From 556598ba543cf655cdc0a6995cc579327f9540ad Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 9 Dec 2015 10:20:50 +0100 Subject: Static documentation rebuilt by staticdocs::build_site() --- inst/web/Extract.mmkin.html | 24 ++++++++++---------- inst/web/index.html | 26 +++++----------------- 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 | 4 ++-- inst/web/vignettes/FOCUS_L.html | 4 ++-- inst/web/vignettes/FOCUS_Z.pdf | Bin 224838 -> 224828 bytes inst/web/vignettes/compiled_models.html | 38 ++++++++++++++++---------------- inst/web/vignettes/mkin.pdf | Bin 160269 -> 160263 bytes vignettes/FOCUS_D.html | 4 ++-- vignettes/FOCUS_L.html | 4 ++-- vignettes/FOCUS_Z.pdf | Bin 224838 -> 224828 bytes vignettes/compiled_models.html | 38 ++++++++++++++++---------------- vignettes/mkin.pdf | Bin 160269 -> 160263 bytes 17 files changed, 79 insertions(+), 95 deletions(-) diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index 4effdf0e..3015a6c8 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -181,7 +181,7 @@ $calls $time user system elapsed - 0.260 0.000 0.259 + 0.264 0.000 0.262 $mkinmod <mkinmod> model generated with @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x36e8dd8> +<environment: 0x4376e58> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x36e8dd8> +<environment: 0x4376e58> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Fri Nov 13 11:14:06 2015" +[1] "Wed Dec 9 10:16:48 2015" attr(,"class") [1] "mkinfit" "modFit" @@ -540,7 +540,7 @@ $calls $time user system elapsed - 0.080 0.008 0.087 + 0.084 0.004 0.086 $mkinmod <mkinmod> model generated with @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x33c0330> +<environment: 0x404d8f8> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x33c0330> +<environment: 0x404d8f8> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Fri Nov 13 11:14:06 2015" +[1] "Wed Dec 9 10:16:47 2015" attr(,"class") [1] "mkinfit" "modFit" @@ -890,7 +890,7 @@ $calls $time user system elapsed - 0.080 0.008 0.087 + 0.084 0.004 0.086 $mkinmod <mkinmod> model generated with @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x33c0330> +<environment: 0x404d8f8> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x33c0330> +<environment: 0x404d8f8> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Fri Nov 13 11:14:06 2015" +[1] "Wed Dec 9 10:16:47 2015" attr(,"class") [1] "mkinfit" "modFit" diff --git a/inst/web/index.html b/inst/web/index.html index bb85e72f..17c5ba6e 100644 --- a/inst/web/index.html +++ b/inst/web/index.html @@ -66,15 +66,6 @@ if several compartments are involved.

install.packages("mkin")
-

If looking for the latest features, you can install directly from -github, e.g. using the devtools package. -Using quick = TRUE skips docs, multiple-architecture builds, demos, and -vignettes, to make installation as fast and painless as possible.

- -
require(devtools)
-install_github("jranke/mkin", quick = TRUE)
-
-

Background

In the regulatory evaluation of chemical substances like plant protection @@ -108,7 +99,7 @@ reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.

  • As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example -plot.mmkin
    • +plot.mmkin.
  • Model solution (forward modelling) in the function mkinpredict is performed either using the analytical solution for the case of @@ -121,10 +112,6 @@ generated C code, see
    The autogeneration of C code was inspired by the ccSolve package. Thanks to Karline Soetaert for her work on that.
    • -
  • Model optimisation with -mkinfit -internally using the modFit function from the FME package, -but using the Port routine nlminb per default.
  • By default, kinetic rate constants and kinetic formation fractions are transformed internally using transform_odeparms @@ -152,9 +139,7 @@ as in KinGUII and CAKE (see below). Simply add the argument componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.
  • When a metabolite decline phase is not described well by SFO kinetics, -either IORE kinetics (often producing failures of the integration algorithm) -or SFORB kinetics (working nicely) can be used for the metabolite, adding one -respectively two parameters to the system.
    • +SFORB kinetics can be used for the metabolite.

    GUI

    @@ -171,9 +156,8 @@ and one for the git

    Credits and historical remarks

    mkin would not be possible without the underlying software stack consisting -of R and the packages deSolve, -minpack.lm and -FME, to say the least.

