From a350a16bb2c11986faf5883a2804d46b03bd7c8f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 10 Sep 2016 05:21:52 +0200 Subject: Static documentation rebuilt with current staticdocs Using hadley/staticdocs commit #8c1069d from 8 days ago --- 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 | 4 ++-- 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 238636 -> 238632 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 e4225ffd..6e32f5a9 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -183,7 +183,7 @@ $calls $time user system elapsed - 0.260 0.000 0.259 + 0.252 0.000 0.252 $mkinmod <mkinmod> model generated with @@ -369,7 +369,7 @@ function (P) } return(mC) } -<environment: 0x37c6c70> +<environment: 0x33d3c70> $cost_notrans function (P) @@ -391,7 +391,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x37c6c70> +<environment: 0x33d3c70> $hessian_notrans parent_0 alpha beta @@ -457,7 +457,7 @@ $bparms.state 99.66619 $date -[1] "Sat Sep 10 04:12:07 2016" +[1] "Sat Sep 10 05:19:30 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -544,7 +544,7 @@ $calls $time user system elapsed - 0.068 0.000 0.069 + 0.068 0.000 0.067 $mkinmod <mkinmod> model generated with @@ -731,7 +731,7 @@ function (P) } return(mC) } -<environment: 0x4cb0ed0> +<environment: 0x48bdf40> $cost_notrans function (P) @@ -753,7 +753,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x4cb0ed0> +<environment: 0x48bdf40> $hessian_notrans parent_0 k_parent_sink @@ -816,7 +816,7 @@ $bparms.state 99.17407 $date -[1] "Sat Sep 10 04:12:07 2016" +[1] "Sat Sep 10 05:19:30 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -896,7 +896,7 @@ $calls $time user system elapsed - 0.068 0.000 0.069 + 0.068 0.000 0.067 $mkinmod <mkinmod> model generated with @@ -1083,7 +1083,7 @@ function (P) } return(mC) } -<environment: 0x4cb0ed0> +<environment: 0x48bdf40> $cost_notrans function (P) @@ -1105,7 +1105,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x4cb0ed0> +<environment: 0x48bdf40> $hessian_notrans parent_0 k_parent_sink @@ -1168,7 +1168,7 @@ $bparms.state 99.17407 $date -[1] "Sat Sep 10 04:12:07 2016" +[1] "Sat Sep 10 05:19:30 2016" attr(,"class") [1] "mkinfit" "modFit" diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index 9972571a..66a8fce2 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -114,8 +114,8 @@
mkin version: 0.9.44.9000 R version: 3.3.1 -Date of fit: Sat Sep 10 04:12:13 2016 -Date of summary: Sat Sep 10 04:12:13 2016 +Date of fit: Sat Sep 10 05:19:35 2016 +Date of summary: Sat Sep 10 05:19:35 2016 Equations: d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -125,7 +125,7 @@ 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 1.456 s +Fitted with method Port using 246 model solutions performed in 1.434 s Weighting: none diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 910a43ec..899f2cc7 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -325,15 +325,15 @@ summary(fit)
mkin version: 0.9.44.9000 R version: 3.3.1 -Date of fit: Sat Sep 10 04:12:15 2016 -Date of summary: Sat Sep 10 04:12:15 2016 +Date of fit: Sat Sep 10 05:19:38 2016 +Date of summary: Sat Sep 10 05:19:38 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 0.148 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 - 1.228 1.216 0.923 + 1.236 1.188 0.911
coef(fit)
diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index fbf06007..d8edeb23 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 0.004 0.005 + 0.004 0.028 0.005
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 - 0.000 0.020 0.002 + 0.016 0.004 0.003
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 - 0.036 0.000 0.036 + 0.032 0.000 0.035
diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index 936350df..53cf5f97 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -159,8 +159,8 @@
mkin version: 0.9.44.9000 R version: 3.3.1 -Date of fit: Sat Sep 10 04:12:23 2016 -Date of summary: Sat Sep 10 04:12:23 2016 +Date of fit: Sat Sep 10 05:19:45 2016 +Date of summary: Sat Sep 10 05:19:45 2016 Equations: d_parent = - k_parent_sink * parent diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html index 43c6cdc2..d016bef5 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: 0.9.44.9000 R version: 3.3.1 -Date of fit: Sat Sep 10 04:12:24 2016 -Date of summary: Sat Sep 10 04:12:24 2016 +Date of fit: Sat Sep 10 05:19:46 2016 +Date of summary: Sat Sep 10 05:19:46 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 0.682 s +Fitted with method Port using 153 model solutions performed in 0.681 s Weighting: none diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html index d02b1b61..9e19315d 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:    0.9.44.9000 
 ## R version:       3.3.1 
-## Date of fit:     Sat Sep 10 04:13:37 2016 
-## Date of summary: Sat Sep 10 04:13:38 2016 
+## Date of fit:     Sat Sep 10 05:20:59 2016 
+## Date of summary: Sat Sep 10 05:20:59 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 0.643 s +## Fitted with method Port using 153 model solutions performed in 0.641 s ## ## Weighting: none ## diff --git a/inst/web/vignettes/FOCUS_L.html b/inst/web/vignettes/FOCUS_L.html index 10d1eb01..8223a3f4 100644 --- a/inst/web/vignettes/FOCUS_L.html +++ b/inst/web/vignettes/FOCUS_L.html @@ -236,15 +236,15 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1) summary(m.L1.SFO) 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
-## Date of fit:     Sat Sep 10 04:13:38 2016 
-## Date of summary: Sat Sep 10 04:13:38 2016 
+## Date of fit:     Sat Sep 10 05:20:59 2016 
+## Date of summary: Sat Sep 10 05:20:59 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.086 s
+## Fitted with method Port using 37 model solutions performed in 0.09 s
 ## 
 ## Weighting: none
 ## 
@@ -329,8 +329,8 @@ summary(m.L1.SFO)
summary(m.L1.FOMC, data = FALSE)
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
-## Date of fit:     Sat Sep 10 04:13:39 2016 
-## Date of summary: Sat Sep 10 04:13:39 2016 
+## Date of fit:     Sat Sep 10 05:21:00 2016 
+## Date of summary: Sat Sep 10 05:21:00 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -342,7 +342,7 @@ summary(m.L1.SFO)
## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.443 s +## Fitted with method Port using 188 model solutions performed in 0.441 s ## ## Weighting: none ## @@ -426,8 +426,8 @@ plot(m.L2.FOMC, show_residuals = TRUE, 
summary(m.L2.FOMC, data = FALSE)
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
-## Date of fit:     Sat Sep 10 04:13:40 2016 
-## Date of summary: Sat Sep 10 04:13:40 2016 
+## Date of fit:     Sat Sep 10 05:21:01 2016 
+## Date of summary: Sat Sep 10 05:21:01 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -496,8 +496,8 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
-## Date of fit:     Sat Sep 10 04:13:41 2016 
-## Date of summary: Sat Sep 10 04:13:41 2016 
+## Date of fit:     Sat Sep 10 05:21:02 2016 
+## Date of summary: Sat Sep 10 05:21:02 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -506,7 +506,7 @@ 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 0.797 s
+## Fitted with method Port using 336 model solutions performed in 0.899 s
 ## 
 ## Weighting: none
 ## 
@@ -585,8 +585,8 @@ plot(mm.L3)

