From b2c75fa1f73167d3e3c9c7db1d561dd482090aab Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 18:01:23 +0200 Subject: Add url: tag to _pkgdown.yml Static documentation rebuilt by pkgdown --- _pkgdown.yml | 2 + build.log | 9 ++ docs/404.html | 6 +- docs/articles/FOCUS_D.html | 6 +- docs/articles/FOCUS_L.html | 42 +++---- docs/articles/web_only/benchmarks.html | 22 ++-- docs/articles/web_only/compiled_models.html | 10 +- docs/pkgdown.yml | 3 + docs/reference/mkinfit.html | 28 ++--- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 +- docs/reference/mmkin.html | 4 +- docs/reference/summary.mkinfit.html | 6 +- docs/sitemap.xml | 183 ++++++++++++++++++++++++++++ vignettes/mkin_benchmarks.rda | Bin 881 -> 885 bytes 15 files changed, 263 insertions(+), 66 deletions(-) create mode 100644 docs/sitemap.xml diff --git a/_pkgdown.yml b/_pkgdown.yml index 89e48585..efe8b6a0 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,3 +1,5 @@ +url: https://pkgdown.jrwb.de/mkin + title: mkin template: diff --git a/build.log b/build.log index 976d27d4..65e585da 100644 --- a/build.log +++ b/build.log @@ -1 +1,10 @@ * checking for file ‘./DESCRIPTION’ ... OK +* preparing ‘mkin’: +* checking DESCRIPTION meta-information ... OK +* installing the package to build vignettes +* creating vignettes ... OK +* checking for LF line-endings in source and make files and shell scripts +* checking for empty or unneeded directories +* looking to see if a ‘data/datalist’ file should be added +* building ‘mkin_0.9.49.6.tar.gz’ + diff --git a/docs/404.html b/docs/404.html index bdc5053f..485641dc 100644 --- a/docs/404.html +++ b/docs/404.html @@ -27,8 +27,8 @@ - - + + @@ -62,7 +62,7 @@ - mkin + mkin 0.9.49.6 diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index b62afbf8..c22eb2c3 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -170,8 +170,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 13:17:00 2019 
-## Date of summary: Wed Sep 18 13:17:00 2019 
+## Date of fit:     Wed Sep 18 17:55:05 2019 
+## Date of summary: Wed Sep 18 17:55:06 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +179,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 1.115 s
+## Fitted using 389 model solutions performed in 1.003 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 0d5667f5..428ca84f 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -116,15 +116,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 13:17:02 2019 
-## Date of summary: Wed Sep 18 13:17:02 2019 
+## Date of fit:     Wed Sep 18 17:55:08 2019 
+## Date of summary: Wed Sep 18 17:55:08 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.297 s
+## Fitted using 133 model solutions performed in 0.293 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -218,8 +218,8 @@
 ## finite result is doubtful
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 13:17:05 2019 
-## Date of summary: Wed Sep 18 13:17:05 2019 
+## Date of fit:     Wed Sep 18 17:55:10 2019 
+## Date of summary: Wed Sep 18 17:55:10 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -231,7 +231,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 2.099 s
+## Fitted using 899 model solutions performed in 1.914 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -323,15 +323,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 13:17:06 2019 
-## Date of summary: Wed Sep 18 13:17:06 2019 
+## Date of fit:     Wed Sep 18 17:55:11 2019 
+## Date of summary: Wed Sep 18 17:55:11 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.554 s
+## Fitted using 239 model solutions performed in 0.511 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -399,8 +399,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 13:17:07 2019 
-## Date of summary: Wed Sep 18 13:17:07 2019 
+## Date of fit:     Wed Sep 18 17:55:12 2019 
+## Date of summary: Wed Sep 18 17:55:12 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -409,7 +409,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.273 s
+## Fitted using 572 model solutions performed in 1.217 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -499,8 +499,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 13:17:09 2019 
-## Date of summary: Wed Sep 18 13:17:09 2019 
+## Date of fit:     Wed Sep 18 17:55:14 2019 
+## Date of summary: Wed Sep 18 17:55:14 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -509,7 +509,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.792 s
+## Fitted using 373 model solutions performed in 0.803 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -605,15 +605,15 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 13:17:10 2019 
-## Date of summary: Wed Sep 18 13:17:11 2019 
+## Date of fit:     Wed Sep 18 17:55:15 2019 
+## Date of summary: Wed Sep 18 17:55:15 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.299 s
+## Fitted using 142 model solutions performed in 0.301 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -670,15 +670,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 13:17:10 2019 
-## Date of summary: Wed Sep 18 13:17:11 2019 
+## Date of fit:     Wed Sep 18 17:55:15 2019 
+## Date of summary: Wed Sep 18 17:55:15 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.488 s
+## Fitted using 224 model solutions performed in 0.458 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 0c78d346..144c4c29 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -204,77 +204,77 @@
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 6.106
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.940
 ##                                                                         t2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 37.249
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.631
 ##                                                                        t3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.739
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.507
 ##                                                                         t4
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.761
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.282
 ##                                                                         t5
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1  9.495
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  6.395
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.675
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.386
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  6.002
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.794
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.727
 ##                                                                        t6
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.702
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.634
 ##                                                                        t7
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.351
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.295
 ##                                                                        t8
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.303
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  8.13
 ##                                                                         t9
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.763
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.339
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.064
 ##                                                                       t10
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  8.12
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.034
 ##                                                                        t11
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  11.22

+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.804

 
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")

 
   
