From a9427a09abdf7ce9aaeae7c7190f90c8f2e5ef52 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 14:08:13 +0100 Subject: Improve README, introductory vignette and some other docs Also bump version to 1.0.3. --- docs/articles/FOCUS_D.html | 22 +-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 79550 -> 79176 bytes .../FOCUS_D_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/articles/FOCUS_L.html | 128 +++++++-------- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../figure-html/unnamed-chunk-10-1.png | Bin 42372 -> 42203 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 82635 -> 82006 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 32949 -> 32751 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 58309 -> 57939 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 35417 -> 35238 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 35848 -> 35640 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 41558 -> 41399 bytes .../FOCUS_L_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/articles/index.html | 2 +- docs/articles/mkin.html | 59 ++++--- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 90521 -> 89958 bytes .../mkin_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/articles/twa.html | 10 +- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../twa_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/articles/web_only/FOCUS_Z.html | 32 ++-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 67049 -> 66640 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 106768 -> 106038 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 105777 -> 105042 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 76400 -> 75626 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 35734 -> 35744 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 67049 -> 66640 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.../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../header-attrs-2.6/header-attrs.js | 12 ++ 61 files changed, 469 insertions(+), 250 deletions(-) create mode 100644 docs/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/mkin_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/twa_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 786b2c47..f3a56065 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -31,7 +31,7 @@ mkin - 1.0.0 + 1.0.3 @@ -94,13 +94,13 @@ -
+

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2021-02-03

+

Last change 31 January 2019 (rebuilt 2021-02-15)

Source: vignettes/FOCUS_D.rmd @@ -185,10 +185,10 @@

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

 summary(fit)
-
## mkin version used for fitting:    1.0.0 
+
## mkin version used for fitting:    1.0.3 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Wed Feb  3 17:32:13 2021 
-## Date of summary: Wed Feb  3 17:32:14 2021 
+## Date of fit:     Mon Feb 15 13:46:23 2021 
+## Date of summary: Mon Feb 15 13:46:23 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -196,7 +196,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 401 model solutions performed in 0.161 s
+## Fitted using 401 model solutions performed in 0.162 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -239,11 +239,11 @@
 ## 
 ## Parameter correlation:
 ##                   parent_0 log_k_parent   log_k_m1 f_parent_qlogis      sigma
-## parent_0         1.000e+00    5.174e-01 -1.688e-01      -5.471e-01 -1.171e-06
-## log_k_parent     5.174e-01    1.000e+00 -3.263e-01      -5.426e-01 -8.481e-07
-## log_k_m1        -1.688e-01   -3.263e-01  1.000e+00       7.478e-01  8.209e-07
+## parent_0         1.000e+00    5.174e-01 -1.688e-01      -5.471e-01 -1.172e-06
+## log_k_parent     5.174e-01    1.000e+00 -3.263e-01      -5.426e-01 -8.483e-07
+## log_k_m1        -1.688e-01   -3.263e-01  1.000e+00       7.478e-01  8.205e-07
 ## f_parent_qlogis -5.471e-01   -5.426e-01  7.478e-01       1.000e+00  1.305e-06
-## sigma           -1.171e-06   -8.481e-07  8.209e-07       1.305e-06  1.000e+00
+## sigma           -1.172e-06   -8.483e-07  8.205e-07       1.305e-06  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
diff --git a/docs/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// 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/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
index 5278038a..abf26715 100644
Binary files a/docs/articles/FOCUS_D_files/figure-html/plot-1.png and b/docs/articles/FOCUS_D_files/figure-html/plot-1.png differ
diff --git a/docs/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js b/docs/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// 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/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 4c3bed4c..53e4e1d3 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
@@ -94,13 +94,13 @@ -
+

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2021-02-03

+

Last change 17 November 2016 (rebuilt 2021-02-15)

Source: vignettes/FOCUS_L.rmd @@ -126,17 +126,17 @@ 
 m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version used for fitting:    1.0.0 
+
## mkin version used for fitting:    1.0.3 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Wed Feb  3 17:32:16 2021 
-## Date of summary: Wed Feb  3 17:32:16 2021 
+## Date of fit:     Mon Feb 15 13:46:25 2021 
+## Date of summary: Mon Feb 15 13:46:25 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.031 s
+## Fitted using 133 model solutions performed in 0.032 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -232,17 +232,17 @@
 
