From 3a5463672c297b37c3c9135c8b144c48744c05d0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 31 Mar 2021 19:42:17 +0200 Subject: Bug fix in plot.mkinfit In residual plots, use xlab and xlim if appropriate --- NEWS.md | 4 +- R/plot.mkinfit.R | 2 +- build.log | 2 +- check.log | 14 ++- docs/articles/FOCUS_D.html | 16 +-- docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 79176 -> 79749 bytes .../FOCUS_D_files/figure-html/plot_2-1.png | Bin 24025 -> 24279 bytes .../FOCUS_D_files/header-attrs-2.7/header-attrs.js | 12 ++ docs/articles/FOCUS_L.html | 62 +++++----- .../figure-html/unnamed-chunk-10-1.png | Bin 42203 -> 42472 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 82006 -> 83163 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 32751 -> 33123 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 57939 -> 58647 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 35238 -> 35678 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 21999 -> 22090 bytes 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docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js diff --git a/NEWS.md b/NEWS.md index 36847cb8..9d03fa3d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,9 @@ # mkin 1.0.4 (Unreleased) -- 'plot.mixed.mmkin': Reset graphical parameters on exit - - All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters +- 'plot.mkinfit': Use xlab and xlim for the residual plot if show_residuals is TRUE + # mkin 1.0.3 (2021-02-15) - Review and update README, the 'Introduction to mkin' vignette and some of the help pages diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 2e319aae..1d4ea543 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -278,7 +278,7 @@ plot.mkinfit <- function(x, fit = x, if (show_residuals) { mkinresplot(fit, obs_vars = row_obs_vars, standardized = standardized, pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars], - legend = FALSE, frame = frame, xlab = xlab) + legend = FALSE, frame = frame, xlab = xlab, xlim = xlim) } # Show error model plot if requested diff --git a/build.log b/build.log index ff0d2fb3..e94b33f0 100644 --- a/build.log +++ b/build.log @@ -6,5 +6,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.0.3.tar.gz’ +* building ‘mkin_1.0.4.tar.gz’ diff --git a/check.log b/check.log index 34732605..0d04e05e 100644 --- a/check.log +++ b/check.log @@ -1,14 +1,16 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.0.3 (2020-10-10) +* using R version 4.0.4 (2021-02-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.0.3’ +* this is package ‘mkin’ version ‘1.0.4’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... NOTE Maintainer: ‘Johannes Ranke ’ + +The Date field is over a month old. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK @@ -67,5 +69,9 @@ Maintainer: ‘Johannes Ranke ’ * checking for detritus in the temp directory ... OK * DONE -Status: OK +Status: 1 NOTE +See + ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ +for details. + diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 08acf58b..1bfba6e5 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -31,7 +31,7 @@ mkin - 1.0.3 + 1.0.4 @@ -94,13 +94,13 @@ -
+

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

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

+

Last change 31 January 2019 (rebuilt 2021-03-31)

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:    1.0.3 
-## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Feb 15 17:50:27 2021 
-## Date of summary: Mon Feb 15 17:50:28 2021 
+
## mkin version used for fitting:    1.0.4 
+## R version used for fitting:       4.0.4 
+## Date of fit:     Wed Mar 31 19:18:28 2021 
+## Date of summary: Wed Mar 31 19:18:29 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 0.159 s
 ## 
 ## Error model: Constant variance 
 ## 
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new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/FOCUS_D_files/header-attrs-2.7/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 ab9739bc..7074816c 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.3
+        1.0.4
@@ -94,13 +94,13 @@ -
+

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

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

+

Last change 17 November 2016 (rebuilt 2021-03-31)

Source: vignettes/FOCUS_L.rmd @@ -126,10 +126,10 @@ 
 m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version used for fitting:    1.0.3 
-## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Feb 15 17:50:30 2021 
-## Date of summary: Mon Feb 15 17:50:30 2021 
+
## mkin version used for fitting:    1.0.4 
+## R version used for fitting:       4.0.4 
+## Date of fit:     Wed Mar 31 19:18:31 2021 
+## Date of summary: Wed Mar 31 19:18:31 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -232,10 +232,10 @@
 
## 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:    1.0.3 
-## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Feb 15 17:50:31 2021 
-## Date of summary: Mon Feb 15 17:50:31 2021 
+
## mkin version used for fitting:    1.0.4 
+## R version used for fitting:       4.0.4 
+## Date of fit:     Wed Mar 31 19:18:32 2021 
+## Date of summary: Wed Mar 31 19:18:32 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -344,10 +344,10 @@
 

