, fixing issues hadley/pgkdown#178 and hadley/pkgdown#213 Remove plot=TRUE from mkinfit calls also in dontrun sections of examples to avoid a flood png files documenting the progress of the fit. --- docs/articles/FOCUS_D.html | 2 +- docs/articles/FOCUS_D_cache/html/__packages | 2 - .../plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData | Bin 0 -> 2756 bytes .../plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb | 0 .../plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx | Bin 0 -> 113 bytes .../plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData | Bin 0 -> 2786 bytes .../html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb | 0 .../html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx | Bin 0 -> 113 bytes docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 95834 -> 38557 bytes .../FOCUS_D_files/figure-html/plot_2-1.png | Bin 14059 -> 6091 bytes docs/articles/FOCUS_L.html | 44 ++++++++++----------- docs/articles/compiled_models.html | 28 ++++++------- .../figure-html/benchmark_FOMC_SFO-1.png | Bin 9514 -> 10757 bytes .../figure-html/benchmark_SFO_SFO-1.png | Bin 11028 -> 10610 bytes docs/articles/mkin.html | 2 +- docs/articles/mkin_cache/html/__packages | 2 - ...-chunk-2_1255937aa4f0d68ff78163262b20b976.RData | Bin 0 -> 3367 bytes ...ed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb | Bin 0 -> 20287 bytes ...ed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx | Bin 0 -> 225 bytes .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 112161 -> 45379 bytes 20 files changed, 38 insertions(+), 42 deletions(-) create mode 100644 docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData create mode 100644 docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb create mode 100644 docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx create mode 100644 docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData create mode 100644 docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb create mode 100644 docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx create mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData create mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb create mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 776e1093..0ce7bd07 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -41,7 +41,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2016-11-17

+

2016-11-18

diff --git a/docs/articles/FOCUS_D_cache/html/__packages b/docs/articles/FOCUS_D_cache/html/__packages index f8bbf624..c3c384b1 100644 --- a/docs/articles/FOCUS_D_cache/html/__packages +++ b/docs/articles/FOCUS_D_cache/html/__packages @@ -8,5 +8,3 @@ inline mkin rmarkdown knitr -microbenchmark -ggplot2 diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData new file mode 100644 index 00000000..36a4095f Binary files /dev/null and b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData differ diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb new file mode 100644 index 00000000..e69de29b diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx new file mode 100644 index 00000000..20f10d9f Binary files /dev/null and b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx differ diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData new file mode 100644 index 00000000..b0731d7b Binary files /dev/null and b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData differ diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb new file mode 100644 index 00000000..e69de29b diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx new file mode 100644 index 00000000..20f10d9f Binary files /dev/null and b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx differ diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png index fc237898..e44c1374 100644 Binary files a/docs/articles/FOCUS_D_files/figure-html/plot-1.png and b/docs/articles/FOCUS_D_files/figure-html/plot-1.png differ diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png index b0a7c26b..c7df3486 100644 Binary files a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png and b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png differ diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index e7ec5308..c3009e4d 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -41,7 +41,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2016-11-17

+

2016-11-18

@@ -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:     Thu Nov 17 22:58:18 2016 
-## Date of summary: Thu Nov 17 22:58:18 2016 
+## Date of fit:     Fri Nov 18 15:22:03 2016 
+## Date of summary: Fri Nov 18 15:22:03 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.103 s
+## Fitted with method Port using 37 model solutions performed in 0.09 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:     Thu Nov 17 22:58:19 2016 
-## Date of summary: Thu Nov 17 22:58:19 2016 
+## Date of fit:     Fri Nov 18 15:22:04 2016 
+## Date of summary: Fri Nov 18 15:22:04 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:     Thu Nov 17 22:58:20 2016 
-## Date of summary: Thu Nov 17 22:58:20 2016 
+## Date of fit:     Fri Nov 18 15:22:05 2016 
+## Date of summary: Fri Nov 18 15:22:05 2016 
 ## 
 ## 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 0.195 s
+## Fitted with method Port using 81 model solutions performed in 0.19 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:     Thu Nov 17 22:58:21 2016 
-## Date of summary: Thu Nov 17 22:58:21 2016 
+## Date of fit:     Fri Nov 18 15:22:06 2016 
+## Date of summary: Fri Nov 18 15:22:06 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -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:     Thu Nov 17 22:58:22 2016 
-## Date of summary: Thu Nov 17 22:58:22 2016 
+## Date of fit:     Fri Nov 18 15:22:07 2016 
+## Date of summary: Fri Nov 18 15:22:07 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -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:     Thu Nov 17 22:58:22 2016 
-## Date of summary: Thu Nov 17 22:58:23 2016 
+## Date of fit:     Fri Nov 18 15:22:08 2016 
+## Date of summary: Fri Nov 18 15:22:08 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.114 s
+## Fitted with method Port using 46 model solutions performed in 0.109 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:     Thu Nov 17 22:58:23 2016 
-## Date of summary: Thu Nov 17 22:58:23 2016 
+## Date of fit:     Fri Nov 18 15:22:08 2016 
+## Date of summary: Fri Nov 18 15:22:08 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.151 s
+## Fitted with method Port using 66 model solutions performed in 0.15 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 1446a357..ce149bc5 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -41,7 +41,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2016-11-17

+            
2016-11-18

           
 
     
@@ -78,21 +78,21 @@ mb.1 <- micr
 print(mb.1)

 
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6251.2433 6291.2435 6315.5160 6331.2438 6347.6524
-##       Eigenvalue based  858.2035  903.1770  926.2132  948.1505  960.2181
-##      deSolve, compiled  721.0067  739.1361  745.9964  757.2656  758.4913
+##  deSolve, not compiled 6341.1795 6363.5977 6373.7748 6386.0158 6390.0724
+##       Eigenvalue based  907.1699  908.8498  921.8335  910.5297  929.1653
+##      deSolve, compiled  747.5311  752.3718  754.2086  757.2125  757.5474
 ##        max neval cld
-##  6364.0611     3   c
-##   972.2856     3  b 
-##   759.7171     3 a

+##  6394.1290     3   c
+##   947.8008     3  b 
+##   757.8823     3 a

 
autoplot(mb.1)

 

 
We see that using the compiled model is by a factor of 8.4 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 8.360665
-## Eigenvalue based      1.252071
+## deSolve, not compiled 8.433585
+## Eigenvalue based      1.202476
 ## deSolve, compiled     1.000000

 
 

@@ -114,11 +114,11 @@ smb.1["median"]/smbprint(mb.2)

 
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.601046 13.602861 13.619563 13.604676 13.628821
-##      deSolve, compiled  1.341581  1.346263  1.348298  1.350944  1.351657
-##       max neval cld
-##  13.65297     3   b
-##   1.35237     3  a

+##  deSolve, not compiled 13.214250 13.248908 13.384577 13.283565 13.469740
+##      deSolve, compiled  1.303868  1.307484  1.332879  1.311099  1.347384
+##        max neval cld
+##  13.655915     3   b
+##   1.383669     3  a

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

 
##   median
 ## 1     NA
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
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diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 4eed053a..8134287b 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -41,7 +41,7 @@
       
mkin - Kinetic evaluation of chemical degradation data

                         
Johannes Ranke

             
-            
2016-11-17

+            
2016-11-18

           
 
     
diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index ff62e6df..ae46e2d7 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -8,5 +8,3 @@ colorout
 setwidth
 nvimcom
 rmarkdown
-microbenchmark
-ggplot2
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData
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