From b7901aac76df753ec1213cb02bebea055965ee87 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Mon, 30 Oct 2023 17:09:21 +0100 Subject: Update static docs --- docs/articles/web_only/FOCUS_Z.html | 7 +- .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 67444 -> 66689 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 107009 -> 105896 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 106098 -> 104799 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 76831 -> 75224 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 37494 -> 36301 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 67444 -> 66689 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 67259 -> 66448 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 81751 -> 80380 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 106406 -> 105172 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 105359 -> 104538 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 89110 -> 88806 bytes docs/articles/web_only/NAFTA_examples.html | 7 +- .../NAFTA_examples_files/figure-html/p10-1.png | Bin 81542 -> 79758 bytes .../NAFTA_examples_files/figure-html/p11-1.png | Bin 77600 -> 76315 bytes .../NAFTA_examples_files/figure-html/p12a-1.png | Bin 83512 -> 81697 bytes .../NAFTA_examples_files/figure-html/p12b-1.png | Bin 71409 -> 70800 bytes .../NAFTA_examples_files/figure-html/p13-1.png | Bin 78613 -> 78121 bytes .../NAFTA_examples_files/figure-html/p14-1.png | Bin 81557 -> 80656 bytes .../NAFTA_examples_files/figure-html/p15a-1.png | Bin 77580 -> 76974 bytes .../NAFTA_examples_files/figure-html/p15b-1.png | Bin 79748 -> 78970 bytes .../NAFTA_examples_files/figure-html/p16-1.png | Bin 94540 -> 93950 bytes .../NAFTA_examples_files/figure-html/p5a-1.png | Bin 83061 -> 82665 bytes .../NAFTA_examples_files/figure-html/p5b-1.png | Bin 81186 -> 80721 bytes .../NAFTA_examples_files/figure-html/p6-1.png | Bin 83142 -> 83052 bytes .../NAFTA_examples_files/figure-html/p7-1.png | Bin 102934 -> 102570 bytes .../NAFTA_examples_files/figure-html/p8-1.png | Bin 93632 -> 92407 bytes .../NAFTA_examples_files/figure-html/p9a-1.png | Bin 78782 -> 78605 bytes .../NAFTA_examples_files/figure-html/p9b-1.png | Bin 76883 -> 76240 bytes docs/articles/web_only/benchmarks.html | 104 ++++++++++++-- docs/articles/web_only/compiled_models.html | 31 +++-- docs/articles/web_only/dimethenamid_2018.html | 154 +++++++++++---------- docs/articles/web_only/multistart.html | 7 +- .../figure-html/unnamed-chunk-3-1.png | Bin 65359 -> 64334 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 53645 -> 52775 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 22804 -> 22131 bytes docs/articles/web_only/saem_benchmarks.html | 85 +++++++++++- 37 files changed, 285 insertions(+), 110 deletions(-) (limited to 'docs/articles/web_only') diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 4cda45e3..f19f59ad 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -33,7 +33,7 @@ mkin - 1.2.4 + 1.2.6 @@ -73,6 +73,9 @@
  • Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
    • +
  • + Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione +
  • Testing hierarchical pathway kinetics with residue data on cyantraniliprole
    • @@ -134,7 +137,7 @@ Ranke

    Last change 16 January 2018 -(rebuilt 2023-05-19)

    +(rebuilt 2023-10-30) Source: vignettes/web_only/FOCUS_Z.rmd diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png index 98bc135b..be652d31 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png index c1011a35..11c158fa 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png index dfd2dd50..fb44de27 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png index 74173f36..4603d247 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png index 1c5793cc..1454c938 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png index 98bc135b..be652d31 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png index 0380ba43..59524035 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png index 8c594ec9..77965455 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png index 84d473d6..5ea3152e 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png index 87af8874..d87105fb 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png index 492cdcc8..06e3ff57 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 87cef18a..1c5be845 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -33,7 +33,7 @@ mkin - 1.2.4 + 1.2.6 @@ -73,6 +73,9 @@
  • Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
    • +
  • + Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione +
  • Testing hierarchical pathway kinetics with residue data on cyantraniliprole
    • @@ -135,7 +138,7 @@ to the US EPA SOP for the NAFTA guidance Ranke