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

-
## mkin version used for fitting:    1.0.3 
-## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Feb 15 17:50:31 2021 
-## Date of summary: Mon Feb 15 17:50:31 2021 
+
## mkin version used for fitting:    1.0.4 
+## R version used for fitting:       4.0.4 
+## Date of fit:     Wed Mar 31 19:18:32 2021 
+## Date of summary: Wed Mar 31 19:18:32 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -425,10 +425,10 @@
 

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

-
## mkin version used for fitting:    1.0.3 
-## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Feb 15 17:50:32 2021 
-## Date of summary: Mon Feb 15 17:50:32 2021 
+
## mkin version used for fitting:    1.0.4 
+## R version used for fitting:       4.0.4 
+## Date of fit:     Wed Mar 31 19:18:33 2021 
+## Date of summary: Wed Mar 31 19:18:33 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -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:    1.0.3 
-## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Feb 15 17:50:32 2021 
-## Date of summary: Mon Feb 15 17:50:32 2021 
+
## mkin version used for fitting:    1.0.4 
+## R version used for fitting:       4.0.4 
+## Date of fit:     Wed Mar 31 19:18:33 2021 
+## Date of summary: Wed Mar 31 19:18:33 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -644,10 +644,10 @@
 
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:    1.0.3 
-## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Feb 15 17:50:33 2021 
-## Date of summary: Mon Feb 15 17:50:33 2021 
+
## mkin version used for fitting:    1.0.4 
+## R version used for fitting:       4.0.4 
+## Date of fit:     Wed Mar 31 19:18:34 2021 
+## Date of summary: Wed Mar 31 19:18:34 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -709,10 +709,10 @@
 ## parent  106  352

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

-
## mkin version used for fitting:    1.0.3 
-## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Feb 15 17:50:33 2021 
-## Date of summary: Mon Feb 15 17:50:33 2021 
+
## mkin version used for fitting:    1.0.4 
+## R version used for fitting:       4.0.4 
+## Date of fit:     Wed Mar 31 19:18:34 2021 
+## Date of summary: Wed Mar 31 19:18:34 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
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new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/FOCUS_L_files/header-attrs-2.7/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/mkin.html b/docs/articles/mkin.html
index 6dbb093d..a0fccc16 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.3
+        1.0.4
@@ -94,13 +94,13 @@ -
+

Introduction to mkin

Johannes Ranke

-

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

+

Last change 15 February 2021 (rebuilt 2021-03-31)

Source: vignettes/mkin.rmd 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 bf38fdd7..8a182047 100644 Binary files a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/docs/articles/mkin_files/header-attrs-2.7/header-attrs.js b/docs/articles/mkin_files/header-attrs-2.7/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/mkin_files/header-attrs-2.7/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/twa.html b/docs/articles/twa.html index 2e3d2f96..167f60d3 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -31,7 +31,7 @@ mkin - 1.0.3 + 1.0.4
@@ -94,13 +94,13 @@ -
+

Calculation of time weighted average concentrations with mkin

Johannes Ranke

-

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

+

Last change 18 September 2019 (rebuilt 2021-03-31)

Source: vignettes/twa.rmd diff --git a/docs/articles/twa_files/header-attrs-2.7/header-attrs.js b/docs/articles/twa_files/header-attrs-2.7/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/twa_files/header-attrs-2.7/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 57fc3545..e4a6cb52 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -31,7 +31,7 @@ mkin - 1.0.3 + 1.0.4
@@ -94,13 +94,13 @@ -
+

Example evaluation of FOCUS dataset Z

Johannes Ranke

-

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

+

Last change 16 January 2018 (rebuilt 2021-03-31)

Source: vignettes/web_only/FOCUS_Z.rmd diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png index 2213c446..2e70b207 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png index 61b04d3a..4a205020 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png index 409f1203..8b07d497 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png index 4d6820cd..4765c9fe 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png index 2e504961..e005446b 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png index 2213c446..2e70b207 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png index 7ab743af..f06ee667 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png index 2e0dce77..b8e0e900 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png index 458299c1..14dd7805 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png index eb833066..414bc941 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png index e7501cbb..0a83f8ea 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-2.7/header-attrs.js b/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.7/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.7/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 e79375b3..65a71b56 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -31,7 +31,7 @@ mkin - 1.0.3 + 1.0.4
@@ -94,13 +94,13 @@ -
+