## Warning in sqrt(1/diag(V)): NaNs produced

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

-
## mkin version used for fitting:    1.0.0 
+
## mkin version used for fitting:    1.0.3 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Wed Feb  3 17:32:16 2021 
-## Date of summary: Wed Feb  3 17:32:16 2021 
+## Date of fit:     Mon Feb 15 13:46:26 2021 
+## Date of summary: Mon Feb 15 13:46:26 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 380 model solutions performed in 0.085 s
+## Fitted using 369 model solutions performed in 0.083 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -270,22 +270,22 @@
 ## 
 ## Results:
 ## 
-##        AIC      BIC    logLik
-##   95.88778 99.44927 -43.94389
+##        AIC      BIC   logLik
+##   95.88781 99.44929 -43.9439
 ## 
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##           Estimate Std. Error  Lower  Upper
 ## parent_0     92.47     1.2820 89.720 95.220
-## log_alpha    16.92        NaN    NaN    NaN
-## log_beta     19.26        NaN    NaN    NaN
-## sigma         2.78     0.4501  1.814  3.745
+## log_alpha    13.78        NaN    NaN    NaN
+## log_beta     16.13        NaN    NaN    NaN
+## sigma         2.78     0.4598  1.794  3.766
 ## 
 ## Parameter correlation:
-##           parent_0 log_alpha log_beta    sigma
-## parent_0  1.000000       NaN      NaN 0.002218
-## log_alpha      NaN         1      NaN      NaN
-## log_beta       NaN       NaN        1      NaN
-## sigma     0.002218       NaN      NaN 1.000000
+##            parent_0 log_alpha log_beta     sigma
+## parent_0  1.0000000       NaN      NaN 0.0001671
+## log_alpha       NaN         1      NaN       NaN
+## log_beta        NaN       NaN        1       NaN
+## sigma     0.0001671       NaN      NaN 1.0000000
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -293,9 +293,9 @@
 ## for estimators of untransformed parameters.
 ##           Estimate t value Pr(>t)  Lower  Upper
 ## parent_0 9.247e+01      NA     NA 89.720 95.220
-## alpha    2.223e+07      NA     NA     NA     NA
-## beta     2.325e+08      NA     NA     NA     NA
-## sigma    2.780e+00      NA     NA  1.814  3.745
+## alpha    9.658e+05      NA     NA     NA     NA
+## beta     1.010e+07      NA     NA     NA     NA
+## sigma    2.780e+00      NA     NA  1.794  3.766
 ## 
 ## FOCUS Chi2 error levels in percent:
 ##          err.min n.optim df
@@ -344,10 +344,10 @@
 

 
 summary(m.L2.FOMC, data = FALSE)

-
## mkin version used for fitting:    1.0.0 
+
## mkin version used for fitting:    1.0.3 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Wed Feb  3 17:32:17 2021 
-## Date of summary: Wed Feb  3 17:32:17 2021 
+## Date of fit:     Mon Feb 15 13:46:26 2021 
+## Date of summary: Mon Feb 15 13:46:26 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -389,10 +389,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09
-## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.617e-07
-## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.386e-07
-## sigma     -7.436e-09 -1.617e-07 -1.386e-07  1.000e+00
+## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09
+## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.602e-07
+## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.372e-07
+## sigma     -7.828e-09 -1.602e-07 -1.372e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -425,10 +425,10 @@
 

 
 summary(m.L2.DFOP, data = FALSE)

-
## mkin version used for fitting:    1.0.0 
+
## mkin version used for fitting:    1.0.3 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Wed Feb  3 17:32:17 2021 
-## Date of summary: Wed Feb  3 17:32:17 2021 
+## Date of fit:     Mon Feb 15 13:46:27 2021 
+## Date of summary: Mon Feb 15 13:46:27 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -437,7 +437,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.133 s
+## Fitted using 581 model solutions performed in 0.134 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -468,18 +468,18 @@
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##          Estimate Std. Error      Lower     Upper
 ## parent_0   93.950  9.998e-01    91.5900   96.3100
-## log_k1      3.117  1.929e+03 -4558.0000 4564.0000
+## log_k1      3.112  1.842e+03 -4353.0000 4359.0000
 ## log_k2     -1.088  6.285e-02    -1.2370   -0.9394
 ## g_qlogis   -0.399  9.946e-02    -0.6342   -0.1638
 ## sigma       1.414  2.886e-01     0.7314    2.0960
 ## 
 ## Parameter correlation:
-##           parent_0     log_k1     log_k2   g_qlogis      sigma
-## parent_0 1.000e+00  6.459e-07  9.147e-11  2.665e-01  8.413e-11
-## log_k1   6.459e-07  1.000e+00  1.061e-04 -2.087e-04 -9.802e-06
-## log_k2   9.147e-11  1.061e-04  1.000e+00 -7.903e-01 -2.429e-09
-## g_qlogis 2.665e-01 -2.087e-04 -7.903e-01  1.000e+00  4.049e-09
-## sigma    8.413e-11 -9.802e-06 -2.429e-09  4.049e-09  1.000e+00
+##            parent_0     log_k1     log_k2   g_qlogis      sigma
+## parent_0  1.000e+00  6.783e-07 -3.390e-10  2.665e-01 -2.967e-10
+## log_k1    6.783e-07  1.000e+00  1.116e-04 -2.196e-04 -1.031e-05
+## log_k2   -3.390e-10  1.116e-04  1.000e+00 -7.903e-01  2.917e-09
+## g_qlogis  2.665e-01 -2.196e-04 -7.903e-01  1.000e+00 -4.408e-09
+## sigma    -2.967e-10 -1.031e-05  2.917e-09 -4.408e-09  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -487,7 +487,7 @@
 ## for estimators of untransformed parameters.
 ##          Estimate   t value    Pr(>t)   Lower   Upper
 ## parent_0  93.9500 9.397e+01 2.036e-12 91.5900 96.3100
-## k1        22.5800 5.303e-04 4.998e-01  0.0000     Inf
+## k1        22.4800 5.553e-04 4.998e-01  0.0000     Inf
 ## k2         0.3369 1.591e+01 4.697e-07  0.2904  0.3909
 ## g          0.4016 1.680e+01 3.238e-07  0.3466  0.4591
 ## sigma      1.4140 4.899e+00 8.776e-04  0.7314  2.0960
@@ -499,7 +499,7 @@
 ## 
 ## Estimated disappearance times:
 ##          DT50  DT90 DT50back DT50_k1 DT50_k2
-## parent 0.5335 5.311    1.599  0.0307   2.058