    26 February 2019 (rebuilt -2023-05-19)

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--git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png index c247fd4e..61359ea6 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png index 99d593fc..85790b1e 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png differ diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 315ad54e..5d6fb6e2 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -33,7 +33,7 @@ mkin - 1.2.4 + 1.2.6 @@ -73,6 +73,9 @@
  • Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
    • +
  • + Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione +
  • Testing hierarchical pathway kinetics with residue data on cyantraniliprole
    • @@ -134,7 +137,7 @@ Ranke

    Last change 17 February 2023 -(rebuilt 2023-05-19)

    +(rebuilt 2023-10-30) Source: vignettes/web_only/benchmarks.rmd @@ -231,7 +234,15 @@ systems. All trademarks belong to their respective owners.

    Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.

    - +
    ++++++++ @@ -433,6 +444,22 @@ models fitted to two datasets, i.e. eight fits for each test.

    + + + + + + + + + + + + + + + +
    OS CPU 1.386 1.960
    LinuxIntel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz4.3.11.2.52.3693.632
    LinuxIntel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz4.3.11.2.62.8564.960
    @@ -443,6 +470,15 @@ models fitted to two datasets, i.e. eight fits for each test.

    by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.

    +++++++++ @@ -669,6 +705,24 @@ for each test.

    + + + + + + + + + + + + + + + + + +
    OS CPU 2.080 1.106
    LinuxIntel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz4.3.11.2.51.8235.5552.404
    LinuxIntel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz4.3.11.2.61.7615.4052.462
    @@ -678,18 +732,18 @@ for each test.

    Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.

    - +
    +++---------++++++ @@ -992,6 +1046,30 @@ dataset, i.e. one fit for each test.

    + + + + + + + + + + + + + + + + + + + + + + + +
    OS 0.712 0.948
    LinuxIntel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz4.3.11.2.50.7981.0961.2173.1731.6342.271
    LinuxIntel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz4.3.11.2.60.8131.1361.2203.1141.5982.255
    diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 3c53b40a..1aa88e05 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -33,7 +33,7 @@ mkin - 1.2.4 + 1.2.6 @@ -73,6 +73,9 @@
  • Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
    • +
  • + Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione +
  • Testing hierarchical pathway kinetics with residue data on cyantraniliprole
    • @@ -134,7 +137,7 @@ definitions in mkin

    Johannes Ranke

    -

    2023-05-19

    +

    2023-10-30

    Source: vignettes/web_only/compiled_models.rmd @@ -152,7 +155,7 @@ compiled from autogenerated C code when defining a model using mkinmod. Starting from version 0.9.49.9, the mkinmod() function checks for presence of a compiler using

    -pkgbuild::has_compiler()
    +pkgbuild::has_compiler()

    In previous versions, it used Sys.which("gcc") for this check.

    On Linux, you need to have the essential build tools like make and @@ -213,10 +216,10 @@ solution is also implemented, which is included in the tests below.

    print("R package rbenchmark is not available") } 
    ##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.099
-## 3     deSolve, compiled            1    1.303   0.129
-## 2      Eigenvalue based            1    1.697   0.168
-## 1 deSolve, not compiled            1   21.475   2.126
    +## 4 analytical 1 1.000 0.213 +## 3 deSolve, compiled 1 1.418 0.302 +## 2 Eigenvalue based 1 2.000 0.426 +## 1 deSolve, not compiled 1 23.535 5.013

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

    @@ -247,15 +250,15 @@ compiled code is available.