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

Johannes Ranke

-

26 February 2019 (rebuilt 2021-02-15)

+

26 February 2019 (rebuilt 2021-03-31)

Source: vignettes/web_only/NAFTA_examples.rmd 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 f5420ce8..b1c874cc 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png index 0ae4bd9f..9dfa26fb 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png index 57a48119..cdae6520 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png and 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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 3ce13a97..efc16dda 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png index e2cf2f83..53addbd2 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png differ diff --git a/docs/articles/web_only/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 new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/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 9908c224..290906c1 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -31,7 +31,7 @@ mkin - 1.0.3 + 1.0.4
@@ -94,13 +94,13 @@ -
+

Benchmark timings for mkin

Johannes Ranke

-

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

+

Last change 13 May 2020 (rebuilt 2021-03-31)

Source: vignettes/web_only/benchmarks.rmd @@ -232,6 +232,11 @@ 1.881 3.504 + +1.0.4 +1.867 +3.450 +
@@ -301,6 +306,12 @@ 6.344 2.798 + +1.0.4 +1.415 +6.364 +2.820 +
@@ -400,6 +411,15 @@ 1.923 2.839 + +1.0.4 +0.785 +1.252 +1.466 +3.091 +1.936 +2.826 +
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 new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/benchmarks_files/header-attrs-2.7/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/news/index.html b/docs/news/index.html index 3a52a093..fae6503a 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -145,8 +145,8 @@

mkin 1.0.4 (Unreleased)

    -

  • ‘plot.mixed.mmkin’: Reset graphical parameters on exit

  • All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters

    • +

  • ‘plot.mkinfit’: Use xlab and xlim for the residual plot if show_residuals is TRUE