+## parent 0.5335 5.311    1.599 0.03084   2.058

 
Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.
@@ -531,10 +531,10 @@

We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

 summary(mm.L3[["DFOP", 1]])
-
## mkin version used for fitting:    1.0.0 
+
## mkin version used for fitting:    1.0.3 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Wed Feb  3 17:32:18 2021 
-## Date of summary: Wed Feb  3 17:32:18 2021 
+## Date of fit:     Mon Feb 15 13:46:27 2021 
+## Date of summary: Mon Feb 15 13:46:28 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -581,11 +581,11 @@
 ## 
 ## Parameter correlation:
 ##            parent_0     log_k1     log_k2   g_qlogis      sigma
-## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -9.671e-08
-## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  7.148e-07
+## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -9.664e-08
+## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  7.147e-07
 ## log_k2    2.282e-02  4.945e-01  1.000e+00 -6.812e-01  1.022e-06
-## g_qlogis  4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -7.929e-07
-## sigma    -9.671e-08  7.148e-07  1.022e-06 -7.929e-07  1.000e+00
+## g_qlogis  4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -7.926e-07
+## sigma    -9.664e-08  7.147e-07  1.022e-06 -7.926e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -644,17 +644,17 @@
 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
 summary(mm.L4[["SFO", 1]], data = FALSE)

-
## mkin version used for fitting:    1.0.0 
+
## mkin version used for fitting:    1.0.3 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Wed Feb  3 17:32:19 2021 
-## Date of summary: Wed Feb  3 17:32:19 2021 
+## Date of fit:     Mon Feb 15 13:46:28 2021 
+## Date of summary: Mon Feb 15 13:46:28 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.03 s
+## Fitted using 142 model solutions performed in 0.031 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -709,17 +709,17 @@
 ## parent  106  352

 
 summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version used for fitting:    1.0.0 
+
## mkin version used for fitting:    1.0.3 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Wed Feb  3 17:32:19 2021 
-## Date of summary: Wed Feb  3 17:32:19 2021 
+## Date of fit:     Mon Feb 15 13:46:28 2021 
+## Date of summary: Mon Feb 15 13:46:28 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.046 s
+## Fitted using 224 model solutions performed in 0.047 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -754,10 +754,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.456e-07
-## log_alpha -4.696e-01  1.000e+00  9.889e-01  2.169e-08
-## log_beta  -5.543e-01  9.889e-01  1.000e+00  4.910e-08
-## sigma     -2.456e-07  2.169e-08  4.910e-08  1.000e+00
+## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07
+## log_alpha -4.696e-01  1.000e+00  9.889e-01  2.478e-08
+## log_beta  -5.543e-01  9.889e-01  1.000e+00  5.211e-08
+## sigma     -2.468e-07  2.478e-08  5.211e-08  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -781,7 +781,7 @@
 

 

 References

-

+

 

 
Ranke, Johannes. 2014. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.

 

diff --git a/docs/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// 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/FOCUS_L_files/header-attrs-2.6/header-attrs.js b/docs/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// 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/index.html b/docs/articles/index.html
index 52770090..22753e8d 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
       
       
         mkin
-        1.0.2
+        1.0.3
       
     

 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index e240323f..6dbb093d 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -94,13 +94,13 @@
 
       
 
-      

+      

   

     

       
Introduction to mkin

                         
Johannes Ranke

             
-            
2021-02-03

+            
Last change 15 February 2021 (rebuilt 2021-02-15)

       
       Source: vignettes/mkin.rmd
       
@@ -148,28 +148,34 @@
 

 

 Background

-
Many approaches are possible regarding the evaluation of chemical degradation data.

-
The mkin package (Ranke 2019) implements the approach recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe (FOCUS Work Group on Degradation Kinetics 2006, 2014) for simple decline data series, data series with transformation products, commonly termed metabolites, and for data series for more than one compartment. It is also possible to include back reactions, so equilibrium reactions and equilibrium partitioning can be specified, although this oftentimes leads to an overparameterisation of the model.

+
The mkin package (Ranke 2021) implements the approach to degradation kinetics recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe (FOCUS Work Group on Degradation Kinetics 2006, 2014). It covers data series describing the decline of one compound, data series with transformation products (commonly termed metabolites) and data series for more than one compartment. It is possible to include back reactions. Therefore, equilibrium reactions and equilibrium partitioning can be specified, although this often leads to an overparameterisation of the model.

 
When the first mkin code was published in 2010, the most commonly used tools for fitting more complex kinetic degradation models to experimental data were KinGUI (Schäfer et al. 2007), a MATLAB based tool with a graphical user interface that was specifically tailored to the task and included some output as proposed by the FOCUS Kinetics Workgroup, and ModelMaker, a general purpose compartment based tool providing infrastructure for fitting dynamic simulation models based on differential equations to data.

-
The code was first uploaded to the BerliOS platform. When this was taken down, the version control history was imported into the R-Forge site (see e.g. the initial commit on 11 May 2010), where the code is still occasionally updated.

-
At that time, the R package FME (Flexible Modelling Environment) (Soetaert and Petzoldt 2010) was already available, and provided a good basis for developing a package specifically tailored to the task. The remaining challenge was to make it as easy as possible for the users (including the author of this vignette) to specify the system of differential equations and to include the output requested by the FOCUS guidance, such as the relative standard deviation that has to be assumed for the residuals, such that the \(\chi^2\) goodness-of-fit test as defined by the FOCUS kinetics workgroup would pass using an significance level \(\alpha\) of 0.05. This relative error, expressed as a percentage, is often termed \(\chi^2\) error level or similar.

