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Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

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+ +
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a/docs/articles/prebuilt/2023_mesotrione_parent.html +++ b/docs/articles/prebuilt/2023_mesotrione_parent.html @@ -1,114 +1,374 @@ - + + + - - - - - -Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione • mkin - - - - - - - + + + + + + + + + +Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Skip to contents - - -
+ +
-
-
-

Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione

-

Johannes -Ranke

- -

Last change on 4 August 2023, -last compiled on 16 November 2023

- - Source: vignettes/prebuilt/2023_mesotrione_parent.rmd -
2023_mesotrione_parent.rmd
-
+
-
-

-

Developed by Johannes Ranke.

-
-
-

-

Site built with pkgdown 2.0.7.

-
-
+ + + + + + + - - + + - + diff --git a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-14-1.png b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-14-1.png index 863a48bd..719bf0e9 100644 Binary files a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-14-1.png and b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-14-1.png differ diff --git a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-19-1.png b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-19-1.png index 256b2b68..6afcac48 100644 Binary files a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-19-1.png and b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-19-1.png differ diff --git a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-25-1.png b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-25-1.png index 59011020..50253fb1 100644 Binary files a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-25-1.png and b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-25-1.png differ diff --git a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-30-1.png b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-30-1.png index f427bc39..c8b77724 100644 Binary files a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-30-1.png and b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-30-1.png differ diff --git a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-8-1.png index 7c3b460b..8fa204a3 100644 Binary files a/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/prebuilt/2023_mesotrione_parent_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 5452a5e5..19bc4761 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -5,86 +5,71 @@ - Calculation of time weighted average concentrations with mkin • mkin - - - - - - + + + + Skip to contents - - 

 print(p9a)
@@ -454,7 +440,7 @@ suggest a simple exponential decline.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p9b)
+plot(p9b)

 print(p9b)
@@ -512,7 +498,7 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p10)
+plot(p10)

 print(p10)
@@ -572,7 +558,7 @@ difference in IORE model parameters between PestDF and mkin.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p11)
+plot(p11) 

 print(p11)
@@ -638,7 +624,7 @@ overparameterisation.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p12a)
+plot(p12a) 

 print(p12a)
@@ -690,15 +676,14 @@ overparameterisation.

## Warning in qt(alpha/2, rdf): NaNs produced
## Warning in qt(1 - alpha/2, rdf): NaNs produced
## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced
-
## Warning in sqrt(1/diag(V)): NaNs produced
-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful
+
## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the
+## non-finite result may be dubious
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-
-plot(p12b)
+
+plot(p12b)

-
+
 print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -742,14 +727,14 @@ overparameterisation.

 

 
Example on page 13
 

-
+
 p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p13)

+
+plot(p13)

 

-
+
 print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -794,18 +779,17 @@ overparameterisation.

 

 
DT50 not observed in the study and DFOP problems in PestDF
 

-
+
 p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])

 
## Warning in sqrt(diag(covar)): NaNs produced

-
## Warning in sqrt(1/diag(V)): NaNs produced

-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful

+
## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the
+## non-finite result may be dubious

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p14)

+
+plot(p14)

 

-
+
 print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -852,18 +836,17 @@ same results in mkin and PestDF.

 

 
N is less than 1 and DFOP fraction parameter is below zero
 

-
+
 p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])

 
## Warning in sqrt(diag(covar)): NaNs produced

-
## Warning in sqrt(1/diag(V)): NaNs produced

-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful

+
## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the
+## non-finite result may be dubious

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p15a)

+
+plot(p15a)

 

-
+
 print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -903,16 +886,16 @@ same results in mkin and PestDF.

 ## 
 ## Representative half-life:
 ## [1] 41.33

-
+
 p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])

 
## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
 ## matrix

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p15b)

+
+plot(p15b)

 

-
+
 print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
@@ -960,16 +943,16 @@ mkin and PestDF.