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 49dceae1..df454e62 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-02-24T14:04Z +last_built: 2021-03-31T17:15Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index e2d47f1b..c59bfad6 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 5a99cf1b..b1c73ba5 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 1cbcb153..17a35806 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index 745d583d..808f1968 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index 19198739..97f650e2 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png index 1028a9c4..21ad6783 100644 Binary files a/docs/reference/Rplot004.png and b/docs/reference/Rplot004.png differ diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png index aa844051..4828f5b2 100644 Binary files a/docs/reference/Rplot005.png and b/docs/reference/Rplot005.png differ diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png index 81525882..4aed2c87 100644 Binary files a/docs/reference/Rplot006.png and b/docs/reference/Rplot006.png differ diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png index 10b7455a..3405a171 100644 Binary files a/docs/reference/Rplot007.png and b/docs/reference/Rplot007.png differ diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png index 9ba106db..70118923 100644 Binary files a/docs/reference/add_err-1.png and b/docs/reference/add_err-1.png differ diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png index 3088c40e..69b820c2 100644 Binary files a/docs/reference/add_err-2.png and b/docs/reference/add_err-2.png differ diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png index 493a761a..1de78fa7 100644 Binary files a/docs/reference/add_err-3.png and b/docs/reference/add_err-3.png differ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 6fbecd14..18ca517e 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -74,7 +74,7 @@ may depend on the predicted value and is specified as a standard deviation." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 06e78459..e81e0c7b 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> mkin - 1.0.3 + 1.0.4
@@ -285,13 +285,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE) system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#> user system elapsed -#> 4.255 1.029 3.937
# Using more cores does not save much time here, as parent_0 takes up most of the time +#> 3.871 0.000 3.871
# Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of # minor interest), we get a nice performance improvement if we use at least 4 cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#> user system elapsed -#> 1.469 0.092 0.911
ci_profile +#> 1.484 0.116 0.923
ci_profile
#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 6845f74f..3b6ae721 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png index 33946ded..5527c07f 100644 Binary files a/docs/reference/experimental_data_for_UBA-1.png and b/docs/reference/experimental_data_for_UBA-1.png differ diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 77f75678..4da8d6c3 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index aa494b27..a0899ac8 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -73,7 +73,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 61f235db..bbacc554 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -73,7 +73,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 9e5b4069..83fb4e48 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error model." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png index 91fe060e..478462ae 100644 Binary files a/docs/reference/mccall81_245T-1.png and b/docs/reference/mccall81_245T-1.png differ diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index b7dca4a7..4f8d3fa0 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -74,7 +74,7 @@ mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png index 28a376f4..b9454c86 100644 Binary files a/docs/reference/mixed-1.png and b/docs/reference/mixed-1.png differ diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index 23d955e3..b4f8db16 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -72,7 +72,7 @@ mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 5111a9e0..fe89012c 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 003e5e8f..a9686e4c 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -75,7 +75,7 @@ dataset if no data are supplied." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png index de2a90a9..e1d0f2f4 100644 Binary files a/docs/reference/mkinfit-1.png and b/docs/reference/mkinfit-1.png differ diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 180f2ee7..2c162e49 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -80,7 +80,7 @@ likelihood function." /> mkin - 1.0.3 + 1.0.4
@@ -431,10 +431,10 @@ doi: 10.3390/environments6 # Use shorthand notation for parent only degradation fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit) -
#> mkin version used for fitting: 1.0.3 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 13:43:26 2021 -#> Date of summary: Mon Feb 15 13:43:26 2021 +
#> mkin version used for fitting: 1.0.4 +#> R version used for fitting: 4.0.4 +#> Date of fit: Wed Mar 31 19:15:41 2021 +#> Date of summary: Wed Mar 31 19:15:41 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -574,10 +574,10 @@ doi: 10.3390/environments6 analytical = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", solution_type = "analytical")) } -
#> test relative elapsed -#> 3 analytical 1.000 0.550 -#> 1 deSolve_compiled 1.731 0.952 -#> 2 eigen 2.662 1.464
# } +
#> Loading required package: rbenchmark
#> test relative elapsed +#> 3 analytical 1.000 0.547 +#> 1 deSolve_compiled 1.717 0.939 +#> 2 eigen 2.644 1.446
# } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO # \dontrun{ @@ -598,10 +598,10 @@ doi: 10.3390/environments6 #> 2 6 -64.983 -1 0.3075 0.5792
# Also, the missing standard error for log_beta and the t-tests for alpha # and beta indicate overparameterisation summary(fit.FOMC_SFO.tc, data = FALSE) -
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful
#> mkin version used for fitting: 1.0.3 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 13:43:38 2021 -#> Date of summary: Mon Feb 15 13:43:38 2021 +
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful
#> mkin version used for fitting: 1.0.4 +#> R version used for fitting: 4.0.4 +#> Date of fit: Wed Mar 31 19:15:53 2021 +#> Date of summary: Wed Mar 31 19:15:53 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -610,7 +610,7 @@ doi: 10.3390/environments6 #> #> Model predictions using solution type deSolve #> -#> Fitted using 3729 model solutions performed in 2.802 s +#> Fitted using 3729 model solutions performed in 2.798 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 4ce9468a..1e8ad60d 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -78,7 +78,7 @@ mkinmod." /> mkin - 1.0.3 + 1.0.4
@@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

parent = mkinsub("SFO", "m1", full_name = "Test compound"), m1 = mkinsub("SFO", full_name = "Metabolite M1"), name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE) -
#> Copied DLL from /tmp/RtmpiJ2M4Z/filee097a4a94a921.so to /home/jranke/.local/share/mkin/SFO_SFO.so
# Now we can save the model and restore it in a new session +
#> Copied DLL from /tmp/Rtmp17EVw2/file269cfd5cc541a9.so to /home/jranke/.local/share/mkin/SFO_SFO.so
# Now we can save the model and restore it in a new session saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds") # Terminate the R session here if you would like to check, and then do library(mkin) @@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

#> }) #> return(predicted) #> } -#> <environment: 0x55555b0c2760>
+#> <environment: 0x55555c17ae90>
# If we have several parallel metabolites # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) m_synth_DFOP_par <- mkinmod( diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 25e26419..5775ba62 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." /> mkin - 1.0.3 + 1.0.4
@@ -410,8 +410,8 @@ as these always return mapped output.