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

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
-## Date of fit:     Sat Sep 10 04:13:42 2016 
-## Date of summary: Sat Sep 10 04:13:42 2016 
+## Date of fit:     Sat Sep 10 05:21:03 2016 
+## Date of summary: Sat Sep 10 05:21:03 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -595,7 +595,7 @@ plot(mm.L3)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.326 s
+## Fitted with method Port using 137 model solutions performed in 0.403 s
 ## 
 ## Weighting: none
 ## 
@@ -685,15 +685,15 @@ plot(mm.L4)
summary(mm.L4[["SFO", 1]], data = FALSE)
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
-## Date of fit:     Sat Sep 10 04:13:42 2016 
-## Date of summary: Sat Sep 10 04:13:42 2016 
+## Date of fit:     Sat Sep 10 05:21:04 2016 
+## Date of summary: Sat Sep 10 05:21:04 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.106 s
+## Fitted with method Port using 46 model solutions performed in 0.109 s
 ## 
 ## Weighting: none
 ## 
@@ -745,15 +745,15 @@ plot(mm.L4)
summary(mm.L4[["FOMC", 1]], data = FALSE)
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
-## Date of fit:     Sat Sep 10 04:13:42 2016 
-## Date of summary: Sat Sep 10 04:13:43 2016 
+## Date of fit:     Sat Sep 10 05:21:04 2016 
+## Date of summary: Sat Sep 10 05:21:04 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 0.15 s
+## Fitted with method Port using 66 model solutions performed in 0.152 s
 ## 
 ## Weighting: none
 ## 
diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf
index 27b9951d..85e50e65 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 004a808c..212b1abb 100644
--- a/inst/web/vignettes/compiled_models.html
+++ b/inst/web/vignettes/compiled_models.html
@@ -251,21 +251,21 @@ mb.1 <- microbenchmark(
 print(mb.1)
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6507.8296 6549.5160 6597.4319 6591.2024 6642.2330
-##       Eigenvalue based  890.5249  917.6589  928.4907  944.7928  947.4735
-##      deSolve, compiled  735.4908  742.0363  749.3996  748.5817  756.3540
+##  deSolve, not compiled 6410.2240 6437.0229 6461.3866 6463.8218 6486.9680
+##       Eigenvalue based  887.5697  915.3026  929.6279  943.0355  950.6570
+##      deSolve, compiled  737.4060  745.6645  749.1956  753.9229  755.0903
 ##        max neval cld
-##  6693.2636     3   c
-##   950.1543     3  b 
-##   764.1264     3 a
+## 6510.1142 3 c +## 958.2786 3 b +## 756.2578 3 a 
autoplot(mb.1)
-

-

We see that using the compiled model is by a factor of 8.8 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 8.6 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:

rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 8.804921
-## Eigenvalue based      1.262110
+## deSolve, not compiled 8.573584
+## Eigenvalue based      1.250838
 ## deSolve, compiled     1.000000
@@ -286,18 +286,18 @@ 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 13.741831 13.74759 13.815509 13.753350 13.852348
-##      deSolve, compiled  1.358402  1.35862  1.368666  1.358838  1.373798
+##                   expr       min        lq      mean    median       uq
+##  deSolve, not compiled 13.370040 13.424534 13.501075 13.479027 13.56659
+##      deSolve, compiled  1.336599  1.336707  1.339399  1.336815  1.34080
 ##        max neval cld
-##  13.951345     3   b
-##   1.388759     3  a
+## 13.654158 3 b +## 1.344784 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 10.1 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 3.3.1 (2016-06-21)
-- 
cgit v1.2.1