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-rw-r--r--docs/reference/DFOP.solution.html9
-rw-r--r--docs/reference/Extract.mmkin.html11
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html9
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html9
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html9
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html9
-rw-r--r--docs/reference/FOCUS_2006_datasets.html9
-rw-r--r--docs/reference/FOMC.solution.html7
-rw-r--r--docs/reference/HS.solution.html7
-rw-r--r--docs/reference/IORE.solution.html7
-rw-r--r--docs/reference/SFO.solution.html7
-rw-r--r--docs/reference/SFORB.solution.html7
-rw-r--r--docs/reference/add_err.html9
-rw-r--r--docs/reference/endpoints.html9
-rw-r--r--docs/reference/geometric_mean.html7
-rw-r--r--docs/reference/ilr.html9
-rw-r--r--docs/reference/mccall81_245T.html29
-rw-r--r--docs/reference/mkin_long_to_wide.html9
-rw-r--r--docs/reference/mkin_wide_to_long.html9
-rw-r--r--docs/reference/mkinerrmin.html9
-rw-r--r--docs/reference/mkinfit.html83
-rw-r--r--docs/reference/mkinmod.html11
-rw-r--r--docs/reference/mkinparplot.html9
-rw-r--r--docs/reference/mkinplot.html6
-rw-r--r--docs/reference/mkinpredict.html15
-rw-r--r--docs/reference/mkinresplot.html6
-rw-r--r--docs/reference/mkinsub.html9
-rw-r--r--docs/reference/mmkin.html13
-rw-r--r--docs/reference/plot.mkinfit.html9
29 files changed, 238 insertions, 113 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index ed30ee50..bad6dd57 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Double First-Order in Parallel kinetics — DFOP.solution • mkin</title>
+<title>
+ — DFOP.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Double First-Order in Parallel kinetics</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 4ef3bb00..0131342a 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -72,6 +72,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -239,7 +242,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.064 0.000 0.065
+#&gt; 0.068 0.000 0.066
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -428,7 +431,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5ce33e0&gt;
+#&gt; &lt;environment: 0x3b9eeb8&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -450,7 +453,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5ce33e0&gt;
+#&gt; &lt;environment: 0x3b9eeb8&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -513,7 +516,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Thu Dec 8 07:56:34 2016&quot;
+#&gt; [1] &quot;Wed Mar 15 09:44:44 2017&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index df8280d7..fff99b6c 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title>
+<title>
+ — FOCUS_2006_DFOP_ref_A_to_B • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 6132388f..5c9feb23 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title>
+<title>
+ — FOCUS_2006_FOMC_ref_A_to_F • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index 86b071cf..8ccbd86a 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin</title>
+<title>
+ — FOCUS_2006_HS_ref_A_to_F • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index b2d199d3..263b9b31 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin</title>
+<title>
+ — FOCUS_2006_SFO_ref_A_to_F • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index cde972b7..71dbe761 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin</title>
+<title>
+ — FOCUS_2006_datasets • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Datasets A to F from the FOCUS Kinetics report from 2006</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 932935b4..8d0ed869 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title>
+<title> First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +72,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +95,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>First-Order Multi-Compartment kinetics</h1>
+ <h1> First-Order Multi-Compartment kinetics </h1>
</div>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 2d0b6e4f..b8e6f524 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Hockey-Stick kinetics — HS.solution • mkin</title>
+<title> Hockey-Stick kinetics — HS.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +72,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +95,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Hockey-Stick kinetics</h1>
+ <h1> Hockey-Stick kinetics </h1>
</div>
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 35e01039..8caef574 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Indeterminate order rate equation kinetics — IORE.solution • mkin</title>
+<title> Indeterminate order rate equation kinetics — IORE.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +72,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +95,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Indeterminate order rate equation kinetics</h1>
+ <h1> Indeterminate order rate equation kinetics </h1>
</div>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 3fa6d1d4..e2c93102 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Single First-Order kinetics — SFO.solution • mkin</title>
+<title> Single First-Order kinetics — SFO.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +72,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +95,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Single First-Order kinetics</h1>
+ <h1> Single First-Order kinetics </h1>
</div>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index d4661cfd..4a73ba9e 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title>
+<title> Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +72,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +95,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Single First-Order Reversible Binding kinetics</h1>
+ <h1> Single First-Order Reversible Binding kinetics </h1>
</div>
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index edced046..aab42f56 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title>
