From cb318ea1067bf18d8ff896cef8d1e847a49e3aa7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 28 Jun 2016 01:43:13 +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 | 6 ++--- 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 | 42 ++++++++++++++++---------------- inst/web/vignettes/FOCUS_Z.pdf | Bin 237947 -> 238788 bytes inst/web/vignettes/compiled_models.html | 32 ++++++++++++------------ 10 files changed, 68 insertions(+), 68 deletions(-) (limited to 'inst') diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index 60697959..81a7a663 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -181,7 +181,7 @@ $calls $time user system elapsed - 0.704 0.000 0.702 + 0.696 0.000 0.695 $mkinmod <mkinmod> model generated with @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x49ead78> +<environment: 0x3431d78> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x49ead78> +<environment: 0x3431d78> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Tue Jun 28 01:17:01 2016" +[1] "Tue Jun 28 01:32:02 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -540,7 +540,7 @@ $calls $time user system elapsed - 0.208 0.004 0.208 + 0.200 0.000 0.204 $mkinmod <mkinmod> model generated with @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x5a6c3b0> +<environment: 0x44b33b0> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x5a6c3b0> +<environment: 0x44b33b0> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 01:17:00 2016" +[1] "Tue Jun 28 01:32:02 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -890,7 +890,7 @@ $calls $time user system elapsed - 0.208 0.004 0.208 + 0.200 0.000 0.204 $mkinmod <mkinmod> model generated with @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x5a6c3b0> +<environment: 0x44b33b0> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x5a6c3b0> +<environment: 0x44b33b0> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 01:17:00 2016" +[1] "Tue Jun 28 01:32:02 2016" attr(,"class") [1] "mkinfit" "modFit" diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index 6596bd70..f073876e 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 01:17:19 2016 -Date of summary: Tue Jun 28 01:17:19 2016 +Date of fit: Tue Jun 28 01:32:20 2016 +Date of summary: Tue Jun 28 01:32:20 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 3.778 s +Fitted with method Port using 246 model solutions performed in 3.912 s Weighting: none diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index dd7f1831..6ebf995c 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 01:17:26 2016 -Date of summary: Tue Jun 28 01:17:26 2016 +Date of fit: Tue Jun 28 01:32:27 2016 +Date of summary: Tue Jun 28 01:32:27 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 0.457 s +Fitted with method Port using 64 model solutions performed in 0.425 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 - 2.868 2.284 2.301 + 2.880 2.292 2.309
coef(fit)
diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index d64a075f..06980d3f 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -304,7 +304,7 @@ 201 20 4.978707 27.46227
user system elapsed - 0.024 0.048 0.010 + 0.020 0.048 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 - 0.008 0.020 0.005 + 0.004 0.000 0.004
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -326,7 +326,7 @@ 201 20 4.978707 27.46227
user system elapsed - 0.132 0.004 0.138 + 0.140 0.000 0.139
diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index 8ade3a21..b8a6d507 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 01:17:46 2016 -Date of summary: Tue Jun 28 01:17:46 2016 +Date of fit: Tue Jun 28 01:32:47 2016 +Date of summary: Tue Jun 28 01:32:47 2016 Equations: d_parent = - k_parent_sink * parent Model predictions using solution type analytical -Fitted with method Port using 35 model solutions performed in 0.27 s +Fitted with method Port using 35 model solutions performed in 0.242 s Weighting: none diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html index 73ff0d08..69e52241 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 01:17:49 2016 -Date of summary: Tue Jun 28 01:17:49 2016 +Date of fit: Tue Jun 28 01:32:50 2016 +Date of summary: Tue Jun 28 01:32:50 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 1.639 s +Fitted with method Port using 153 model solutions performed in 1.694 s Weighting: none diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html index 48ae4654..7f564ad8 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 01:22:20 2016 
