From b6e278759127dab5bb78bc3016926a66e8a9758f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 14 May 2020 17:10:59 +0200 Subject: Test markdown link, article update due to .rmd extension --- R/nlme.R | 2 +- cran-comments.md | 5 ---- docs/articles/FOCUS_D.html | 15 ++++++---- docs/articles/FOCUS_L.html | 43 +++++++++++++++------------- docs/articles/mkin.html | 9 ++++-- docs/articles/twa.html | 9 ++++-- docs/articles/web_only/FOCUS_Z.html | 9 ++++-- docs/articles/web_only/NAFTA_examples.html | 9 ++++-- docs/articles/web_only/benchmarks.html | 24 ++++++++-------- docs/articles/web_only/compiled_models.html | 23 ++++++++------- docs/pkgdown.yml | 2 +- docs/reference/nlme-1.png | Bin 71651 -> 70555 bytes docs/reference/nlme.html | 25 +++++++++------- man/nlme.Rd | 2 +- vignettes/web_only/mkin_benchmarks.rda | Bin 854 -> 856 bytes 15 files changed, 98 insertions(+), 79 deletions(-) diff --git a/R/nlme.R b/R/nlme.R index fa69db3c..3ee7b9fd 100644 --- a/R/nlme.R +++ b/R/nlme.R @@ -3,7 +3,7 @@ #' These functions facilitate setting up a nonlinear mixed effects model for #' an mmkin row object. An mmkin row object is essentially a list of mkinfit #' objects that have been obtained by fitting the same model to a list of -#' datasets. +#' datasets. They are used internally by the [nlme.mmkin()] method. #' #' @param object An mmkin row object containing several fits of the same model to different datasets #' @import nlme diff --git a/cran-comments.md b/cran-comments.md index e630e0a8..e69de29b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +0,0 @@ -Update of yesterdays release, addressing a platform specific test outcome on Solaris that -was revealed by the CRAN checks. - -This update also fixes a number of spelling errors that were found with the help of -devtools::spell_check(). diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 10b8f685..243ebee1 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -68,6 +68,9 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • +
  • + Some benchmark timings +
  • @@ -97,10 +100,10 @@

    Example evaluation of FOCUS Example Dataset D

    Johannes Ranke

    -

    2020-05-12

    +

    2020-05-14

    - Source: vignettes/FOCUS_D.Rmd - + Source: vignettes/FOCUS_D.rmd + @@ -177,8 +180,8 @@ 
    summary(fit)
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 12 15:31:36 2020 
-## Date of summary: Tue May 12 15:31:36 2020 
+## Date of fit:     Thu May 14 17:07:12 2020 
+## Date of summary: Thu May 14 17:07:12 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -186,7 +189,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 421 model solutions performed in 0.165 s
+## Fitted using 421 model solutions performed in 0.167 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 742718cb..df5c77c4 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -68,6 +68,9 @@
     
  • 
       Example evaluation of NAFTA SOP Attachment examples
     
    • 
+    
  • 
+      Some benchmark timings
+    
    •
  • @@ -97,10 +100,10 @@

    Example evaluation of FOCUS Laboratory Data L1 to L3

    Johannes Ranke

    -

    2020-05-12

    +

    2020-05-14

    - Source: vignettes/FOCUS_L.Rmd - + Source: vignettes/FOCUS_L.rmd + @@ -123,15 +126,15 @@ summary(m.L1.SFO) 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 12 15:31:38 2020 
-## Date of summary: Tue May 12 15:31:38 2020 
+## Date of fit:     Thu May 14 17:07:14 2020 
+## Date of summary: Thu May 14 17:07:14 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.03 s
+## Fitted using 133 model solutions performed in 0.032 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -224,8 +227,8 @@
 ## doubtful
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 12 15:31:38 2020 
-## Date of summary: Tue May 12 15:31:38 2020 
+## Date of fit:     Thu May 14 17:07:14 2020 
+## Date of summary: Thu May 14 17:07:14 2020 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -332,8 +335,8 @@
 
    summary(m.L2.FOMC, data = FALSE)
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 12 15:31:39 2020 
-## Date of summary: Tue May 12 15:31:39 2020 
+## Date of fit:     Thu May 14 17:07:15 2020 
+## Date of summary: Thu May 14 17:07:15 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -411,8 +414,8 @@
 