    } 
    ## Temporary DLL for differentials generated and loaded
    ##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.165
-## 1 deSolve, not compiled            1   22.673   3.741
    -

    Here we get a performance benefit of a factor of 23 using the version +## 2 deSolve, compiled 1 1.000 0.492 +## 1 deSolve, not compiled 1 20.398 10.036 +

    Here we get a performance benefit of a factor of 20 using the version of the differential equation model compiled from C code!

    -

    This vignette was built with mkin 1.2.4 on

    -
    ## R version 4.3.0 Patched (2023-05-18 r84448)
+
    This vignette was built with mkin 1.2.6 on
    
+
    ## R version 4.3.1 (2023-06-16)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Debian GNU/Linux 12 (bookworm)
    
-
    ## CPU model: AMD Ryzen 9 7950X 16-Core Processor
    
+## Running under: Ubuntu 22.04.3 LTS
    +
    ## CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz
    diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index a89631a2..1cffd561 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -33,7 +33,7 @@ mkin - 1.2.4 + 1.2.6 @@ -73,6 +73,9 @@
  • Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
    • +
  • + Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione +
  • Testing hierarchical pathway kinetics with residue data on cyantraniliprole
    • @@ -135,7 +138,7 @@ from 2018 Ranke

    Last change 1 July 2022, -built on 19 May 2023

    +built on 30 Oct 2023 Source: vignettes/web_only/dimethenamid_2018.rmd @@ -222,12 +225,12 @@ least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):

    -plot(mixed(f_parent_mkin_const["SFO", ]))
    +plot(mixed(f_parent_mkin_const["SFO", ]))

    Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:

    -plot(mixed(f_parent_mkin_const["DFOP", ]))
    +plot(mixed(f_parent_mkin_const["DFOP", ]))

    The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 @@ -239,7 +242,7 @@ dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:

    -plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)
    +plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)

    While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual @@ -251,7 +254,7 @@ degradation model and the error model (see below).

    predicted residues is reduced by using the two-component error model:

    -plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)
    +plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)

    However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by @@ -263,7 +266,7 @@ Status of individual fits: dataset model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot - DFOP OK OK C OK C OK + DFOP OK OK OK OK C OK C: Optimisation did not converge: iteration limit reached without convergence (10) @@ -319,7 +322,7 @@ indicates that this difference is significant as the p-value is below 

                            Model df    AIC    BIC  logLik   Test L.Ratio p-value
 f_parent_nlme_sfo_const     1  5 796.60 811.82 -393.30                       
 f_parent_nlme_sfo_tc        2  6 798.60 816.86 -393.30 1 vs 2    0.00   0.998
-f_parent_nlme_dfop_tc       3 10 671.91 702.34 -325.96 2 vs 3  134.69  <.0001
    +f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.95 2 vs 3 134.69 <.0001

    In addition to these fits, attempts were also made to include correlations between random effects by using the log Cholesky parameterisation of the matrix specifying them. The code used for these @@ -341,7 +344,7 @@ effects does not improve the fits.

    The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.

    -plot(f_parent_nlme_dfop_tc)
    +plot(f_parent_nlme_dfop_tc)

    @@ -358,8 +361,17 @@ implemented in the saemix package, the convergence plots need to be manually checked for every fit. We define control settings that work well for all the parent data fits shown in this vignette.

    -library(saemix)
-saemix_control <- saemixControl(nbiter.saemix = c(800, 300), nb.chains = 15,
+library(saemix)
    +
    Loading required package: npde
    +
    Package saemix, version 3.2
+  please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr
    +
    
+Attaching package: 'saemix'
    +
    The following objects are masked from 'package:npde':
+
+    kurtosis, skewness
    +
    +saemix_control <- saemixControl(nbiter.saemix = c(800, 300), nb.chains = 15,
     print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
 saemix_control_moreiter <- saemixControl(nbiter.saemix = c(1600, 300), nb.chains = 15,
     print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
@@ -367,7 +379,7 @@ well for all the parent data fits shown in this vignette.
    
     print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)

    The convergence plot for the SFO model using constant variance is shown below.