 

 
The DFOP fraction parameter is greater than 1
 

-
+
 p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The representative half-life of the IORE model is longer than the one corresponding

 
## to the terminal degradation rate found with the DFOP model.

 
## The representative half-life obtained from the DFOP model may be used

-
-plot(p16)

+
+plot(p16)

 

-
+
 print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -1010,10 +993,12 @@ mkin and PestDF.

 ## Representative half-life:
 ## [1] 8.93

 
In PestDF, the DFOP fit seems to have stuck in a local minimum, as
-mkin finds a solution with a much lower \(\chi^2\) error level. As the half-life from
-the slower rate constant of the DFOP model is larger than the IORE
-derived half-life, the NAFTA recommendation obtained with mkin is to use
-the DFOP representative half-life of 8.9 days.

+mkin finds a solution with a much lower
+χ2\chi^2
+error level. As the half-life from the slower rate constant of the DFOP
+model is larger than the IORE derived half-life, the NAFTA
+recommendation obtained with mkin is to use the DFOP representative
+half-life of 8.9 days.

 

 

 
Conclusions
@@ -1038,28 +1023,26 @@ Pesticide Degradation.” 

 
 
 
     
 

 
-  
 
-  
+
+
 
   
 
diff --git a/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
deleted file mode 100644
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--- a/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
+++ /dev/null
@@ -1,15 +0,0 @@
-// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});
diff --git a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 17c2f8d8..3566be42 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -5,86 +5,71 @@
 
 
 
-
 Benchmark timings for mkin • mkin
 
-
-
-
-
-
-
+
+
+
+
 
 
     Skip to contents
-    
 
-    

 
 
 
     

-  

-
Developed by Johannes Ranke.

+  
Developed by Johannes Ranke.

 

 
 

-  

-
Site built with pkgdown 2.0.7.

+  
Site built with pkgdown 2.1.1.

 

 
     

 

 
-  
 
-  
+
+
 
   
 
diff --git a/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
deleted file mode 100644
index ca349fd6..00000000
--- a/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
+++ /dev/null
@@ -1,15 +0,0 @@
-// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});
diff --git a/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js b/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 210ddaf7..bbf6e897 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -5,86 +5,71 @@
 
 
 
-
 Performance benefit by using compiled model definitions in mkin • mkin
 
-
-
-
-
-
-
+
+
+
+
 
 
     Skip to contents
-    
 
-    

 
##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.109
-## 3     deSolve, compiled            1    1.284   0.140
-## 2      Eigenvalue based            1    1.670   0.182
-## 1 deSolve, not compiled            1   21.927   2.390

+## 4            analytical            1    1.000   0.105
+## 3     deSolve, compiled            1    1.333   0.140
+## 2      Eigenvalue based            1    1.667   0.175
+## 1 deSolve, not compiled            1   22.486   2.361

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

 

@@ -209,38 +195,36 @@ compiled code is available.

 }

 
## Temporary DLL for differentials generated and loaded

 
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.181
-## 1 deSolve, not compiled            1   23.646   4.280

+## 2     deSolve, compiled            1    1.000   0.175
+## 1 deSolve, not compiled            1   23.937   4.189

 
Here we get a performance benefit of a factor of 24 using the version
 of the differential equation model compiled from C code!

-
This vignette was built with mkin 1.2.6 on

-
## R version 4.3.2 (2023-10-31)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
This vignette was built with mkin 1.2.9 on

+
## R version 4.4.2 (2024-10-31)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Debian GNU/Linux 12 (bookworm)

 
## CPU model: AMD Ryzen 9 7950X 16-Core Processor

 

-  

 
 
 
     

-  

-
Developed by Johannes Ranke.

+  
Developed by Johannes Ranke.

 

 
 

-  

-
Site built with pkgdown 2.0.7.

+  
Site built with pkgdown 2.1.1.