+<title>
+ — add_err • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Add normally distributed errors to simulated kinetic degradation data</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 38a6a400..4145825a 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin</title>
+<title>
+ — endpoints • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 03b9f54b..828ec471 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Calculate the geometric mean — geometric_mean • mkin</title>
+<title> Calculate the geometric mean — geometric_mean • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +72,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +95,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Calculate the geometric mean</h1>
+ <h1> Calculate the geometric mean </h1>
</div>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 85f203ed..4262fa81 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to perform isometric log-ratio transformation — ilr • mkin</title>
+<title>
+ — ilr • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to perform isometric log-ratio transformation</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 123af096..4fa32b30 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title>
+<title>
+ — mccall81_245T • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1>
+ <h1>
+</h1>
</div>
@@ -128,10 +133,10 @@
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
-#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:56:42 2016
-#&gt; Date of summary: Thu Dec 8 07:56:42 2016
+#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:44:52 2017
+#&gt; Date of summary: Wed Mar 15 09:44:52 2017
#&gt;
#&gt;
#&gt; Warning: Optimisation by method Port did not converge.
@@ -146,7 +151,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 590 model solutions performed in 3.474 s
+#&gt; Fitted with method Port using 590 model solutions performed in 3.519 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -223,10 +228,10 @@
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:56:44 2016
-#&gt; Date of summary: Thu Dec 8 07:56:44 2016
+ <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:44:54 2017
+#&gt; Date of summary: Wed Mar 15 09:44:54 2017
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -236,7 +241,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.44 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.449 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index af7daf7a..9b37726e 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Convert a dataframe from long to wide format — mkin_long_to_wide • mkin</title>
+<title>
+ — mkin_long_to_wide • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Convert a dataframe from long to wide format</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 75417aec..378d3691 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin</title>
+<title>
+ — mkin_wide_to_long • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Convert a dataframe with observations over time into long format</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index a69920fd..97616a41 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title>
+<title>
+ — mkinerrmin • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Calculate the minimum error to assume in order to pass the variance test</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 3dd701d3..01c930e2 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title>
+<title>
+ — mkinfit • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Fit a kinetic model to data with one or more state variables</h1>
+ <h1>
+</h1>
</div>
@@ -372,17 +377,17 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:56:46 2016
-#&gt; Date of summary: Thu Dec 8 07:56:46 2016
+<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:44:56 2017
+#&gt; Date of summary: Wed Mar 15 09:44:56 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.145 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.146 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -451,7 +456,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; user system elapsed
-#&gt; 1.172 1.232 0.904 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 1.216 1.268 0.942 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -528,7 +533,7 @@
#&gt; Model cost at call 152 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; user system elapsed
-#&gt; 0.712 0.044 0.709 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.712 0.040 0.703 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -569,10 +574,10 @@
<span class='co'># Weighted fits, including IRLS</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:56:57 2016
-#&gt; Date of summary: Thu Dec 8 07:56:57 2016
+<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:45:07 2017
+#&gt; Date of summary: Wed Mar 15 09:45:07 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -580,7 +585,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.77 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.753 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -690,10 +695,10 @@
#&gt; 100 m1 33.13 3.198e+01 1.148e+00
#&gt; 120 m1 25.15 2.879e+01 -3.640e+00
#&gt; 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:56:59 2016
-#&gt; Date of summary: Thu Dec 8 07:56:59 2016
+<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:45:09 2017
+#&gt; Date of summary: Wed Mar 15 09:45:09 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -701,7 +706,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 486 model solutions performed in 2.019 s
+#&gt; Fitted with method Port using 486 model solutions performed in 2.091 s
#&gt;
#&gt; Weighting: none then iterative reweighting method obs
#&gt;
@@ -811,10 +816,10 @@
#&gt; 100 m1 33.13 3.199e+01 1.140e+00 2.722
#&gt; 120 m1 25.15 2.881e+01 -3.659e+00 2.722
#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:57:00 2016
-#&gt; Date of summary: Thu Dec 8 07:57:00 2016
