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 docs/reference/Extract.mmkin.html | 24 ++++++------ docs/reference/mccall81_245T.html | 6 +-- docs/reference/mkinfit.html | 8 ++-- docs/reference/mkinpredict.html | 6 +-- docs/reference/summary.mkinfit.html | 6 +-- docs/reference/transform_odeparms.html | 6 +-- 15 files changed, 69 insertions(+), 64 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 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)
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
index 57730131..c52ccd5d 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png differ
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index 50adff32..c89ef9a5 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png differ
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
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData
new file mode 100644
index 00000000..d11ccf31
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new file mode 100644
index 00000000..5ac4f484
Binary files /dev/null and b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx
new file mode 100644
index 00000000..8983f69e
Binary files /dev/null and b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx differ
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index d34e3805..2e7e2244 100644
Binary files a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png differ
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index ad4614fb..4b6545db 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -193,7 +193,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.264   0.000   0.262 
+#>   0.260   0.000   0.261 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -379,7 +379,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x50d32d0>
+#> <environment: 0x5bbb4a8>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -401,7 +401,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x50d32d0>
+#> <environment: 0x5bbb4a8>
 #> 
 #> $hessian_notrans
 #>            parent_0     alpha       beta
@@ -467,7 +467,7 @@
 #> 99.66619 
 #> 
 #> $date
-#> [1] "Fri Nov  4 17:08:52 2016"
+#> [1] "Fri Nov  4 17:12:26 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
  fits["SFO", "B"]
#>      dataset
@@ -546,7 +546,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.068   0.000   0.067 
+#>   0.068   0.000   0.071 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -733,7 +733,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x4f17408>
+#> <environment: 0x5719c08>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -755,7 +755,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x4f17408>
+#> <environment: 0x5719c08>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -818,7 +818,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Nov  4 17:08:51 2016"
+#> [1] "Fri Nov  4 17:12:26 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
  fits["SFO", "B", drop = TRUE]
#> [[1]]
@@ -894,7 +894,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.068   0.000   0.067 
+#>   0.068   0.000   0.071 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -1081,7 +1081,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x4f17408>
+#> <environment: 0x5719c08>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -1103,7 +1103,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x4f17408>
+#> <environment: 0x5719c08>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -1166,7 +1166,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Nov  4 17:08:51 2016"
+#> [1] "Fri Nov  4 17:12:26 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 6eb4741b..40c21d3c 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -122,8 +122,8 @@
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Fri Nov  4 17:08:59 2016 
-#> Date of summary: Fri Nov  4 17:08:59 2016 
+#> Date of fit:     Fri Nov  4 17:12:32 2016 
+#> Date of summary: Fri Nov  4 17:12:32 2016 
 #> 
 #> Equations:
 #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -133,7 +133,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.497 s
+#> Fitted with method Port using 246 model solutions performed in 1.502 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 93185eff..32083843 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -359,15 +359,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Fri Nov  4 17:09:01 2016 
-#> Date of summary: Fri Nov  4 17:09:01 2016 
+#> Date of fit:     Fri Nov  4 17:12:35 2016 
+#> Date of summary: Fri Nov  4 17:12:35 2016 
 #> 
 #> Equations:
 #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.156 s
+#> Fitted with method Port using 64 model solutions performed in 0.147 s
 #> 
 #> Weighting: none
 #> 
@@ -436,7 +436,7 @@
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#>    user  system elapsed 
-#>   1.256   1.216   0.946 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   1.208   1.256   0.935 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 9f00dab7..e8302508 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -275,17 +275,17 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.004   0.028   0.004 
  system.time(
+#>   0.008   0.016   0.005 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.000   0.020   0.003 
  system.time(
+#>   0.000   0.016   0.002 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.052   0.000   0.052 

+#>   0.036   0.000   0.035