 

 
     

 

 
-  
 
-  
+
+
 
   
 
diff --git a/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
deleted file mode 100644
index ca349fd6..00000000
--- a/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
+++ /dev/null
@@ -1,15 +0,0 @@
-// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});
diff --git a/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html
index 4221ba07..5d39704d 100644
--- a/docs/articles/web_only/dimethenamid_2018.html
+++ b/docs/articles/web_only/dimethenamid_2018.html
@@ -5,86 +5,71 @@
 
 
 
-
 Example evaluations of the dimethenamid data from 2018 • mkin
 
-
-
-
-
-
-
+
+
+
+
 
 
     Skip to contents
-    
 
-    

 

 
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
@@ -201,7 +187,7 @@ 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 @@ -213,7 +199,7 @@ 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 @@ -303,7 +289,7 @@ 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)

@@ -320,8 +306,17 @@ 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 3.3, March 2024
+  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)
@@ -329,7 +324,7 @@ 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")

@@ -337,19 +332,19 @@ 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:
@@ -385,14 +380,14 @@ 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:
@@ -413,11 +408,11 @@ 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
+a.1        1.06463   0.87979   1.2495
+b.1        0.02964   0.02266   0.0366
+SD.DMTA_0  2.03611   0.40361   3.6686
 SD.k1      0.59534   0.25692   0.9338
-SD.k2      0.00042 -73.01372  73.0146
+SD.k2      0.00042 -73.00540  73.0062
 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
@@ -434,7 +429,7 @@ 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,
@@ -442,7 +437,7 @@ 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)

@@ -456,7 +451,7 @@ DFOP tc more iterations 665.85 663.76

 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(
@@ -480,7 +475,7 @@ 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)
@@ -500,7 +495,7 @@ 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"),
@@ -511,7 +506,7 @@ 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)

 
@@ -574,10 +569,10 @@ satisfactory precision.

 
Session Info
 

-
+
-
R version 4.3.2 (2023-10-31)
-Platform: x86_64-pc-linux-gnu (64-bit)
+
R version 4.4.2 (2024-10-31)
+Platform: x86_64-pc-linux-gnu
 Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
@@ -599,23 +594,22 @@ attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] saemix_3.2   npde_3.3     nlme_3.1-163 mkin_1.2.6   knitr_1.42  
+[1] saemix_3.3   npde_3.5     nlme_3.1-166 mkin_1.2.9   knitr_1.49  
 
 loaded via a namespace (and not attached):
- [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
- [5] lattice_0.21-8    digest_0.6.31     magrittr_2.0.3    evaluate_0.21    
- [9] grid_4.3.2        fastmap_1.1.1     rprojroot_2.0.3   jsonlite_1.8.4   
-[13] DBI_1.1.3         mclust_6.0.0      gridExtra_2.3     purrr_1.0.1      
-[17] fansi_1.0.4       scales_1.2.1      codetools_0.2-19  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_4.3.2       parallel_4.3.2   
-[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          MASS_7.3-60       ragg_1.2.5       
-[41] pkgconfig_2.0.3   desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2      
-[45] pillar_1.9.0      gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4
-[49] highr_0.10        xfun_0.39         tibble_3.2.1      lmtest_0.9-40    
-[53] tidyselect_1.2.0  htmltools_0.5.5   rmarkdown_2.21    compiler_4.3.2   