-## Date of summary: Tue Jun 28 01:22:21 2016 
+## Date of fit:     Tue Jun 28 01:37:23 2016 
+## Date of summary: Tue Jun 28 01:37:23 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 1.759 s +## Fitted with method Port using 153 model solutions performed in 1.704 s ## ## Weighting: none ## diff --git a/inst/web/vignettes/FOCUS_L.html b/inst/web/vignettes/FOCUS_L.html index 7026e3ce..154ac896 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 01:22:22 2016 
-## Date of summary: Tue Jun 28 01:22:22 2016 
+## Date of fit:     Tue Jun 28 01:37:25 2016 
+## Date of summary: Tue Jun 28 01:37:25 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.253 s
+## Fitted with method Port using 37 model solutions performed in 0.244 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 01:22:24 2016 
-## Date of summary: Tue Jun 28 01:22:24 2016 
+## Date of fit:     Tue Jun 28 01:37:27 2016 
+## Date of summary: Tue Jun 28 01:37:27 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 1.241 s +## Fitted with method Port using 188 model solutions performed in 1.236 s ## ## Weighting: none ## @@ -425,15 +425,15 @@ 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 01:22:27 2016 
-## Date of summary: Tue Jun 28 01:22:27 2016 
+## Date of fit:     Tue Jun 28 01:37:29 2016 
+## Date of summary: Tue Jun 28 01:37:29 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 0.541 s
+## Fitted with method Port using 81 model solutions performed in 0.534 s
 ## 
 ## Weighting: none
 ## 
@@ -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 01:22:30 2016 
-## Date of summary: Tue Jun 28 01:22:30 2016 
+## Date of fit:     Tue Jun 28 01:37:32 2016 
+## Date of summary: Tue Jun 28 01:37:32 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 2.29 s
+## Fitted with method Port using 336 model solutions performed in 2.323 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 01:22:33 2016 
-## Date of summary: Tue Jun 28 01:22:33 2016 
+## Date of fit:     Tue Jun 28 01:37:35 2016 
+## Date of summary: Tue Jun 28 01:37:35 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 0.959 s
+## Fitted with method Port using 137 model solutions performed in 0.909 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 01:22:34 2016 
-## Date of summary: Tue Jun 28 01:22:35 2016 
+## Date of fit:     Tue Jun 28 01:37:36 2016 
+## Date of summary: Tue Jun 28 01:37:37 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.302 s
+## Fitted with method Port using 46 model solutions performed in 0.312 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 01:22:35 2016 
-## Date of summary: Tue Jun 28 01:22:35 2016 
+## Date of fit:     Tue Jun 28 01:37:37 2016 
+## Date of summary: Tue Jun 28 01:37:37 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 0.438 s
+## Fitted with method Port using 66 model solutions performed in 0.417 s
 ## 
 ## Weighting: none
 ## 
diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf
index d21f7cb9..ac3af921 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 3a81c6c3..9e2dff36 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 25.634645 25.717260 25.925956 25.799875 26.071612
-##       Eigenvalue based  2.235689  2.237675  2.246796  2.239661  2.252349
-##      deSolve, compiled  1.869556  1.881345  1.887495  1.893133  1.896465
+##  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
 ##        max neval cld
-##  26.343349     3   b
-##   2.265038     3  a 
-##   1.899797     3  a
+## 25.736998 3 b +## 2.262771 3 a +## 1.880606 3 a 
autoplot(mb.1)
-

-

We see that using the compiled model is by a factor of 13.6 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 13.8 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:

rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                          median
-## deSolve, not compiled 13.628133
-## Eigenvalue based       1.183044
+## deSolve, not compiled 13.750973
+## Eigenvalue based       1.207962
 ## 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 53.993961 54.012379 54.225054 54.030797 54.340600
-##      deSolve, compiled  3.450737  3.535551  3.583034  3.620364  3.649183
+##                   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
 ##        max neval cld
-##  54.650403     3   b
-##   3.678001     3  a
+## 55.105678 3 b +## 3.722071 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