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 99b05623..6594c3e6 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -165,9 +165,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.153    1.000     3.152        0
-## 1 deSolve, not compiled            3  28.771    9.125    28.756        0
-## 2      Eigenvalue based            3   4.444    1.409     4.443        0
+## 3     deSolve, compiled            3   3.143    1.000     3.141        0
+## 1 deSolve, not compiled            3  28.853    9.180    28.839        0
+## 2      Eigenvalue based            3   4.427    1.409     4.425        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -216,8 +216,8 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.978    1.000     4.975    0.000
-## 1 deSolve, not compiled            3  54.194   10.887    54.160    0.004
+## 2     deSolve, compiled            3   4.956    1.000     4.952        0
+## 1 deSolve, not compiled            3  53.338   10.762    53.312        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 76c7efa6..a1377251 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,4 +10,7 @@ articles:
   NAFTA_examples: web_only/NAFTA_examples.html
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
+urls:
+  reference: https://pkgdown.jrwb.de/mkin/reference
+  article: https://pkgdown.jrwb.de/mkin/articles
 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index c1cfc228..954086b5 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -408,15 +408,15 @@ Per default, parameters in the kinetic models are internally transformed in
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 13:14:54 2019 
-#> Date of summary: Wed Sep 18 13:14:54 2019 
+#> Date of fit:     Wed Sep 18 17:53:04 2019 
+#> Date of summary: Wed Sep 18 17:53:04 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.475 s
+#> Fitted using 222 model solutions performed in 0.467 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -490,7 +490,7 @@ Per default, parameters in the kinetic models are internally transformed in
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.561       0.000       1.568 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.524       0.000       1.527 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -563,7 +563,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>        1.06        0.00        1.06 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.115       0.000       1.116 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -599,8 +599,8 @@ Per default, parameters in the kinetic models are internally transformed in
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 13:15:10 2019 
-#> Date of summary: Wed Sep 18 13:15:10 2019 
+#> Date of fit:     Wed Sep 18 17:53:19 2019 
+#> Date of summary: Wed Sep 18 17:53:19 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -608,7 +608,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.095 s
+#> Fitted using 421 model solutions performed in 1.167 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -718,8 +718,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   120       m1    25.15  28.78984 -3.640e+00
 #>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 13:15:12 2019 
-#> Date of summary: Wed Sep 18 13:15:12 2019 
+#> Date of fit:     Wed Sep 18 17:53:22 2019 
+#> Date of summary: Wed Sep 18 17:53:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -727,7 +727,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.639 s
+#> Fitted using 979 model solutions performed in 2.583 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -850,8 +850,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   120       m1    25.15  28.80429 -3.654e+00
 #>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 13:15:22 2019 
-#> Date of summary: Wed Sep 18 13:15:22 2019 
+#> Date of fit:     Wed Sep 18 17:53:31 2019 
+#> Date of summary: Wed Sep 18 17:53:31 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -859,7 +859,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.723 s
+#> Fitted using 2289 model solutions performed in 9.35 s
 #> 
 #> Error model: Two-component variance function 
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index ca243e3c..4c73a0db 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -239,7 +239,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file4e7a49f4ff50.c 2> file4e7a49f4ff50.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file195c26c6bf0a.c 2> file195c26c6bf0a.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index f5401c1d..f2c6f87f 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -332,17 +332,17 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.004       0.000       0.004 
  system.time(
+#>       0.003       0.000       0.003 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.002       0.000       0.002 
  system.time(
+#>       0.001       0.000       0.001 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.021       0.000       0.021 

+#>       0.022       0.000       0.022 

   # \dontrun{
     # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index ea695d9a..eac99579 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -199,8 +199,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.007       0.031       4.920 
time_1
#>        User      System verstrichen 
-#>      19.290       0.000      19.301 

+#>       0.013       0.027       5.014 
time_1
#>        User      System verstrichen 
+#>      19.047       0.000      19.057 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340481   0.2659519   0.7505684   0.2494316 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index a10859fc..cc2ac55a 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -215,15 +215,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 13:16:44 2019 
-#> Date of summary: Wed Sep 18 13:16:44 2019 
+#> Date of fit:     Wed Sep 18 17:54:50 2019 
+#> Date of summary: Wed Sep 18 17:54:50 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.273 s
+#> Fitted using 131 model solutions performed in 0.27 s
 #> 
 #> Error model: Constant variance 
 #> 
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
new file mode 100644
index 00000000..e75a0097
--- /dev/null
+++ b/docs/sitemap.xml
@@ -0,0 +1,183 @@
+
+
+  
+    https://pkgdown.jrwb.de/mkin/index.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/AIC.mmkin.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/CAKE_export.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/DFOP.solution.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/Extract.mmkin.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_HS_ref_A_to_F.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_SFO_ref_A_to_F.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_datasets.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/HS.solution.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/IORE.solution.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_2015.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_Attachment.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/SFO.solution.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/SFORB.solution.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/add_err.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/endpoints.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/experimental_data_for_UBA.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/geometric_mean.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/ilr.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mccall81_245T.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkin_long_to_wide.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkin_wide_to_long.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinds.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinerrplot.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinfit.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinmod.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinparplot.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinplot.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinresplot.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mkinsub.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/mmkin.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/nafta.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/print.mkinds.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/print.mkinmod.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/print.nafta.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/test_data_from_UBA_2014.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/articles/FOCUS_D.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/articles/mkin.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/articles/twa.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/articles/web_only/FOCUS_Z.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html
+  
+  
+    https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html
+  
+
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
index c2a5076b..764c874c 100644
Binary files a/vignettes/mkin_benchmarks.rda and b/vignettes/mkin_benchmarks.rda differ
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