    +of R and the packages deSolve +and FME, to say the least.

    It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories @@ -187,7 +171,7 @@ as detailed in their guidance document from 2006, slightly updated in 2011 and BayerCropScience, which is based on the MatLab runtime environment.

    The companion package -kinfit was +kinfit (now deprecated) was started in 2008 and first published on CRAN on 01 May 2010.

    diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index c959f114..ef7753f1 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -114,8 +114,8 @@
    mkin version: 0.9.41.9000 R version: 3.2.2 -Date of fit: Fri Nov 13 11:14:13 2015 -Date of summary: Fri Nov 13 11:14:13 2015 +Date of fit: Wed Dec 9 10:16:55 2015 +Date of summary: Wed Dec 9 10:16:55 2015 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 1.369 s +Fitted with method Port using 246 model solutions performed in 1.383 s Weighting: none diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index c2998ae6..3c48dcc0 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -317,15 +317,15 @@ summary(fit)
    mkin version: 0.9.41.9000 R version: 3.2.2 -Date of fit: Fri Nov 13 11:14:16 2015 -Date of summary: Fri Nov 13 11:14:16 2015 +Date of fit: Wed Dec 9 10:16:57 2015 +Date of summary: Wed Dec 9 10:16:57 2015 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 0.171 s +Fitted with method Port using 64 model solutions performed in 0.189 s Weighting: none @@ -401,7 +401,7 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))
    user system elapsed - 1.200 1.188 0.898 + 1.184 1.180 0.891
    coef(fit)
    diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index ee452a18..393c1e26 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -304,7 +304,7 @@ 201 20 4.978707 27.46227
    user system elapsed - 0.004 0.028 0.005 + 0.012 0.016 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 - 0.016 0.004 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 - 0.056 0.000 0.054 + 0.048 0.004 0.053
    diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index 1c63e7b9..9771ff5b 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -159,15 +159,15 @@
    mkin version: 0.9.41.9000 R version: 3.2.2 -Date of fit: Fri Nov 13 11:14:26 2015 -Date of summary: Fri Nov 13 11:14:26 2015 +Date of fit: Wed Dec 9 10:17:07 2015 +Date of summary: Wed Dec 9 10:17:07 2015 Equations: d_parent = - k_parent_sink * parent Model predictions using solution type analytical -Fitted with method Port using 35 model solutions performed in 0.151 s +Fitted with method Port using 35 model solutions performed in 0.15 s Weighting: none diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html index 49639b47..50ce71a7 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: 0.9.41.9000 R version: 3.2.2 -Date of fit: Fri Nov 13 11:14:27 2015 -Date of summary: Fri Nov 13 11:14:27 2015 +Date of fit: Wed Dec 9 10:17:08 2015 +Date of summary: Wed Dec 9 10:17:08 2015 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 0.619 s +Fitted with method Port using 153 model solutions performed in 0.626 s Weighting: none diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html index d9fc6e18..076ab4c5 100644 --- a/inst/web/vignettes/FOCUS_D.html +++ b/inst/web/vignettes/FOCUS_D.html @@ -10,7 +10,7 @@ - + Example evaluation of FOCUS Example Dataset D @@ -64,7 +64,7 @@ img { diff --git a/inst/web/vignettes/FOCUS_L.html b/inst/web/vignettes/FOCUS_L.html index 9584aee5..9797e2f1 100644 --- a/inst/web/vignettes/FOCUS_L.html +++ b/inst/web/vignettes/FOCUS_L.html @@ -10,7 +10,7 @@ - + Example evaluation of FOCUS Laboratory Data L1 to L3 @@ -65,7 +65,7 @@ img {
    diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf index 1d08173a..ba30cb0c 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 c7f4fbea..bd39ae2d 100644 --- a/inst/web/vignettes/compiled_models.html +++ b/inst/web/vignettes/compiled_models.html @@ -10,7 +10,7 @@ - + Performance benefit by using compiled model definitions in mkin @@ -65,7 +65,7 @@ img {
    @@ -104,21 +104,21 @@ smb.1 <- summary(mb.1) print(mb.1) 
    ## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 9538.4007 9570.3211 9605.6503 9602.2416 9639.2752
-##       Eigenvalue based  881.9438  885.9337  901.1558  889.9236  910.7618
-##      deSolve, compiled  692.0913  695.6109  697.9629  699.1304  700.8987
+##  deSolve, not compiled 9508.4631 9522.5843 9634.9196 9536.7055 9698.1479
+##       Eigenvalue based  872.6560  877.4544  888.3598  882.2527  896.2117
+##      deSolve, compiled  698.8148  700.5031  708.8625  702.1914  713.8864
 ##        max neval cld
-##  9676.3087     3   c
-##   931.5999     3  b 
-##   702.6669     3 a
    +## 9859.5902 3 b +## 910.1707 3 a +## 725.5815 3 a 
    autoplot(mb.1)
    -

