Bug fix in plot.mkinfit

In residual plots, use xlab and xlim if appropriate

33 files changed, 65 insertions, 9 deletions

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 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
       </span>
     </div>
 
@@ -94,13 +94,13 @@
 
       
 
-      </header><script src="FOCUS_Z_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+      </header><script src="FOCUS_Z_files/header-attrs-2.7/header-attrs.js"></script><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">Last change 16 January 2018 (rebuilt 2021-02-15)</h4>
+            <h4 class="date">Last change 16 January 2018 (rebuilt 2021-03-31)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_Z.rmd</code></div>
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
--- 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
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
--- 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
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
--- 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
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
--- 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
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
--- 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
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
--- 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
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
--- 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
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
--- 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
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
--- 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
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
--- 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
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
--- 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
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 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
       </span>
     </div>
 
@@ -94,13 +94,13 @@
 
       
 
-      </header><script src="NAFTA_examples_files/header-attrs-2.6/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+      </header><script src="NAFTA_examples_files/header-attrs-2.7/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</h4>
+            <h4 class="date">26 February 2019 (rebuilt 2021-03-31)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
       <div class="hidden name"><code>NAFTA_examples.rmd</code></div>
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
--- 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
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
--- 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
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
--- 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
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
index c42d45f0..57672896 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
index 52dea51e..1e4995a8 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
index ca1f29be..93bb7173 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png
index f69e6d3b..a2ee7966 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
index 71fcd257..a40bd581 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
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
index 820501a3..690c91ef 100644
--- 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
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png
index e264d2ea..c1284b83 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png
index e5b656a4..d40ad7e7 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png
index c9664c77..8c2ae01b 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png
index a81f814c..fbf566f7 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png
index 75d72e7c..1e137ddf 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png
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 3ce13a97..efc16dda 100644
--- 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
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
--- 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
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 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
       </span>
     </div>
 
@@ -94,13 +94,13 @@
 
       
 
-      </header><script src="benchmarks_files/header-attrs-2.6/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+      </header><script src="benchmarks_files/header-attrs-2.7/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">Last change 13 May 2020 (rebuilt 2021-02-15)</h4>
+            <h4 class="date">Last change 13 May 2020 (rebuilt 2021-03-31)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -232,6 +232,11 @@
 <td align="right">1.881</td>
 <td align="right">3.504</td>
 </tr>
+<tr class="even">
+<td align="left">1.0.4</td>
+<td align="right">1.867</td>
+<td align="right">3.450</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -301,6 +306,12 @@
 <td align="right">6.344</td>
 <td align="right">2.798</td>
 </tr>
+<tr class="even">
+<td align="left">1.0.4</td>
+<td align="right">1.415</td>
+<td align="right">6.364</td>
+<td align="right">2.820</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -400,6 +411,15 @@
 <td align="right">1.923</td>
 <td align="right">2.839</td>
 </tr>
+<tr class="even">
+<td align="left">1.0.4</td>
+<td align="right">0.785</td>
+<td align="right">1.252</td>
+<td align="right">1.466</td>
+<td align="right">3.091</td>
+<td align="right">1.936</td>
+<td align="right">2.826</td>
+</tr>
 </tbody>
 </table>
 </div>
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);
+  }
+});