    -
    +
     f_parent_saemix_sfo_const <- mkin::saem(f_parent_mkin_const["SFO", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_sfo_const$so, plot.type = "convergence")
    
@@ -375,19 +387,19 @@ shown below.
    
 
    Obviously the selected number of iterations is sufficient to reach
 convergence. This can also be said for the SFO fit using the
 two-component error model.
    
-
    +
     f_parent_saemix_sfo_tc <- mkin::saem(f_parent_mkin_tc["SFO", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_sfo_tc$so, plot.type = "convergence")
    
 
    
 
    When fitting the DFOP model with constant variance (see below),
 parameter convergence is not as unambiguous.
    
-
    +
     f_parent_saemix_dfop_const <- mkin::saem(f_parent_mkin_const["DFOP", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_dfop_const$so, plot.type = "convergence")
    
 
    
-
    +
     print(f_parent_saemix_dfop_const)
    
 
    Kinetic nonlinear mixed-effects model fit by SAEM
 Structural model:
@@ -408,11 +420,11 @@ DMTA_0    97.99583 96.50079 99.4909
 k1         0.06377  0.03432  0.0932
 k2         0.00848  0.00444  0.0125
 g          0.95701  0.91313  1.0009
-a.1        1.82141  1.65122  1.9916
-SD.DMTA_0  1.64787  0.45772  2.8380
+a.1        1.82141  1.60516  2.0377
+SD.DMTA_0  1.64787  0.45729  2.8384
 SD.k1      0.57439  0.24731  0.9015
-SD.k2      0.03296 -2.50195  2.5679
-SD.g       1.10266  0.32369  1.8816
    
+SD.k2      0.03296 -2.50524  2.5712
+SD.g       1.10266  0.32354  1.8818
    
 
    While the other parameters converge to credible values, the variance
 of k2 (omega2.k2) converges to a very small value. The
 printout of the saem.mmkin model shows that the estimated
@@ -423,14 +435,14 @@ this model.
    
 also observe that the estimated variance of k2 becomes very small, while
 being ill-defined, as illustrated by the excessive confidence interval
 of SD.k2.
    
-
    +
     f_parent_saemix_dfop_tc <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 f_parent_saemix_dfop_tc_moreiter <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
   control = saemix_control_moreiter, transformations = "saemix")
 plot(f_parent_saemix_dfop_tc$so, plot.type = "convergence")
    
 
    
-
    +
     print(f_parent_saemix_dfop_tc)
    
 
    Kinetic nonlinear mixed-effects model fit by SAEM
 Structural model:
@@ -446,17 +458,17 @@ Likelihood computed by importance sampling
   666 664   -323
 
 Fitted parameters:
-          estimate    lower    upper
-DMTA_0    98.27617  96.3088 100.2436
-k1         0.06437   0.0337   0.0950
-k2         0.00880   0.0063   0.0113
-g          0.95249   0.9100   0.9949
-a.1        1.06161   0.8625   1.2607
-b.1        0.02967   0.0226   0.0367
-SD.DMTA_0  2.06075   0.4187   3.7028
-SD.k1      0.59357   0.2561   0.9310
-SD.k2      0.00292 -10.2960  10.3019
-SD.g       1.05725   0.3808   1.7337
    
+          estimate     lower    upper
+DMTA_0    98.24165  96.29190 100.1914
+k1         0.06421   0.03352   0.0949
+k2         0.00866   0.00617   0.0111
+g          0.95340   0.91218   0.9946
+a.1        1.06463   0.86503   1.2642
+b.1        0.02964   0.02259   0.0367
+SD.DMTA_0  2.03611   0.40416   3.6681
+SD.k1      0.59534   0.25692   0.9338
+SD.k2      0.00042 -73.01372  73.0146
+SD.g       1.04234   0.37189   1.7128
    
 
    Doubling the number of iterations in the first phase of the algorithm
 leads to a slightly lower likelihood, and therefore to slightly higher
 AIC and BIC values. With even more iterations, the algorithm stops with
@@ -472,7 +484,7 @@ message.
    
