From 1b2bdb8c02b1090f6c20f3ce9f7b461aab26e21c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 28 Jun 2016 05:32:21 +0200 Subject: Static documentation rebuilt by staticdocs::build_site() --- inst/web/Extract.mmkin.html | 24 +++++++++---------- inst/web/mccall81_245T.html | 6 ++--- inst/web/mkinfit.html | 8 +++---- inst/web/mkinpredict.html | 4 ++-- inst/web/summary.mkinfit.html | 6 ++--- inst/web/transform_odeparms.html | 6 ++--- inst/web/vignettes/FOCUS_D.html | 6 ++--- inst/web/vignettes/FOCUS_L.html | 40 ++++++++++++++++---------------- inst/web/vignettes/FOCUS_Z.pdf | Bin 238788 -> 238788 bytes inst/web/vignettes/compiled_models.html | 32 ++++++++++++------------- 10 files changed, 66 insertions(+), 66 deletions(-) (limited to 'inst') diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index 81a7a663..d165e11a 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -181,7 +181,7 @@ $calls $time user system elapsed - 0.696 0.000 0.695 + 0.712 0.000 0.711 $mkinmod <mkinmod> model generated with @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x3431d78> +<environment: 0x498a868> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x3431d78> +<environment: 0x498a868> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Tue Jun 28 01:32:02 2016" +[1] "Tue Jun 28 01:54:25 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -540,7 +540,7 @@ $calls $time user system elapsed - 0.200 0.000 0.204 + 0.224 0.000 0.224 $mkinmod <mkinmod> model generated with @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x44b33b0> +<environment: 0x5658dc0> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x44b33b0> +<environment: 0x5658dc0> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 01:32:02 2016" +[1] "Tue Jun 28 01:54:24 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -890,7 +890,7 @@ $calls $time user system elapsed - 0.200 0.000 0.204 + 0.224 0.000 0.224 $mkinmod <mkinmod> model generated with @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x44b33b0> +<environment: 0x5658dc0> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x44b33b0> +<environment: 0x5658dc0> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 01:32:02 2016" +[1] "Tue Jun 28 01:54:24 2016" attr(,"class") [1] "mkinfit" "modFit" diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index f073876e..20328b34 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -114,8 +114,8 @@
mkin version: 0.9.43 R version: 3.3.1 -Date of fit: Tue Jun 28 01:32:20 2016 -Date of summary: Tue Jun 28 01:32:20 2016 +Date of fit: Tue Jun 28 01:54:43 2016 +Date of summary: Tue Jun 28 01:54:43 2016 Equations: d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -124,7 +124,7 @@ d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole Model predictions using solution type deSolve -Fitted with method Port using 246 model solutions performed in 3.912 s +Fitted with method Port using 246 model solutions performed in 3.74 s Weighting: none diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 6ebf995c..9e0162c5 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -325,15 +325,15 @@ summary(fit)
mkin version: 0.9.43 R version: 3.3.1 -Date of fit: Tue Jun 28 01:32:27 2016 -Date of summary: Tue Jun 28 01:32:27 2016 +Date of fit: Tue Jun 28 01:54:49 2016 +Date of summary: Tue Jun 28 01:54:49 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 0.425 s +Fitted with method Port using 64 model solutions performed in 0.433 s Weighting: none @@ -409,7 +409,7 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))
user system elapsed - 2.880 2.292 2.309 + 2.788 2.280 2.257
coef(fit)
diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index 06980d3f..be761407 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -304,7 +304,7 @@ 201 20 4.978707 27.46227
user system elapsed - 0.020 0.048 0.011 + 0.028 0.044 0.011
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -315,7 +315,7 @@ 201 20 4.978707 27.46227
user system elapsed - 0.004 0.000 0.004 + 0.024 0.000 0.005
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index b8a6d507..724e470d 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -159,15 +159,15 @@
mkin version: 0.9.43 R version: 3.3.1 -Date of fit: Tue Jun 28 01:32:47 2016 -Date of summary: Tue Jun 28 01:32:47 2016 +Date of fit: Tue Jun 28 01:55:10 2016 +Date of summary: Tue Jun 28 01:55:10 2016 Equations: d_parent = - k_parent_sink * parent Model predictions using solution type analytical -Fitted with method Port using 35 model solutions performed in 0.242 s +Fitted with method Port using 35 model solutions performed in 0.244 s Weighting: none diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html index 69e52241..aa7e22f3 100644 --- a/inst/web/transform_odeparms.html +++ b/inst/web/transform_odeparms.html @@ -135,8 +135,8 @@ summary(fit, data=FALSE) # See transformed and backtransformed parameters
mkin version: 0.9.43 R version: 3.3.1 -Date of fit: Tue Jun 28 01:32:50 2016 -Date of summary: Tue Jun 28 01:32:50 2016 +Date of fit: Tue Jun 28 01:55:12 2016 +Date of summary: Tue Jun 28 01:55:12 2016 Equations: d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -144,7 +144,7 @@ d_m1 = + k_parent_m1 * parent - k_m1_sink * m1 Model predictions using solution type deSolve -Fitted with method Port using 153 model solutions performed in 1.694 s +Fitted with method Port using 153 model solutions performed in 1.624 s Weighting: none diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html index 7f564ad8..e01c5869 100644 --- a/inst/web/vignettes/FOCUS_D.html +++ b/inst/web/vignettes/FOCUS_D.html @@ -192,8 +192,8 @@ print(FOCUS_2006_D) 
summary(fit)
## mkin version:    0.9.43 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:37:23 2016 
-## Date of summary: Tue Jun 28 01:37:23 2016 
+## Date of fit:     Tue Jun 28 01:59:43 2016 
+## Date of summary: Tue Jun 28 01:59:44 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -201,7 +201,7 @@ print(FOCUS_2006_D)
## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 1.704 s +## Fitted with method Port using 153 model solutions performed in 1.698 s ## ## Weighting: none ## diff --git a/inst/web/vignettes/FOCUS_L.html b/inst/web/vignettes/FOCUS_L.html index 154ac896..828d9def 100644 --- a/inst/web/vignettes/FOCUS_L.html +++ b/inst/web/vignettes/FOCUS_L.html @@ -235,15 +235,15 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1) summary(m.L1.SFO) 
## mkin version:    0.9.43 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:37:25 2016 
-## Date of summary: Tue Jun 28 01:37:25 2016 
+## Date of fit:     Tue Jun 28 01:59:45 2016 
+## Date of summary: Tue Jun 28 01:59:45 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.244 s
+## Fitted with method Port using 37 model solutions performed in 0.243 s
 ## 
 ## Weighting: none
 ## 
@@ -328,8 +328,8 @@ summary(m.L1.SFO)
summary(m.L1.FOMC, data = FALSE)
## mkin version:    0.9.43 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:37:27 2016 
-## Date of summary: Tue Jun 28 01:37:27 2016 
+## Date of fit:     Tue Jun 28 01:59:47 2016 
+## Date of summary: Tue Jun 28 01:59:47 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -341,7 +341,7 @@ summary(m.L1.SFO)
## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 1.236 s +## Fitted with method Port using 188 model solutions performed in 1.241 s ## ## Weighting: none ## @@ -425,8 +425,8 @@ plot(m.L2.FOMC, show_residuals = TRUE, 
summary(m.L2.FOMC, data = FALSE)
## mkin version:    0.9.43 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:37:29 2016 
-## Date of summary: Tue Jun 28 01:37:29 2016 
+## Date of fit:     Tue Jun 28 01:59:49 2016 
+## Date of summary: Tue Jun 28 01:59:49 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -495,8 +495,8 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.43 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:37:32 2016 
-## Date of summary: Tue Jun 28 01:37:32 2016 
+## Date of fit:     Tue Jun 28 01:59:52 2016 
+## Date of summary: Tue Jun 28 01:59:52 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -505,7 +505,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 2.323 s
+## Fitted with method Port using 336 model solutions performed in 2.286 s
 ## 
 ## Weighting: none
 ## 
@@ -584,8 +584,8 @@ plot(mm.L3)