    summary(m.L2.DFOP, data = FALSE)
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 12 15:31:39 2020 
-## Date of summary: Tue May 12 15:31:39 2020 
+## Date of fit:     Thu May 14 17:07:15 2020 
+## Date of summary: Thu May 14 17:07:15 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -421,7 +424,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 0.13 s
+## Fitted using 572 model solutions performed in 0.131 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -514,8 +517,8 @@
 
    summary(mm.L3[["DFOP", 1]])
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 12 15:31:39 2020 
-## Date of summary: Tue May 12 15:31:40 2020 
+## Date of fit:     Thu May 14 17:07:16 2020 
+## Date of summary: Thu May 14 17:07:16 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -623,8 +626,8 @@
 
    summary(mm.L4[["SFO", 1]], data = FALSE)
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 12 15:31:40 2020 
-## Date of summary: Tue May 12 15:31:40 2020 
+## Date of fit:     Thu May 14 17:07:16 2020 
+## Date of summary: Thu May 14 17:07:16 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -687,15 +690,15 @@
 
    summary(mm.L4[["FOMC", 1]], data = FALSE)
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 12 15:31:40 2020 
-## Date of summary: Tue May 12 15:31:40 2020 
+## Date of fit:     Thu May 14 17:07:16 2020 
+## Date of summary: Thu May 14 17:07:16 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.044 s
+## Fitted using 224 model solutions performed in 0.043 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 0d4ced0f..37b7b1a1 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -68,6 +68,9 @@
     
  • 
       Example evaluation of NAFTA SOP Attachment examples
     
    • 
+    
  • 
+      Some benchmark timings
+    
    •
  • @@ -97,10 +100,10 @@

    Introduction to mkin

    Johannes Ranke

    -

    2020-05-12

    +

    2020-05-14

    - Source: vignettes/mkin.Rmd - + Source: vignettes/mkin.rmd + diff --git a/docs/articles/twa.html b/docs/articles/twa.html index b58306f1..c231e17d 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -68,6 +68,9 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • +
  • + Some benchmark timings +
  • @@ -97,10 +100,10 @@

    Calculation of time weighted average concentrations with mkin

    Johannes Ranke

    -

    2020-05-12

    +

    2020-05-14

    - Source: vignettes/twa.Rmd - + Source: vignettes/twa.rmd + diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 0c34d77d..3427afb6 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -68,6 +68,9 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • +
  • + Some benchmark timings +
  • @@ -97,10 +100,10 @@

    Example evaluation of FOCUS dataset Z

    Johannes Ranke

    -

    2020-05-12

    +

    2020-05-14

    - Source: vignettes/web_only/FOCUS_Z.Rmd - + Source: vignettes/web_only/FOCUS_Z.rmd + diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 411341b8..46cb7aa5 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -68,6 +68,9 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • +
  • + Some benchmark timings +
  • @@ -97,10 +100,10 @@

    Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

    Johannes Ranke

    -

    2020-05-12

    +

    2020-05-14

    - Source: vignettes/web_only/NAFTA_examples.Rmd - + Source: vignettes/web_only/NAFTA_examples.rmd + diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 202ec25f..97e22303 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -100,7 +100,7 @@

    Benchmark timings for mkin

    Johannes Ranke

    -

    2020-05-13

    +

    2020-05-14

    Source: vignettes/web_only/benchmarks.rmd @@ -210,8 +210,8 @@ 0.9.50.2 -1.704 -3.909 +1.714 +3.971 @@ -260,9 +260,9 @@ 0.9.50.2 -1.370 -6.147 -2.747 +1.402 +6.174 +2.764 @@ -329,12 +329,12 @@ 0.9.50.2 -0.761 -1.213 -1.287 -2.886 -2.054 -2.984 +0.777 +1.236 +1.332 +2.872 +2.069 +2.987 diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 85134720..837b288b 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -68,6 +68,9 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • +
  • + Some benchmark timings +
  • @@ -97,10 +100,10 @@

    Performance benefit by using compiled model definitions in mkin

    Johannes Ranke

    -

    2020-05-12

    +

    2020-05-14

    - Source: vignettes/web_only/compiled_models.Rmd - + Source: vignettes/web_only/compiled_models.rmd + @@ -149,10 +152,10 @@ print("R package rbenchmark is not available") } 
    ##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.190
-## 3     deSolve, compiled            1    1.774   0.337
-## 2      Eigenvalue based            1    2.105   0.400
-## 1 deSolve, not compiled            1   42.763   8.125
    +## 4 analytical 1 1.000 0.191 +## 3 deSolve, compiled 1 1.801 0.344 +## 2 Eigenvalue based 1 2.105 0.402 +## 1 deSolve, not compiled 1 42.864 8.187

    We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.