+ [1] gtable_0.3.6      jsonlite_1.8.9    dplyr_1.1.4       compiler_4.4.2   
+ [5] tidyselect_1.2.1  parallel_4.4.2    gridExtra_2.3     jquerylib_0.1.4  
+ [9] systemfonts_1.1.0 scales_1.3.0      textshaping_0.4.1 yaml_2.3.10      
+[13] fastmap_1.2.0     lattice_0.22-6    ggplot2_3.5.1     R6_2.5.1         
+[17] generics_0.1.3    lmtest_0.9-40     MASS_7.3-61       htmlwidgets_1.6.4
+[21] tibble_3.2.1      desc_1.4.3        munsell_0.5.1     bslib_0.8.0      
+[25] pillar_1.9.0      rlang_1.1.4       utf8_1.2.4        cachem_1.1.0     
+[29] xfun_0.49         fs_1.6.5          sass_0.4.9        cli_3.6.3        
+[33] pkgdown_2.1.1     magrittr_2.0.3    digest_0.6.37     grid_4.4.2       
+[37] mclust_6.1.1      lifecycle_1.0.4   vctrs_0.6.5       evaluate_1.0.1   
+[41] glue_1.8.0        codetools_0.2-20  ragg_1.3.3        zoo_1.8-12       
+[45] fansi_1.0.6       colorspace_2.1-1  rmarkdown_2.29    pkgconfig_2.0.3  
+[49] tools_4.4.2       htmltools_0.5.8.1

 

 

 
References
@@ -640,28 +634,26 @@ November 2017.” 

 
 
 
     
 

 
-  
 
-  
+
+
 
   
diff --git a/docs/articles/web_only/dimethenamid_2018_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/dimethenamid_2018_files/accessible-code-block-0.0.1/empty-anchor.js
deleted file mode 100644
index ca349fd6..00000000
--- a/docs/articles/web_only/dimethenamid_2018_files/accessible-code-block-0.0.1/empty-anchor.js
+++ /dev/null
@@ -1,15 +0,0 @@
-// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});
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diff --git a/docs/articles/web_only/dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png b/docs/articles/web_only/dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png
index a799b14c..6bcf3434 100644
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diff --git a/docs/articles/web_only/mkin_benchmarks.rda b/docs/articles/web_only/mkin_benchmarks.rda
deleted file mode 100644
index e26caf64..00000000
Binary files a/docs/articles/web_only/mkin_benchmarks.rda and /dev/null differ
diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html
index 4438adc3..f6ab46de 100644
--- a/docs/articles/web_only/multistart.html
+++ b/docs/articles/web_only/multistart.html
@@ -5,86 +5,71 @@
 
 
 
-
 Short demo of the multistart method • mkin
 
-
-
-
-
-
-
+
+
+
+
 
 
     Skip to contents
-    
 
-    

 

 Degradation model
 
 

@@ -405,6 +391,16 @@ systems. All trademarks belong to their respective owners.

+
+
+
+
+
+
+
+
+
+

 

 
 2.406
 2.478
 
Ryzen 9 7950XLinux1.2.93.31.0861.9911.9492.411

 
 

 
Two-component error fits for SFO, DFOP, SFORB and HS.

@@ -520,6 +516,16 @@ systems. All trademarks belong to their respective owners.

 3.669
 3.153
 
+
+Ryzen 9 7950X
+Linux
+1.2.9
+3.3
+2.426
+3.196
+3.256
+3.322
+
 
 
 

@@ -617,6 +623,14 @@ systems. All trademarks belong to their respective owners.

 12.007
 286.757
 
+
+Ryzen 9 7950X
+Linux
+1.2.9
+3.3
+12.420
+289.338
+
 
 
 

@@ -703,32 +717,37 @@ systems. All trademarks belong to their respective owners.

 3.2
 480.577
 
+
+Ryzen 9 7950X
+Linux
+1.2.9
+3.3
+485.836
+
 
 
 

 

-  

 
 
 
     

-  

-
Developed by Johannes Ranke.

+  
Developed by Johannes Ranke.

 

 
 

-  

-
Site built with pkgdown 2.0.7.

+  
Site built with pkgdown 2.1.1.

 

 
     

 

 
-  
 
-  
+
+
 
   
 
diff --git a/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
deleted file mode 100644
index ca349fd6..00000000
--- a/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
+++ /dev/null
@@ -1,15 +0,0 @@
-// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});
-- 
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