#> test relative elapsed #> 2 deSolve_compiled 1.0 0.005 #> 4 analytical 1.0 0.005 -#> 1 eigen 4.4 0.022 -#> 3 deSolve 47.0 0.235
+#> 1 eigen 4.0 0.020 +#> 3 deSolve 46.2 0.231
# \dontrun{ # Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE) diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png index ffd34f6f..963aa5b7 100644 Binary files a/docs/reference/mkinresplot-1.png and b/docs/reference/mkinresplot-1.png differ diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 04ff15b8..fe3150e7 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -75,7 +75,7 @@ argument show_residuals = TRUE." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png index 0db3379f..26586ab9 100644 Binary files a/docs/reference/mmkin-1.png and b/docs/reference/mmkin-1.png differ diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png index 024a9892..dbcdd8ee 100644 Binary files a/docs/reference/mmkin-2.png and b/docs/reference/mmkin-2.png differ diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png index a23d7cb9..80245fc6 100644 Binary files a/docs/reference/mmkin-3.png and b/docs/reference/mmkin-3.png differ diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png index 89975db5..328aa564 100644 Binary files a/docs/reference/mmkin-4.png and b/docs/reference/mmkin-4.png differ diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png index a2f34983..9ce5e919 100644 Binary files a/docs/reference/mmkin-5.png and b/docs/reference/mmkin-5.png differ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index c9800fe7..c73d14bf 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -75,7 +75,7 @@ datasets specified in its first two arguments." /> mkin - 1.0.3 + 1.0.4
@@ -234,9 +234,9 @@ plotting.

time_default
#> user system elapsed -#> 4.630 0.415 1.717
time_1 +#> 5.387 0.413 1.864
time_1
#> user system elapsed -#> 5.694 0.000 5.694
+#> 5.786 0.008 5.794
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png index 728cc557..cca4ce0a 100644 Binary files a/docs/reference/nlme-1.png and b/docs/reference/nlme-1.png differ diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png index e8167455..c0d8e857 100644 Binary files a/docs/reference/nlme-2.png and b/docs/reference/nlme-2.png differ diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 7b0c6a97..c6b43aab 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png index 9186c135..90ede880 100644 Binary files a/docs/reference/nlme.mmkin-1.png and b/docs/reference/nlme.mmkin-1.png differ diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png index d395fe02..0d140fd1 100644 Binary files a/docs/reference/nlme.mmkin-2.png and b/docs/reference/nlme.mmkin-2.png differ diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png index 40518a59..8a60b52b 100644 Binary files a/docs/reference/nlme.mmkin-3.png and b/docs/reference/nlme.mmkin-3.png differ diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 189e34ef..03448606 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/parms.html b/docs/reference/parms.html index e45d6a5c..b4346b13 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png index e5da9f1c..54e5c46f 100644 Binary files a/docs/reference/plot.mkinfit-1.png and b/docs/reference/plot.mkinfit-1.png differ diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png index a11d1680..ff8418a3 100644 Binary files a/docs/reference/plot.mkinfit-2.png and b/docs/reference/plot.mkinfit-2.png differ diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png index c976d4b1..54f2b981 100644 Binary files a/docs/reference/plot.mkinfit-3.png and b/docs/reference/plot.mkinfit-3.png differ diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png index c8bc00fe..7a7bfc6c 100644 Binary files a/docs/reference/plot.mkinfit-4.png and b/docs/reference/plot.mkinfit-4.png differ diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png index 6631aa68..6a6741e7 100644 Binary files a/docs/reference/plot.mkinfit-5.png and b/docs/reference/plot.mkinfit-5.png differ diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png index 946b20c5..c4d0b9c7 100644 Binary files a/docs/reference/plot.mkinfit-6.png and b/docs/reference/plot.mkinfit-6.png differ diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png index 10807ea8..802b00ef 100644 Binary files a/docs/reference/plot.mkinfit-7.png and b/docs/reference/plot.mkinfit-7.png differ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index b80c672d..ff6da93e 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png index 647dfb8a..d06d683c 100644 Binary files a/docs/reference/plot.mmkin-1.png and b/docs/reference/plot.mmkin-1.png differ diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png index 1bc1c9db..d3678aca 100644 Binary files a/docs/reference/plot.mmkin-2.png and b/docs/reference/plot.mmkin-2.png differ diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png index 50d6ffac..f84d5782 100644 Binary files a/docs/reference/plot.mmkin-3.png and b/docs/reference/plot.mmkin-3.png differ diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png index e049fa16..9919dacb 100644 Binary files a/docs/reference/plot.mmkin-4.png and b/docs/reference/plot.mmkin-4.png differ diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png index 2421995b..945b863f 100644 Binary files a/docs/reference/plot.mmkin-5.png and b/docs/reference/plot.mmkin-5.png differ diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 20f9033d..3348e050 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -76,7 +76,7 @@ the fit of at least one model to the same dataset is shown." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 864c4ff9..c6d716a1 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -79,7 +79,7 @@ below to see their documentation. mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/sigma_twocomp-1.png b/docs/reference/sigma_twocomp-1.png index 6e61684e..fddb86a7 100644 Binary files a/docs/reference/sigma_twocomp-1.png and b/docs/reference/sigma_twocomp-1.png differ diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 397582f0..1b4e45e4 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -73,7 +73,7 @@ dependence of the measured value \(y\):" /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index d6840425..8df9011d 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally mkin - 1.0.3 + 1.0.4 @@ -265,10 +265,10 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