 
    The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and
 the version with increased iterations can be compared using the model
 comparison function of the saemix package:
    
-
    +
     AIC_parent_saemix <- saemix::compare.saemix(
   f_parent_saemix_sfo_const$so,
   f_parent_saemix_sfo_tc$so,
@@ -480,7 +492,7 @@ comparison function of the saemix package:
    
   f_parent_saemix_dfop_tc$so,
   f_parent_saemix_dfop_tc_moreiter$so)
    
 
    Likelihoods calculated by importance sampling
    
-
    +
     rownames(AIC_parent_saemix) <- c(
   "SFO const", "SFO tc", "DFOP const", "DFOP tc", "DFOP tc more iterations")
 print(AIC_parent_saemix)
    
@@ -488,13 +500,13 @@ comparison function of the saemix package:
    
 SFO const               796.38 795.34
 SFO tc                  798.38 797.13
 DFOP const              705.75 703.88
-DFOP tc                 665.65 663.57
-DFOP tc more iterations 665.88 663.80
    
+DFOP tc                 665.67 663.59
+DFOP tc more iterations 665.85 663.76
    
 
    In order to check the influence of the likelihood calculation
 algorithms implemented in saemix, the likelihood from Gaussian
 quadrature is added to the best fit, and the AIC values obtained from
 the three methods are compared.
    
-
    +
     f_parent_saemix_dfop_tc$so <-
   saemix::llgq.saemix(f_parent_saemix_dfop_tc$so)
 AIC_parent_saemix_methods <- c(
@@ -504,7 +516,7 @@ the three methods are compared.
    
 )
 print(AIC_parent_saemix_methods)
    
 
        is     gq    lin 
-665.65 665.68 665.11 
    
+665.67 665.74 665.13 
    
 
    The AIC values based on importance sampling and Gaussian quadrature
 are very similar. Using linearisation is known to be less accurate, but
 still gives a similar value.
    
@@ -518,7 +530,7 @@ iterations makes a lot of difference. When using the LAPACK version
 coming with Debian Bullseye, the AIC based on Gaussian quadrature is
 almost the same as the one obtained with the other methods, also when
 using defaults for the fit.
    
-
    +
     f_parent_saemix_dfop_tc_defaults <- mkin::saem(f_parent_mkin_tc["DFOP", ])
 f_parent_saemix_dfop_tc_defaults$so <-
   saemix::llgq.saemix(f_parent_saemix_dfop_tc_defaults$so)
@@ -529,7 +541,7 @@ using defaults for the fit.
    
 )
 print(AIC_parent_saemix_methods_defaults)
    
 
        is     gq    lin 
-669.77 669.36 670.95 
    
+670.09 669.37 671.29 
    
 
    
 
    
 
    
@@ -538,7 +550,7 @@ using defaults for the fit.
    
 
    The following table gives the AIC values obtained with both backend
 packages using the same control parameters (800 iterations burn-in, 300
 iterations second phase, 15 chains).
    
-
    +
     AIC_all <- data.frame(
   check.names = FALSE,
   "Degradation model" = c("SFO", "SFO", "DFOP", "DFOP"),
@@ -549,7 +561,7 @@ iterations second phase, 15 chains).
    
   saemix_is = sapply(list(f_parent_saemix_sfo_const$so, f_parent_saemix_sfo_tc$so,
     f_parent_saemix_dfop_const$so, f_parent_saemix_dfop_tc$so), AIC, method = "is")
 )
-kable(AIC_all)
    
+kable(AIC_all)
    
 
@@ -577,15 +589,15 @@ iterations second phase, 15 chains).
    