 
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.43 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:37:35 2016 
-## Date of summary: Tue Jun 28 01:37:35 2016 
+## Date of fit:     Tue Jun 28 01:59:55 2016 
+## Date of summary: Tue Jun 28 01:59:56 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -594,7 +594,7 @@ plot(mm.L3)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.909 s
+## Fitted with method Port using 137 model solutions performed in 0.907 s
 ## 
 ## Weighting: none
 ## 
@@ -684,15 +684,15 @@ plot(mm.L4)
summary(mm.L4[["SFO", 1]], data = FALSE)
## mkin version:    0.9.43 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:37:36 2016 
-## Date of summary: Tue Jun 28 01:37:37 2016 
+## Date of fit:     Tue Jun 28 01:59:57 2016 
+## Date of summary: Tue Jun 28 01:59:58 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.312 s
+## Fitted with method Port using 46 model solutions performed in 0.306 s
 ## 
 ## Weighting: none
 ## 
@@ -744,15 +744,15 @@ plot(mm.L4)
summary(mm.L4[["FOMC", 1]], data = FALSE)
## mkin version:    0.9.43 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:37:37 2016 
-## Date of summary: Tue Jun 28 01:37:37 2016 
+## Date of fit:     Tue Jun 28 01:59:57 2016 
+## Date of summary: Tue Jun 28 01:59:58 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 0.417 s
+## Fitted with method Port using 66 model solutions performed in 0.42 s
 ## 
 ## Weighting: none
 ## 
diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf
index ac3af921..efda950f 100644
Binary files a/inst/web/vignettes/FOCUS_Z.pdf and b/inst/web/vignettes/FOCUS_Z.pdf differ
diff --git a/inst/web/vignettes/compiled_models.html b/inst/web/vignettes/compiled_models.html
index 9e2dff36..5e426a7f 100644
--- a/inst/web/vignettes/compiled_models.html
+++ b/inst/web/vignettes/compiled_models.html
@@ -250,21 +250,21 @@ mb.1 <- microbenchmark(
 print(mb.1)
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 25.160343 25.384579 25.502052 25.608814 25.672906
-##       Eigenvalue based  2.219737  2.234679  2.244043  2.249621  2.256196
-##      deSolve, compiled  1.825299  1.843813  1.856078  1.862327  1.871467
+##  deSolve, not compiled 25.042204 25.078629 25.467550 25.115054 25.680223
+##       Eigenvalue based  2.273059  2.277424  2.285719  2.281790  2.292049
+##      deSolve, compiled  1.878785  1.883750  1.891594  1.888716  1.897998
 ##        max neval cld
-##  25.736998     3   b
-##   2.262771     3  a 
-##   1.880606     3  a
+## 26.245391 3 b +## 2.302308 3 a +## 1.907281 3 a 
autoplot(mb.1)
-