    @@ -178,9 +181,9 @@ }
    ## Successfully compiled differential equation model from auto-generated C code.
    ##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.476
-## 1 deSolve, not compiled            1   30.103  14.329
    -

    Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!

    +## 2 deSolve, compiled 1 1.000 0.466 +## 1 deSolve, not compiled 1 30.942 14.419     +

    Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!

    This vignette was built with mkin 0.9.50.2 on

    ## R version 4.0.0 (2020-04-24)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 922e556c..eb3f0f6e 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   NAFTA_examples: web_only/NAFTA_examples.html
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
-last_built: 2020-05-13T14:16Z
+last_built: 2020-05-14T15:07Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png
index 8db1f999..68ccb43f 100644
Binary files a/docs/reference/nlme-1.png and b/docs/reference/nlme-1.png differ
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index 8ef7e7c9..b2d415dc 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -43,7 +43,7 @@
 
+datasets. They are used internally by the nlme.mmkin() method." />
 
 
 
@@ -112,6 +112,9 @@ datasets." />
     
  • 
       Example evaluation of NAFTA SOP Attachment examples
     
    • 
+    
  • 
+      Some benchmark timings
+    
    •
  • @@ -147,7 +150,7 @@ datasets." />

    These functions facilitate setting up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of -datasets.

    +datasets. They are used internally by the nlme.mmkin() method.

    nlme_function(object)
@@ -222,28 +225,28 @@ nlme for the case of a single grouping variable ds?
    
 #>   Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) 
 #>  Data: grouped_data 
 #>        AIC      BIC    logLik
-#>   252.7798 262.1358 -121.3899
+#>   298.2781 307.7372 -144.1391
 #> 
 #> Random effects:
 #>  Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
 #>  Level: ds
 #>  Structure: Diagonal
-#>             parent_0 log_k_parent_sink Residual
-#> StdDev: 0.0006768135         0.6800777 2.489397
+#>          parent_0 log_k_parent_sink Residual
+#> StdDev: 0.9374733         0.7098105  3.83543
 #> 
 #> Fixed effects: parent_0 + log_k_parent_sink ~ 1 
-#>                       Value Std.Error DF   t-value p-value
-#> parent_0          101.74884 0.6456014 44 157.60321       0
-#> log_k_parent_sink  -3.05575 0.4015811 44  -7.60929       0
+#>                       Value Std.Error DF  t-value p-value
+#> parent_0          101.76838 1.1445444 45 88.91606       0
+#> log_k_parent_sink  -3.05444 0.4195622 45 -7.28008       0
 #>  Correlation: 
 #>                   prnt_0
-#> log_k_parent_sink 0.026 
+#> log_k_parent_sink 0.034 
 #> 
 #> Standardized Within-Group Residuals:
 #>        Min         Q1        Med         Q3        Max 
-#> -2.1317488 -0.6878121  0.0828385  0.8592270  2.9529864 
+#> -2.6169360 -0.2185329  0.0574070  0.5720937  3.0459868 
 #> 
-#> Number of Observations: 48
+#> Number of Observations: 49
 #> Number of Groups: 3 
    plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))
    # augPred does not seem to work on fits with more than one state
 # variable
 
diff --git a/man/nlme.Rd b/man/nlme.Rd
index bf527320..5e981a14 100644
--- a/man/nlme.Rd
+++ b/man/nlme.Rd
@@ -31,7 +31,7 @@ A \code{\link{groupedData}} object
 These functions facilitate setting up a nonlinear mixed effects model for
 an mmkin row object. An mmkin row object is essentially a list of mkinfit
 objects that have been obtained by fitting the same model to a list of
-datasets.
+datasets. They are used internally by the \code{\link[=nlme.mmkin]{nlme.mmkin()}} method.
 }
 \examples{
 sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index c88ca4d6..a95680c0 100644
Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ
-- 
cgit v1.2.1