-
Also, mkin introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to mkin for the case of linear differential equations (i.e. where the FOMC or DFOP models were not used for the parent compound), greatly improving the optimization speed for these cases. This, however, has become somehow obsolete, as the use of compiled code described below gives even smaller execution times.

+
The ‘mkin’ code was first uploaded to the BerliOS development platform. When this was taken down, the version control history was imported into the R-Forge site (see e.g. the initial commit on 11 May 2010), where the code is still being updated.

+
At that time, the R package FME (Flexible Modelling Environment) (Soetaert and Petzoldt 2010) was already available, and provided a good basis for developing a package specifically tailored to the task. The remaining challenge was to make it as easy as possible for the users (including the author of this vignette) to specify the system of differential equations and to include the output requested by the FOCUS guidance, such as the \(\chi^2\) error level as defined in this guidance.

+
Also, mkin introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to mkin for the case of linear differential equations (i.e. where the FOMC or DFOP models were not used for the parent compound), greatly improving the optimization speed for these cases. This, has become somehow obsolete, as the use of compiled code described below gives even faster execution times.

 
The possibility to specify back-reactions and a biphasic model (SFORB) for metabolites were present in mkin from the very beginning.

 

 

 Derived software tools

-
Soon after the publication of mkin, two derived tools were published, namely KinGUII (available from Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical user interface (GUI), and added fitting by iteratively reweighted least squares (IRLS) and characterisation of likely parameter distributions by Markov Chain Monte Carlo (MCMC) sampling.

-
CAKE focuses on a smooth use experience, sacrificing some flexibility in the model definition, originally allowing only two primary metabolites in parallel. The current version 3.3 of CAKE release in March 2016 uses a basic scheme for up to six metabolites in a flexible arrangement, but does not support back-reactions (non-instantaneous equilibria) or biphasic kinetics for metabolites.

+
Soon after the publication of mkin, two derived tools were published, namely KinGUII (developed at Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical user interface (GUI), and added fitting by iteratively reweighted least squares (IRLS) and characterisation of likely parameter distributions by Markov Chain Monte Carlo (MCMC) sampling.

+
CAKE focuses on a smooth use experience, sacrificing some flexibility in the model definition, originally allowing only two primary metabolites in parallel. The current version 3.4 of CAKE released in May 2020 uses a scheme for up to six metabolites in a flexible arrangement and supports biphasic modelling of metabolites, but does not support back-reactions (non-instantaneous equilibria).

 
KinGUI offers an even more flexible widget for specifying complex kinetic models. Back-reactions (non-instantaneous equilibria) were supported early on, but until 2014, only simple first-order models could be specified for transformation products. Starting with KinGUII version 2.1, biphasic modelling of metabolites was also available in KinGUII.

 
A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named gmkin. Please see its documentation page and manual for further information.

 
A comparison of scope, usability and numerical results obtained with these tools has been recently been published by Ranke, Wöltjen, and Meinecke (2018).

 

-

-

-Recent developments

-
Currently (July 2019), the main features available in mkin which are not present in KinGUII or CAKE, are the speed increase by using compiled code when a compiler is present, parallel model fitting on multicore machines using the mmkin function, and the estimation of parameter confidence intervals based on transformed parameters.

-
In addition, the possibility to use two alternative error models to constant variance have been integrated. The variance by variable error model introduced by Gao et al. (2011) has been available via an iteratively reweighted least squares (IRLS) procedure since mkin version 0.9-22. With release 0.9.49.5, the IRLS algorithm has been replaced by direct or step-wise maximisation of the likelihood function, which makes it possible not only to fit the variance by variable error model but also a two-component error model inspired by error models developed in analytical chemistry.

 

+

+

+Unique features

+
Currently, the main unique features available in mkin are

+
    
+
  • the speed increase by using compiled code when a compiler is present,
    • 
+
  • parallel model fitting on multicore machines using the mmkin function,
    • 
+
  • the estimation of parameter confidence intervals based on transformed parameters (see below) and
    • 
+
  • the possibility to use the two-component error model
+
    • 
+

+
The iteratively reweighted least squares fitting of different variances for each variable as introduced by Gao et al. (2011) has been available in mkin since version 0.9-22. With release 0.9.49.5, the IRLS algorithm has been complemented by direct or step-wise maximisation of the likelihood function, which makes it possible not only to fit the variance by variable error model but also a two-component error model inspired by error models developed in analytical chemistry (Ranke and Meinecke 2019).

 

 

 

@@ -177,13 +183,13 @@
 
For rate constants, the log transformation is used, as proposed by Bates and Watts (1988, 77, 149). Approximate intervals are constructed for the transformed rate constants (compare Bates and Watts 1988, 135), i.e. for their logarithms. Confidence intervals for the rate constants are then obtained using the appropriate backtransformation using the exponential function.

 
In the first version of mkin allowing for specifying models using formation fractions, a home-made reparameterisation was used in order to ensure that the sum of formation fractions would not exceed unity.

 
This method is still used in the current version of KinGUII (v2.1 from April 2014), with a modification that allows for fixing the pathway to sink to zero. CAKE uses penalties in the objective function in order to enforce this constraint.

-
In 2012, an alternative reparameterisation of the formation fractions was proposed together with René Lehmann (Ranke and Lehmann 2012), based on isometric logratio transformation (ILR). The aim was to improve the validity of the linear approximation of the objective function during the parameter estimation procedure as well as in the subsequent calculation of parameter confidence intervals.