#> iteration limit reached without convergence (10)
f_nlme <- nlme(f_mmkin)
#> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
summary(f_nlme, data = TRUE)
#> nlme version used for fitting: 3.1.152 -#> mkin version used for pre-fitting: 1.0.3 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 13:46:13 2021 -#> Date of summary: Mon Feb 15 13:46:13 2021 +#> mkin version used for pre-fitting: 1.0.4 +#> R version used for fitting: 4.0.4 +#> Date of fit: Wed Mar 31 19:18:24 2021 +#> Date of summary: Wed Mar 31 19:18:24 2021 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -278,7 +278,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

#> #> Model predictions using solution type analytical #> -#> Fitted in 0.553 s using 4 iterations +#> Fitted in 0.537 s using 4 iterations #> #> Variance model: Two-component variance function #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index c3c756f6..bbaad91e 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." /> mkin - 1.0.3 + 1.0.4
diff --git a/test.log b/test.log index 80b64269..b49088e5 100644 --- a/test.log +++ b/test.log @@ -3,14 +3,14 @@ Loading required package: parallel Testing mkin ✔ | OK F W S | Context ✔ | 5 | AIC calculation -✔ | 2 | Export dataset for reading into CAKE [0.2 s] +✔ | 2 | Export dataset for reading into CAKE ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] -✔ | 7 | Fitting the SFORB model [3.4 s] +✔ | 7 | Fitting the SFORB model [3.5 s] ✔ | 5 | Analytical solutions for coupled models [3.1 s] ✔ | 5 | Calculation of Akaike weights -✔ | 12 | Confidence intervals and p-values [1.1 s] -✔ | 14 | Error model fitting [4.1 s] +✔ | 12 | Confidence intervals and p-values [1.0 s] +✔ | 14 | Error model fitting [4.2 s] ✔ | 5 | Time step normalisation ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] @@ -19,10 +19,27 @@ Testing mkin ✔ | 1 | mkinfit features [0.3 s] ✔ | 10 | Special cases of mkinfit calls [0.3 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] -✔ | 3 | Model predictions with mkinpredict [0.3 s] +✔ | 3 | Model predictions with mkinpredict [0.4 s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] ✔ | 9 | Nonlinear mixed-effects models [7.9 s] -✔ | 14 | Plotting [1.7 s] +✖ | 10 4 | Plotting [1.7 s] +──────────────────────────────────────────────────────────────────────────────── +Failure (test_plot.R:20:3): Plotting mkinfit, mmkin and mixed model objects is reproducible +Figures don't match: mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg + + +Failure (test_plot.R:21:3): Plotting mkinfit, mmkin and mixed model objects is reproducible +Figures don't match: plot-res-for-focus-c.svg + + +Failure (test_plot.R:22:3): Plotting mkinfit, mmkin and mixed model objects is reproducible +Figures don't match: mkinfit-plot-for-focus-c-with-sep-true.svg + + +Failure (test_plot.R:30:3): Plotting mkinfit, mmkin and mixed model objects is reproducible +Figures don't match: plot-res-for-focus-d.svg + +──────────────────────────────────────────────────────────────────────────────── ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s] ✔ | 4 | Summary [0.1 s] @@ -32,6 +49,6 @@ Testing mkin ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.5 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 40.9 s +Duration: 41.0 s -[ FAIL 0 | WARN 0 | SKIP 0 | PASS 174 ] +[ FAIL 4 | WARN 0 | SKIP 0 | PASS 170 ] diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index f1f078db..f740cfc0 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -60,6 +60,15 @@ if (!!window.navigator.userAgent.match("MSIE 8")) { !function(a){"use strict";a.matchMedia=a.matchMedia||function(a){var b,c=a.documentElement,d=c.firstElementChild||c.firstChild,e=a.createElement("body"),f=a.createElement("div");return f.id="mq-test-1",f.style.cssText="position:absolute;top:-100em",e.style.background="none",e.appendChild(f),function(a){return 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