-
+
-
-
+
+
    
 
    
 Degradation model
 DFOP
 const
 NA709.26704.95
 705.75
 
    
 
    
 DFOP
 tc
 671.91665.11665.65665.13665.67
 
    
 
 
    
@@ -612,48 +624,48 @@ satisfactory precision.
    
 
    
 
    Session Info
 
    
-
    +
-
    R version 4.3.0 Patched (2023-05-18 r84448)
+
    R version 4.3.1 (2023-06-16)
 Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Debian GNU/Linux 12 (bookworm)
+Running under: Ubuntu 22.04.3 LTS
 
 Matrix products: default
-BLAS:   /home/jranke/svn/R/r-patched/build/lib/libRblas.so 
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3;  LAPACK version 3.11.0
+BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
 
 locale:
- [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
- [3] LC_TIME=C                  LC_COLLATE=de_DE.UTF-8    
- [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
- [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
+ [3] LC_TIME=C                  LC_COLLATE=en_US.UTF-8    
+ [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
+ [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
-[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
+[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
 
-time zone: Europe/Berlin
+time zone: Europe/Zurich
 tzcode source: system (glibc)
 
 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] nlme_3.1-162 mkin_1.2.4   knitr_1.42  
+[1] saemix_3.2   npde_3.3     nlme_3.1-163 mkin_1.2.6   knitr_1.44  
 
 loaded via a namespace (and not attached):
- [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    saemix_3.2       
- [5] stringi_1.7.12    lattice_0.21-8    digest_0.6.31     magrittr_2.0.3   
- [9] evaluate_0.21     grid_4.3.0        fastmap_1.1.1     rprojroot_2.0.3  
-[13] jsonlite_1.8.4    DBI_1.1.3         mclust_6.0.0      gridExtra_2.3    
-[17] purrr_1.0.1       fansi_1.0.4       scales_1.2.1      textshaping_0.3.6
-[21] jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1       munsell_0.5.0    
-[25] cachem_1.0.8      yaml_2.3.7        tools_4.3.0       parallel_4.3.0   
-[29] memoise_2.0.1     dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2    
-[33] vctrs_0.6.2       R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3  
-[37] stringr_1.5.0     fs_1.6.2          ragg_1.2.5        pkgconfig_2.0.3  
-[41] desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2       pillar_1.9.0     
-[45] gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4 xfun_0.39        
-[49] tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0  npde_3.3         
-[53] htmltools_0.5.5   rmarkdown_2.21    compiler_4.3.0   
    
+ [1] sass_0.4.7        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
+ [5] lattice_0.21-9    digest_0.6.33     magrittr_2.0.3    evaluate_0.22    
+ [9] grid_4.3.1        fastmap_1.1.1     rprojroot_2.0.3   jsonlite_1.8.7   
+[13] mclust_6.0.0      gridExtra_2.3     purrr_1.0.1       fansi_1.0.4      
+[17] scales_1.2.1      codetools_0.2-19  textshaping_0.3.6 jquerylib_0.1.4  
+[21] cli_3.6.1         rlang_1.1.1       munsell_0.5.0     cachem_1.0.8     
+[25] yaml_2.3.7        tools_4.3.1       parallel_4.3.1    memoise_2.0.1    
+[29] dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2     vctrs_0.6.3      
+[33] R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3   stringr_1.5.0    
+[37] fs_1.6.3          MASS_7.3-60       ragg_1.2.5        pkgconfig_2.0.3  
+[41] desc_1.4.2        pkgdown_2.0.7     bslib_0.5.1       pillar_1.9.0     
+[45] gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4 xfun_0.40        
+[49] tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0  rstudioapi_0.15.0
+[53] htmltools_0.5.6.1 rmarkdown_2.23    compiler_4.3.1   
    
 
    
 
    