+
In 2012, an alternative reparameterisation of the formation fractions was proposed together with René Lehmann (Ranke and Lehmann 2012), based on isometric logratio transformation (ILR). The aim was to improve the validity of the linear approximation of the objective function during the parameter estimation procedure as well as in the subsequent calculation of parameter confidence intervals. In the current version of mkin, a logit transformation is used for parameters that are bound between 0 and 1, such as the g parameter of the DFOP model.

 

 

 Confidence intervals based on transformed parameters

 
In the first attempt at providing improved parameter confidence intervals introduced to mkin in 2013, confidence intervals obtained from FME on the transformed parameters were simply all backtransformed one by one to yield asymmetric confidence intervals for the backtransformed parameters.

 
However, while there is a 1:1 relation between the rate constants in the model and the transformed parameters fitted in the model, the parameters obtained by the isometric logratio transformation are calculated from the set of formation fractions that quantify the paths to each of the compounds formed from a specific parent compound, and no such 1:1 relation exists.

-
Therefore, parameter confidence intervals for formation fractions obtained with this method only appear valid for the case of a single transformation product, where only one formation fraction is to be estimated, directly corresponding to one component of the ilr transformed parameter.

+
Therefore, parameter confidence intervals for formation fractions obtained with this method only appear valid for the case of a single transformation product, where currently the logit transformation is used for the formation fraction.

 
The confidence intervals obtained by backtransformation for the cases where a 1:1 relation between transformed and original parameter exist are considered by the author of this vignette to be more accurate than those obtained using a re-estimation of the Hessian matrix after backtransformation, as implemented in the FME package.

 

 

@@ -198,36 +204,39 @@
 

 References

 
-

+

 

 
Bates, D., and D. Watts. 1988. Nonlinear Regression and Its Applications. Wiley-Interscience.

 

 

-
FOCUS Work Group on Degradation Kinetics. 2006. Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. Report of the Focus Work Group on Degradation Kinetics. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

+
FOCUS Work Group on Degradation Kinetics. 2006. Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. Report of the Focus Work Group on Degradation Kinetics. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

 

 

-
———. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

+
———. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

 

 

-
Gao, Z., J.W. Green, J. Vanderborght, and W. Schmitt. 2011. “Improving Uncertainty Analysis in Kinetic Evaluations Using Iteratively Reweighted Least Squares.” Journal. Environmental Science and Technology 45: 4429–37.

+
Gao, Z., J. W. Green, J. Vanderborght, and W. Schmitt. 2011. “Improving Uncertainty Analysis in Kinetic Evaluations Using Iteratively Reweighted Least Squares.” Journal. Environmental Science and Technology 45: 4429–37.

 

 

-
Ranke, J. 2019. ‘mkin‘: Kinetic Evaluation of Chemical Degradation Data. https://CRAN.R-project.org/package=mkin.

+
Ranke, J. 2021. ‘mkin‘: Kinetic Evaluation of Chemical Degradation Data. https://CRAN.R-project.org/package=mkin.

 

 

 
Ranke, J., and R. Lehmann. 2012. “Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.” In SETAC World 20-24 May. Berlin.

 

 

-
———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In XV Symposium on Pesticide Chemistry 2-4 September 2015. Piacenza. http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf.

+
———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In XV Symposium on Pesticide Chemistry 2-4 September 2015. Piacenza. http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf.

+

+

+
Ranke, Johannes, and Stefan Meinecke. 2019. “Error Models for the Kinetic Evaluation of Chemical Degradation Data.” Environments 6 (12). https://doi.org/10.3390/environments6120124.

 

 

-
Ranke, Johannes, Janina Wöltjen, and Stefan Meinecke. 2018. “Comparison of Software Tools for Kinetic Evaluation of Chemical Degradation Data.” Environmental Sciences Europe 30 (1): 17. https://doi.org/10.1186/s12302-018-0145-1.

+
Ranke, Johannes, Janina Wöltjen, and Stefan Meinecke. 2018. “Comparison of Software Tools for Kinetic Evaluation of Chemical Degradation Data.” Environmental Sciences Europe 30 (1): 17. https://doi.org/10.1186/s12302-018-0145-1.

 

 

 
Schäfer, D., B. Mikolasch, P. Rainbird, and B. Harvey. 2007. “KinGUI: A New Kinetic Software Tool for Evaluations According to FOCUS Degradation Kinetics.” In Proceedings of the Xiii Symposium Pesticide Chemistry, edited by Del Re A. A. M., Capri E., Fragoulis G., and Trevisan M., 916–23. Piacenza.

 

 

-
Soetaert, Karline, and Thomas Petzoldt. 2010. “Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME.” Journal of Statistical Software 33 (3): 1–28. https://www.jstatsoft.org/v33/i03/.

+
Soetaert, Karline, and Thomas Petzoldt. 2010. “Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME.” Journal of Statistical Software 33 (3): 1–28. https://www.jstatsoft.org/v33/i03/.

 

 

 

diff --git a/docs/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// 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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+  }
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diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index 8acd92af..bf38fdd7 100644
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diff --git a/docs/articles/mkin_files/header-attrs-2.6/header-attrs.js b/docs/articles/mkin_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/mkin_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// 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);
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+});
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index c270659b..2e3d2f96 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -94,13 +94,13 @@
 
       
 
-      

+      

   

     

       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2021-02-03

+            
Last change 18 September 2019 (rebuilt 2021-02-15)

       
       Source: vignettes/twa.rmd
       
@@ -141,9 +141,9 @@
   \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
   \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) \]

 
Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the max_twa_parent() function. If the same is needed for metabolites, the function pfm::max_twa() from the ‘pfm’ package can be used.

