From a04cc65a18998ff5d107a52d23c9a4aad21a03aa Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 23 Mar 2016 18:33:37 +0100 Subject: Static documentation rebuilt by staticdocs::build_site() --- inst/web/Extract.mmkin.html | 24 ++++++++++++------------ inst/web/index.html | 2 +- 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_Z.pdf | Bin 225028 -> 225040 bytes inst/web/vignettes/compiled_models.html | 32 ++++++++++++++++---------------- inst/web/vignettes/mkin.pdf | Bin 160263 -> 160263 bytes vignettes/FOCUS_Z.pdf | Bin 225028 -> 225040 bytes vignettes/compiled_models.html | 32 ++++++++++++++++---------------- vignettes/mkin.pdf | Bin 160263 -> 160263 bytes 13 files changed, 61 insertions(+), 61 deletions(-) diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index 68cfaf9a..fd99aa8b 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -181,7 +181,7 @@ $calls $time user system elapsed - 0.280 0.000 0.279 + 0.288 0.000 0.288 $mkinmod <mkinmod> model generated with @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x2d2bae8> +<environment: 0x23d9ae8> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x2d2bae8> +<environment: 0x23d9ae8> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Wed Mar 23 16:59:33 2016" +[1] "Wed Mar 23 18:10:37 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -540,7 +540,7 @@ $calls $time user system elapsed - 0.096 0.004 0.102 + 0.092 0.004 0.096 $mkinmod <mkinmod> model generated with @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x4975b58> +<environment: 0x4023b58> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x4975b58> +<environment: 0x4023b58> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Wed Mar 23 16:59:32 2016" +[1] "Wed Mar 23 18:10:36 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -890,7 +890,7 @@ $calls $time user system elapsed - 0.096 0.004 0.102 + 0.092 0.004 0.096 $mkinmod <mkinmod> model generated with @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x4975b58> +<environment: 0x4023b58> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x4975b58> +<environment: 0x4023b58> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Wed Mar 23 16:59:32 2016" +[1] "Wed Mar 23 18:10:36 2016" attr(,"class") [1] "mkinfit" "modFit" diff --git a/inst/web/index.html b/inst/web/index.html index 09310304..7d034fc9 100644 --- a/inst/web/index.html +++ b/inst/web/index.html @@ -51,7 +51,7 @@

mkin

-

+

The R package mkin provides calculation routines for the analysis of chemical degradation data, including multicompartment kinetics as diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index 598f4d76..5b191184 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -114,8 +114,8 @@

mkin version: 0.9.42 R version: 3.2.4 -Date of fit: Wed Mar 23 16:59:40 2016 -Date of summary: Wed Mar 23 16:59:40 2016 +Date of fit: Wed Mar 23 18:10:44 2016 +Date of summary: Wed Mar 23 18:10:44 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 1.469 s +Fitted with method Port using 246 model solutions performed in 1.482 s Weighting: none diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 75d8be8b..5b843ae2 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -325,15 +325,15 @@ summary(fit)
mkin version: 0.9.42 R version: 3.2.4 -Date of fit: Wed Mar 23 16:59:43 2016 -Date of summary: Wed Mar 23 16:59:43 2016 +Date of fit: Wed Mar 23 18:10:46 2016 +Date of summary: Wed Mar 23 18:10:46 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 0.195 s +Fitted with method Port using 64 model solutions performed in 0.191 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 - 1.200 1.272 0.936 + 1.204 1.280 0.942
coef(fit)
diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index 34c715f8..76814960 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 0.024 0.004
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 0.003 + 0.016 0.004 0.002
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 - 0.052 0.000 0.052 + 0.048 0.008 0.055
diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index 69edb2fe..40e3ca63 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -159,15 +159,15 @@
mkin version: 0.9.42 R version: 3.2.4 -Date of fit: Wed Mar 23 16:59:53 2016 -Date of summary: Wed Mar 23 16:59:53 2016 +Date of fit: Wed Mar 23 18:10:56 2016 +Date of summary: Wed Mar 23 18:10:56 2016 Equations: d_parent = - k_parent_sink * parent Model predictions using solution type analytical -Fitted with method Port using 35 model solutions performed in 0.102 s +Fitted with method Port using 35 model solutions performed in 0.109 s Weighting: none diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html index 81d3927f..34428004 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: 0.9.42 R version: 3.2.4 -Date of fit: Wed Mar 23 16:59:54 2016 -Date of summary: Wed Mar 23 16:59:54 2016 +Date of fit: Wed Mar 23 18:10:57 2016 +Date of summary: Wed Mar 23 18:10:57 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 0.667 s +Fitted with method Port using 153 model solutions performed in 0.669 s Weighting: none diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf index e2ecd1e3..8103cba4 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 81d26b0f..756a2753 100644 --- a/inst/web/vignettes/compiled_models.html +++ b/inst/web/vignettes/compiled_models.html @@ -104,21 +104,21 @@ smb.1 <- summary(mb.1) print(mb.1) 
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 9494.5137 9596.5859 9663.5380 9698.6581 9748.0502
-##       Eigenvalue based  955.2669  964.7481  985.7901  974.2293 1001.0517
-##      deSolve, compiled  728.4599  736.3608  750.6479  744.2616  761.7419
+##  deSolve, not compiled 9539.3064 9543.1547 9554.1987 9547.0031 9561.6448
+##       Eigenvalue based  927.5569  928.1716  943.8293  928.7864  951.9656
+##      deSolve, compiled  734.6125  737.3273  739.0161  740.0420  741.2179
 ##        max neval cld
-##  9797.4422     3   c
-##  1027.8741     3  b 
-##   779.2221     3 a
+## 9576.2865 3 c +## 975.1447 3 b +## 742.3938 3 a 
autoplot(mb.1)
-