 
    References
diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html
index b9224bb0..dff087e4 100644
--- a/docs/articles/web_only/multistart.html
+++ b/docs/articles/web_only/multistart.html
@@ -33,7 +33,7 @@
       
       
         mkin
-        1.2.4
+        1.2.6
       
     
    
 
@@ -73,6 +73,9 @@
     
  • 
       Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
     
    • 
+    
  • 
+      Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+    
    • 
     
  • 
       Testing hierarchical pathway kinetics with residue data on cyantraniliprole
     
    • 
@@ -134,7 +137,7 @@
 Ranke
             
             
    Last change 20 April 2023
-(rebuilt 2023-05-19)
    
+(rebuilt 2023-10-30)
       
       Source: vignettes/web_only/multistart.rmd
       
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
index f41dc889..8be6ba61 100644
Binary files a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png differ
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
index 9e206791..bc518c0c 100644
Binary files a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png differ
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
index c8e918cd..9ecdf4c9 100644
Binary files a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/docs/articles/web_only/saem_benchmarks.html b/docs/articles/web_only/saem_benchmarks.html
index a9637876..095a37e2 100644
--- a/docs/articles/web_only/saem_benchmarks.html
+++ b/docs/articles/web_only/saem_benchmarks.html
@@ -33,7 +33,7 @@
       
       
         mkin
-        1.2.4
+        1.2.6
       
     
    
 
@@ -73,6 +73,9 @@
     
  • 
       Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
     
    • 
+    
  • 
+      Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+    
    • 
     
  • 
       Testing hierarchical pathway kinetics with residue data on cyantraniliprole
     
    • 
@@ -134,7 +137,7 @@
 Ranke
             
             
    Last change 17 February 2023
-(rebuilt 2023-05-19)
    
+(rebuilt 2023-10-30)
       
       Source: vignettes/web_only/saem_benchmarks.rmd
       
@@ -190,7 +193,7 @@ explanation of the following preprocessing.
    
 
     anova(
   sfo_const, dfop_const, sforb_const, hs_const,
-  sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1)
    
+  sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1)
    
 
@@ -330,7 +333,17 @@ systems. All trademarks belong to their respective owners.
    Parent only
 
    Constant variance for SFO, DFOP, SFORB and HS.
    
-
    
 
    
 
 
 
    
+
    
++++++++++
@@ -412,10 +425,30 @@ systems. All trademarks belong to their respective owners.
    
+
+
+
+
+
+
+
+
+
+
    









 
    
 CPU
 OS
 1.987
 2.055
 
    Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHzLinux1.2.63.22.9986.5236.1264.721
    
 
 
    
 
    Two-component error fits for SFO, DFOP, SFORB and HS.
    
-
+
    
++++++++++
@@ -497,6 +530,16 @@ systems. All trademarks belong to their respective owners.
    
+
+
+
+
+
+
+
+
+
+
    









 
    
 CPU
 OS
 3.433
 3.595
 
    Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHzLinux1.2.63.25.0708.4648.5257.599
    
 
 
    
 
    
@@ -505,6 +548,14 @@ systems. All trademarks belong to their respective owners.
    
 
 
    Two-component error for DFOP-SFO and SFORB-SFO.
    
 
++++++++
@@ -570,6 +621,14 @@ systems. All trademarks belong to their respective owners.
    
+
+
+
+
+
+
+
+
    







 
    
 CPU
 OS
 12.160
 265.934
 
    Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHzLinux1.2.63.230.168748.675
    
 
 
    
 
    
@@ -577,7 +636,14 @@ systems. All trademarks belong to their respective owners.
    
 
    Three metabolites
 
    
 
    Two-component error for SFORB-SFO3-plus
    
-
+
    
+++++++
@@ -635,6 +701,13 @@ systems. All trademarks belong to their respective owners.
    
+
+
+
+
+
+
+
    






 
    
 CPU
 OS
 3.2
 456.252
 
    Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHzLinux1.2.63.21235.028
    
 
 
    
 
    
-- 
cgit v1.2.1