-

+

 

-
FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

+
FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

 

 

   

diff --git a/docs/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// 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/twa_files/header-attrs-2.6/header-attrs.js b/docs/articles/twa_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/twa_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// 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/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 8bdcbe30..57fc3545 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -94,13 +94,13 @@
 
       
 
-      

+      

   

     

       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2021-02-03

+            
Last change 16 January 2018 (rebuilt 2021-02-15)

       
       Source: vignettes/web_only/FOCUS_Z.rmd
       
@@ -237,12 +237,12 @@
 
 summary(m.Z.FOCUS, data = FALSE)$bpar

 
##             Estimate se_notrans t value     Pr(>t)     Lower      Upper
-## Z0_0       96.839001   1.994273 48.5585 4.0276e-42 92.827060 100.850943
-## k_Z0        2.215367   0.118456 18.7021 1.0410e-23  1.989432   2.466960
-## k_Z1        0.478310   0.028258 16.9265 6.2430e-22  0.424712   0.538673
-## k_Z2        0.451628   0.042139 10.7176 1.6313e-14  0.374337   0.544877
-## k_Z3        0.058692   0.015245  3.8498 1.7806e-04  0.034806   0.098972
-## f_Z2_to_Z3  0.471498   0.058350  8.0805 9.6614e-11  0.357741   0.588294
+## Z0_0       96.838822   1.994274 48.5584 4.0280e-42 92.826981 100.850664
+## k_Z0        2.215393   0.118458 18.7019 1.0413e-23  1.989456   2.466989
+## k_Z1        0.478305   0.028258 16.9266 6.2418e-22  0.424708   0.538666
+## k_Z2        0.451627   0.042139 10.7176 1.6314e-14  0.374339   0.544872
+## k_Z3        0.058692   0.015245  3.8499 1.7803e-04  0.034808   0.098965
+## f_Z2_to_Z3  0.471502   0.058351  8.0805 9.6608e-11  0.357769   0.588274
 ## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736

 
 endpoints(m.Z.FOCUS)

@@ -253,9 +253,9 @@
 ## $distimes
 ##        DT50    DT90
 ## Z0  0.31288  1.0394
-## Z1  1.44916  4.8140
+## Z1  1.44917  4.8141
 ## Z2  1.53478  5.0984
-## Z3 11.80983 39.2314

+## Z3 11.80986 39.2315

 
This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.
@@ -351,13 +351,13 @@ ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471371 0.0075126 0.0800070 0.0000000 +## 2.4471322 0.0075125 0.0800069 0.0000000 ## ## $distimes ## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.35666 0.28325 92.265 NA NA +## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA ## Z1 1.5148 5.0320 NA NA NA NA NA -## Z2 1.6414 5.4525 NA NA NA NA NA +## Z2 1.6414 5.4526 NA NA NA NA NA ## Z3 NA NA NA NA NA 8.6636 Inf

It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.

@@ -365,9 +365,9 @@

References

-
+
-

FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

+

FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

diff --git a/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// 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 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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 47d46a9f..e7501cbb 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/FOCUS_Z_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// 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.html b/docs/articles/web_only/NAFTA_examples.html index d3e23253..e79375b3 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -31,7 +31,7 @@ mkin - 1.0.0 + 1.0.3
@@ -94,13 +94,13 @@ -
+

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

Johannes Ranke

-

2021-02-03

+

26 February 2019 (rebuilt 2021-02-15)

Source: vignettes/web_only/NAFTA_examples.rmd @@ -156,7 +156,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.42e-12 5.00e-01 0.0000 Inf +## k2 2.26e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## @@ -165,7 +165,7 @@ ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.22e+11 2.86e+11 +## DFOP 55.5 5.59e+11 3.07e+11 ## ## Representative half-life: ## [1] 321.51 @@ -207,7 +207,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 1.10e-11 5.00e-01 0.0000 Inf +## k2 8.63e-12 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -216,7 +216,7 @@ ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.03e+11 6.29e+10 +## DFOP 83.6 1.32e+11 8.04e+10 ## ## Representative half-life: ## [1] 215.87 @@ -258,7 +258,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.60e-11 5.00e-01 0.0000 Inf +## k2 3.22e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## @@ -267,7 +267,7 @@ ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 9.07e+09 1.93e+10 +## DFOP 34.1 1.01e+10 2.15e+10 ## ## Representative half-life: ## [1] 53.17 @@ -309,7 +309,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 2.89e-10 5.00e-01 0.0000 Inf +## k2 3.63e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## @@ -318,7 +318,7 @@ ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 4.75e+09 2.40e+09 +## DFOP 96.4 3.77e+09 1.91e+09 ## ## Representative half-life: ## [1] 454.55 @@ -420,7 +420,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 9.03e-13 5.00e-01 0.000 Inf +## k2 9.02e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## @@ -429,7 +429,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.38e+12 7.67e+11 +## DFOP 10.5 1.38e+12 7.69e+11 ## ## Representative half-life: ## [1] 101.43 @@ -441,15 +441,16 @@ 
 p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])
## Warning in sqrt(diag(covar)): NaNs produced
+
## Warning in sqrt(diag(covar_notrans)): 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
## 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)

 