-

We see that using the compiled model is by a factor of 13 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 12.9 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 13.031249
-## Eigenvalue based       1.308988
+## deSolve, not compiled 12.900624
+## Eigenvalue based       1.255046
 ## deSolve, compiled      1.000000
@@ -137,18 +137,18 @@ smb.2 <- summary(mb.2) print(mb.2) 
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 20.473617 20.530414 20.676143 20.587210 20.777405
-##      deSolve, compiled  1.332632  1.334693  1.336846  1.336755  1.338953
+##  deSolve, not compiled 20.728228 20.867978 20.959811 21.007729 21.075602
+##      deSolve, compiled  1.343219  1.382365  1.399697  1.421511  1.427936
 ##        max neval cld
-##  20.967601     3   b
-##   1.341152     3  a
+## 21.143476 3 b +## 1.434362 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 15.4 using the version of the differential equation model compiled from C code using the inline package!

+

+

Here we get a performance benefit of a factor of 14.8 using the version of the differential equation model compiled from C code using the inline package!

This vignette was built with mkin 0.9.42 on

## R version 3.2.4 Revised (2016-03-16 r70336)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/inst/web/vignettes/mkin.pdf b/inst/web/vignettes/mkin.pdf
index 455fedcb..b07cdc72 100644
Binary files a/inst/web/vignettes/mkin.pdf and b/inst/web/vignettes/mkin.pdf differ
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index e2ecd1e3..8103cba4 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 81d26b0f..756a2753 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -104,21 +104,21 @@ smb.1 <- summary(mb.1)
 print(mb.1)
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 9494.5137 9596.5859 9663.5380 9698.6581 9748.0502
-##       Eigenvalue based  955.2669  964.7481  985.7901  974.2293 1001.0517
-##      deSolve, compiled  728.4599  736.3608  750.6479  744.2616  761.7419
+##  deSolve, not compiled 9539.3064 9543.1547 9554.1987 9547.0031 9561.6448
+##       Eigenvalue based  927.5569  928.1716  943.8293  928.7864  951.9656
+##      deSolve, compiled  734.6125  737.3273  739.0161  740.0420  741.2179
 ##        max neval cld
-##  9797.4422     3   c
-##  1027.8741     3  b 
-##   779.2221     3 a
+## 9576.2865 3 c +## 975.1447 3 b +## 742.3938 3 a 
autoplot(mb.1)
-

-

We see that using the compiled model is by a factor of 13 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 12.9 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 13.031249
-## Eigenvalue based       1.308988
+## deSolve, not compiled 12.900624
+## Eigenvalue based       1.255046
 ## deSolve, compiled      1.000000
@@ -137,18 +137,18 @@ smb.2 <- summary(mb.2) print(mb.2) 
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 20.473617 20.530414 20.676143 20.587210 20.777405
-##      deSolve, compiled  1.332632  1.334693  1.336846  1.336755  1.338953
+##  deSolve, not compiled 20.728228 20.867978 20.959811 21.007729 21.075602
+##      deSolve, compiled  1.343219  1.382365  1.399697  1.421511  1.427936
 ##        max neval cld
-##  20.967601     3   b
-##   1.341152     3  a
+## 21.143476 3 b +## 1.434362 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 15.4 using the version of the differential equation model compiled from C code using the inline package!

+

+

Here we get a performance benefit of a factor of 14.8 using the version of the differential equation model compiled from C code using the inline package!

This vignette was built with mkin 0.9.42 on

## R version 3.2.4 Revised (2016-03-16 r70336)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 455fedcb..b07cdc72 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
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