    -

    We see that using the compiled model is by a factor of 13.7 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 13.6 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 13.734549
-## Eigenvalue based       1.272901
+## deSolve, not compiled 13.581348
+## Eigenvalue based       1.256428
 ## deSolve, compiled      1.000000
    @@ -136,19 +136,19 @@ 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 20.475764 20.494740 20.507391 20.513716 20.523205
-##      deSolve, compiled  1.244022  1.244327  1.261983  1.244631  1.270963
+##                   expr       min        lq      mean    median       uq
+##  deSolve, not compiled 21.324080 21.368031 21.460777 21.411981 21.52913
+##      deSolve, compiled  1.376772  1.414208  1.461651  1.451643  1.50409
 ##        max neval cld
-##  20.532695     3   b
-##   1.297295     3  a
    +## 21.646269 3 b +## 1.556538 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 16.5 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 0.9.41.9000 on

    ## R version 3.2.2 (2015-08-14)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/inst/web/vignettes/mkin.pdf b/inst/web/vignettes/mkin.pdf
index e9ee9ed1..00940a35 100644
Binary files a/inst/web/vignettes/mkin.pdf and b/inst/web/vignettes/mkin.pdf differ
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index d9fc6e18..076ab4c5 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Example evaluation of FOCUS Example Dataset D
 
@@ -64,7 +64,7 @@ img {
 
 
 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 9584aee5..9797e2f1 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Example evaluation of FOCUS Laboratory Data L1 to L3
 
@@ -65,7 +65,7 @@ img {
 
 
 
    
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 1d08173a..ba30cb0c 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 c7f4fbea..bd39ae2d 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Performance benefit by using compiled model definitions in mkin
 
@@ -65,7 +65,7 @@ img {
 
 
 
    
@@ -104,21 +104,21 @@ smb.1 <- summary(mb.1)
 print(mb.1)
    ## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 9538.4007 9570.3211 9605.6503 9602.2416 9639.2752
-##       Eigenvalue based  881.9438  885.9337  901.1558  889.9236  910.7618
-##      deSolve, compiled  692.0913  695.6109  697.9629  699.1304  700.8987
+##  deSolve, not compiled 9508.4631 9522.5843 9634.9196 9536.7055 9698.1479
+##       Eigenvalue based  872.6560  877.4544  888.3598  882.2527  896.2117
+##      deSolve, compiled  698.8148  700.5031  708.8625  702.1914  713.8864
 ##        max neval cld
-##  9676.3087     3   c
-##   931.5999     3  b 
-##   702.6669     3 a
    +## 9859.5902 3 b +## 910.1707 3 a +## 725.5815 3 a 
    autoplot(mb.1)
    -

    -

    We see that using the compiled model is by a factor of 13.7 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 13.6 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 13.734549
-## Eigenvalue based       1.272901
+## deSolve, not compiled 13.581348
+## Eigenvalue based       1.256428
 ## deSolve, compiled      1.000000
    @@ -136,19 +136,19 @@ 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 20.475764 20.494740 20.507391 20.513716 20.523205
-##      deSolve, compiled  1.244022  1.244327  1.261983  1.244631  1.270963
+##                   expr       min        lq      mean    median       uq
+##  deSolve, not compiled 21.324080 21.368031 21.460777 21.411981 21.52913
+##      deSolve, compiled  1.376772  1.414208  1.461651  1.451643  1.50409
 ##        max neval cld
-##  20.532695     3   b
-##   1.297295     3  a
    +## 21.646269 3 b +## 1.556538 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 16.5 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 0.9.41.9000 on

    ## R version 3.2.2 (2015-08-14)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index e9ee9ed1..00940a35 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
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