+<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:45:10 2017
+#&gt; Date of summary: Wed Mar 15 09:45:10 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -822,7 +827,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.65 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.661 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -933,10 +938,10 @@
#&gt; 120 m1 25.15 28.824128 -3.674128
#&gt; 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:57:01 2016
-#&gt; Date of summary: Thu Dec 8 07:57:01 2016
+<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:45:11 2017
+#&gt; Date of summary: Wed Mar 15 09:45:11 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -944,7 +949,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.713 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.724 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1055,10 +1060,10 @@
<span class='no'>errors</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'>&lt;-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>]
<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:57:02 2016
-#&gt; Date of summary: Thu Dec 8 07:57:02 2016
+<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:45:12 2017
+#&gt; Date of summary: Wed Mar 15 09:45:12 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1066,7 +1071,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 316 model solutions performed in 1.322 s
+#&gt; Fitted with method Port using 316 model solutions performed in 1.31 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1177,10 +1182,10 @@
#&gt; 120 m1 25.15 28.760615 -3.610615 2
#&gt; 120 m1 33.31 28.760615 4.549385 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Dec 8 07:57:05 2016
-#&gt; Date of summary: Thu Dec 8 07:57:05 2016
+<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
+#&gt; R version: 3.3.3
+#&gt; Date of fit: Wed Mar 15 09:45:15 2017
+#&gt; Date of summary: Wed Mar 15 09:45:15 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1188,7 +1193,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 648 model solutions performed in 2.818 s
+#&gt; Fitted with method Port using 648 model solutions performed in 2.766 s
#&gt;
#&gt; Weighting: manual then iterative reweighting method obs
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 1044af6b..1343abcc 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title>
+<title>
+ — mkinmod • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to set up a kinetic model with one or more state variables</h1>
+ <h1>
+</h1>
</div>
@@ -188,7 +193,7 @@
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file386742883b12.c 2&gt; file386742883b12.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file2ac5b2884c1.c 2&gt; file2ac5b2884c1.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 744de866..0682211b 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin</title>
+<title>
+ — mkinparplot • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to plot the confidence intervals obtained using mkinfit</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 898b1b9f..fdc61af4 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin</title>
+<title>
+ — mkinplot • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -95,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Plot the observed data and the fitted model of an mkinfit object</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 766b6613..2348d40e 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title>
+<title>
+ — mkinpredict • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Produce predictions from a kinetic model using specific parameters</h1>
+ <h1>
+</h1>
</div>
@@ -290,17 +295,17 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.012 0.020 0.005 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.016 0.016 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.000 0.020 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.016 0.004 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.032 0.000 0.035 </div></pre>
+#&gt; 0.032 0.000 0.034 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index a6527aa4..fd5722bc 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title>
+<title>
+ — mkinresplot • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -95,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to plot residuals stored in an mkin object</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index bad034ee..aff0b593 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to set up a kinetic submodel for one state variable — mkinsub • mkin</title>
+<title>
+ — mkinsub • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to set up a kinetic submodel for one state variable</h1>
+ <h1>
+</h1>
</div>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 0127f114..67397827 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title>
+<title>
+ — mmkin • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1>
+ <h1>
+</h1>
</div>
@@ -158,8 +163,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_default</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 16.776 0.108 9.353 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 22.696 0.000 22.701 </div><div class='input'>
+#&gt; 16.360 0.128 9.017 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 21.888 0.004 21.892 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340479 0.2659521 0.7505687 0.2494313
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 9969e198..e77b7b54 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -6,7 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title>
+<title>
+ — plot.mkinfit • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -72,6 +73,9 @@
</li>
</ul>
</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -92,7 +96,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Plot the observed data and the fitted model of an mkinfit object</h1>
+ <h1>
+</h1>
</div>

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