-

We see that using the compiled model is by a factor of 13.8 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:

+

+

We see that using the compiled model is by a factor of 13.3 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 13.750973
-## Eigenvalue based       1.207962
+## deSolve, not compiled 13.297425
+## Eigenvalue based       1.208117
 ## deSolve, compiled      1.000000
@@ -285,18 +285,18 @@ smb.1["median"]/smb.1["deSolve, compiled", "median" 
smb.2 <- summary(mb.2)
 print(mb.2)
## Unit: seconds
-##                   expr       min        lq      mean   median        uq
-##  deSolve, not compiled 54.725198 54.787875 54.893809 54.85055 54.978114
-##      deSolve, compiled  3.618315  3.644838  3.670582  3.67136  3.696716
+##                   expr      min        lq      mean    median        uq
+##  deSolve, not compiled 53.69252 53.938844 54.137601 54.185167 54.360141
+##      deSolve, compiled  3.42508  3.526298  3.588392  3.627516  3.670048
 ##        max neval cld
-##  55.105678     3   b
-##   3.722071     3  a
+## 54.535116 3 b +## 3.712579 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 14.9 using the version of the differential equation model compiled from C code!

This vignette was built with mkin 0.9.43 on

## R version 3.3.1 (2016-06-21)
-- 
cgit v1.2.1