-
+
 print(p9b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -473,12 +474,12 @@
 ## sigma             1.288 1.76e-04  0.7456  1.830
 ## 
 ## $DFOP
-##          Estimate Pr(>t)   Lower   Upper
-## parent_0  94.7123     NA 93.1355 96.2891
-## k1         0.0389     NA  0.0266  0.0569
-## k2         0.0389     NA  0.0255  0.0592
-## g          0.5256     NA      NA      NA
-## sigma      1.5957     NA  0.9135  2.2779
+##          Estimate   Pr(>t)   Lower   Upper
+## parent_0  94.7123 1.61e-16 93.1355 96.2891
+## k1         0.0389 1.08e-04  0.0266  0.0569
+## k2         0.0389 2.23e-04  0.0255  0.0592
+## g          0.5256      NaN      NA      NA
+## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
 ## DTx values:
@@ -494,15 +495,18 @@
 

 

 Example on page 10

-
+
 p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])

-
## Warning in sqrt(diag(covar_notrans)): NaNs produced

+
## 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

 
## 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)

 

-
+
 print(p10)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -528,9 +532,9 @@
 ## $DFOP
 ##          Estimate   Pr(>t)   Lower    Upper
 ## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## k1         0.0495 5.63e-03  0.0240   0.1020
-## k2         0.0495 1.93e-03  0.0272   0.0903
-## g          0.4487      NaN  0.0000   1.0000
+## k1         0.0495 6.58e-03  0.0303   0.0809
+## k2         0.0495 2.60e-03  0.0410   0.0598
+## g          0.4487 5.00e-01      NA       NA
 ## sigma      8.0152 2.50e-04  4.5886  11.4418
 ## 
 ## 
@@ -551,14 +555,14 @@
 

 

 Example on page 11

-
+
 p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])

 
## 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)

 

-
+
 print(p11)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -594,10 +598,10 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.16e+02 7.18e+02 2.16e+02
 ## IORE 9.73e+02 1.37e+08 4.11e+07
-## DFOP 3.07e+11 1.93e+12 6.97e+11
+## DFOP 3.07e+11 1.93e+12 6.98e+11
 ## 
 ## Representative half-life:
-## [1] 41148171

+## [1] 41148170

 
In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.

 

 

@@ -608,19 +612,21 @@
 

 

 Example on page 12, upper panel

-
+
 p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])

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

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

+
## Warning in sqrt(diag(covar_notrans)): 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

 
## 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)

 

-
+
 print(p12a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -644,12 +650,12 @@
 ## sigma             3.965     NA    NA    NA
 ## 
 ## $DFOP
-##          Estimate   Pr(>t) Lower Upper
-## parent_0  100.521 2.74e-10    NA    NA
-## k1          0.124 2.53e-05    NA    NA
-## k2          0.124 2.52e-02    NA    NA
-## g           0.793 5.00e-01    NA    NA
-## sigma       7.048 2.50e-04    NA    NA
+##          Estimate   Pr(>t)   Lower   Upper
+## parent_0  100.521 2.74e-10 92.2366 108.805
+## k1          0.124 2.53e-05  0.0908   0.170
+## k2          0.124 2.52e-02  0.0456   0.339
+## g           0.793      NaN      NA      NA
+## sigma       7.048 2.50e-04  4.0349  10.061
 ## 
 ## 
 ## DTx values:
@@ -664,20 +670,18 @@
 

 

 Example on page 12, lower panel

-
+
 p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])

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

 
## Warning in qt(alpha/2, rdf): NaNs produced

 
## Warning in qt(1 - alpha/2, rdf): 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 sqrt(diag(covar_notrans)): NaNs produced

+
## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced

 
## 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)

 

-
+
 print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -702,11 +706,11 @@
 ## 
 ## $DFOP
 ##          Estimate Pr(>t) Lower Upper
-## parent_0  97.6840     NA   NaN   NaN
-## k1         0.0589     NA    NA    NA
-## k2         0.0589     NA    NA    NA
-## g          0.6473     NA    NA    NA
-## sigma      3.4323     NA   NaN   NaN
+## parent_0  97.6840    NaN   NaN   NaN
+## k1         0.0589    NaN    NA    NA
+## k2         0.0589    NaN    NA    NA
+## g          0.6473    NaN    NA    NA
+## sigma      3.4323    NaN   NaN   NaN
 ## 
 ## 
 ## DTx values:
@@ -721,18 +725,14 @@
 

 

 Example on page 13

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

-
## 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

 
## 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)

 

-
+
 print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -758,9 +758,9 @@
 ## $DFOP
 ##          Estimate Pr(>t)    Lower    Upper
 ## parent_0 92.73500     NA 8.95e+01 95.92118
-## k1        0.00258     NA 4.25e-04  0.01569
-## k2        0.00258     NA 1.76e-03  0.00379
-## g         0.16452     NA       NA       NA
+## k1        0.00258     NA 4.14e-04  0.01611
+## k2        0.00258     NA 1.74e-03  0.00383
+## g         0.16452     NA 0.00e+00  1.00000
 ## sigma     3.41172     NA 2.02e+00  4.79960
 ## 
 ## 
@@ -777,7 +777,7 @@
 

 

 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

@@ -785,10 +785,10 @@
 ## doubtful

 
## 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)

 

-
+
 print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -815,7 +815,7 @@
 ##          Estimate   Pr(>t)    Lower    Upper
 ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768
 ## k1       9.53e-03 1.20e-01  0.00638   0.0143
-## k2       5.33e-12 5.00e-01  0.00000      Inf
+## k2       6.08e-12 5.00e-01  0.00000      Inf
 ## g        3.98e-01 2.19e-01  0.30481   0.4998
 ## sigma    1.17e+00 7.68e-06  0.77406   1.5610
 ## 
@@ -824,7 +824,7 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.48e+02 8.25e+02 2.48e+02
 ## IORE 4.34e+02 2.22e+04 6.70e+03
-## DFOP 3.48e+10 3.37e+11 1.30e+11
+## DFOP 3.05e+10 2.95e+11 1.14e+11
 ## 
 ## Representative half-life:
 ## [1] 6697.44

@@ -833,14 +833,14 @@
 

 

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

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

 
## 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)

 

-
+
 print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -864,12 +864,12 @@
 ## sigma             3.105 1.78e-04  1.795  4.416
 ## 
 ## $DFOP
-##          Estimate Pr(>t)    Lower    Upper
-## parent_0 97.96751     NA 94.21913 101.7159
-## k1        0.00952     NA  0.00221   0.0411
-## k2        0.00952     NA  0.00626   0.0145
-## g         0.21241     NA  0.00000   1.0000
-## sigma     4.18778     NA  2.39747   5.9781
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0 97.96751 2.85e-13 94.21913 101.7159
+## k1        0.00952 6.28e-02  0.00250   0.0363
+## k2        0.00952 1.27e-04  0.00646   0.0140
+## g         0.21241 5.00e-01  0.00000   1.0000
+## sigma     4.18778 2.50e-04  2.39747   5.9781
 ## 
 ## 
 ## DTx values:
@@ -880,7 +880,7 @@
 ## 
 ## Representative half-life:
 ## [1] 41.33

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

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

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

@@ -888,10 +888,10 @@
 ## doubtful

 
## 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)

 

-
+
 print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
@@ -909,7 +909,7 @@
 ## 
 ## $IORE
 ##                Estimate   Pr(>t)    Lower  Upper
-## parent_0          99.83 1.81e-16 97.51348 102.14
+## parent_0          99.83 1.81e-16 97.51349 102.14
 ## k__iore_parent     0.38 3.22e-01  0.00352  41.05
 ## N_parent           0.00 5.00e-01 -1.07696   1.08
 ## sigma              2.21 2.57e-04  1.23245   3.19
@@ -936,16 +936,16 @@
 

 

 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)

 

-
+
 print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -996,7 +996,7 @@
 

 

 References

-

+

 

 
US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing 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
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// 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/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
index bfe9b278..f5420ce8 100644
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diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png
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diff --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 0d111357..3ce13a97 100644
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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 73b85767..e2cf2f83 100644
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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
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// 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 e15358a0..d7b81f20 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -94,13 +94,13 @@
 
       
 
-      

+      

   

     

       
Benchmark timings for mkin

                         
Johannes Ranke

             
-            
2021-02-03

+            
Last change 13 May 2020 (rebuilt 2021-02-15)

       
       Source: vignettes/web_only/benchmarks.rmd
       
@@ -135,17 +135,11 @@
   m1 = mkinsub("SFO"))
 t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]
 t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
-    error_model = "tc"))[["elapsed"]]

-
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## iteration limit reached without convergence (10)
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## iteration limit reached without convergence (10)

-
-t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
+    error_model = "tc"))[["elapsed"]]
+t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
     error_model = "obs"))[["elapsed"]]

 
Two metabolites, synthetic data:

-
+
 m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
                            M2 = mkinsub("SFO"),
@@ -172,7 +166,7 @@
     error_model = "obs"))[["elapsed"]]
 t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
     error_model = "obs"))[["elapsed"]]

-
+
 mkin_benchmarks[system_string, paste0("t", 1:11)] <-
   c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
 save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")

@@ -234,9 +228,9 @@
 3.729
 
 
-1.0.0
-1.770
-3.703
+1.0.3
+1.722
+3.419
 
 
 
@@ -302,10 +296,10 @@
 2.810
 
 
-1.0.0
-1.373
-7.127
-2.762
+1.0.3
+1.402
+6.343
+2.802
 
 
 
@@ -313,7 +307,7 @@
 

 

 Two metabolites

-
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.

+
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.

 
@@ -398,13 +392,13 @@
 
-
-
-
-
-
-
-
+
+
+
+
+
+
+

 

 mkin version3.105
 

 
1.0.00.7751.2691.4673.7671.9192.9421.0.30.7711.2511.4643.0741.9402.831
 

 
 

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
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// 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
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// 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 e45655b6..ce8d8481 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -94,13 +94,13 @@
 
       
 
-      

+      

   

     

       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2021-02-03

+            
2021-02-15

       
       Source: vignettes/web_only/compiled_models.rmd
       
@@ -159,9 +159,9 @@
 }

 
##                    test replications relative elapsed
 ## 4            analytical            1    1.000   0.181
-## 3     deSolve, compiled            1    1.818   0.329
-## 2      Eigenvalue based            1    2.061   0.373
-## 1 deSolve, not compiled            1   43.923   7.950

+## 3     deSolve, compiled            1    1.812   0.328
+## 2      Eigenvalue based            1    2.088   0.378
+## 1 deSolve, not compiled            1   45.923   8.312

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

 

 

@@ -188,13 +188,13 @@
 }

 
## Temporary DLL for differentials generated and loaded

 
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.474
-## 1 deSolve, not compiled            1   30.179  14.305

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

-
This vignette was built with mkin 1.0.0 on

+## 2     deSolve, compiled            1    1.000   0.486
+## 1 deSolve, not compiled            1   31.597  15.356

+
Here we get a performance benefit of a factor of 32 using the version of the differential equation model compiled from C code!

+
This vignette was built with mkin 1.0.3 on

 
## R version 4.0.3 (2020-10-10)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Debian GNU/Linux 10 (buster)

+## Running under: Debian GNU/Linux bullseye/sid

 
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor

 

   

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
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// 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
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// 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);
+  }
+});
-- 
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