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-rw-r--r--docs/reference/index.html6
-rw-r--r--docs/reference/mkinfit.html576
-rw-r--r--docs/reference/sigma_rl.html167
3 files changed, 466 insertions, 283 deletions
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 54886c94..4675748c 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -337,6 +337,12 @@
<p><code><a href="ilr.html">ilr</a></code> <code><a href="ilr.html">invilr</a></code> </p>
</td>
<td><p>Function to perform isometric log-ratio transformation</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="sigma_rl.html">sigma_rl</a></code> </p>
+ </td>
+ <td><p>Two component error model of Rocke and Lorenzato</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index cdf7c7ef..0102aecb 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -70,6 +70,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +86,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -130,7 +128,9 @@
<span class='kw'>control.modFit</span> <span class='kw'>=</span> <span class='fu'>list</span>(),
<span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"none"</span>,
+ <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>weight</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"none"</span>, <span class='st'>"std"</span>, <span class='st'>"mean"</span>, <span class='st'>"tc"</span>),
+ <span class='kw'>tc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>sigma_low</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>rsd_high</span> <span class='kw'>=</span> <span class='fl'>0.07</span>),
<span class='kw'>scaleVar</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>,
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
@@ -293,7 +293,13 @@
<tr>
<th>weight</th>
<td><p>only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of "none",
- "std", "mean", see details of <code>modCost</code>.</p></td>
+ "std", "mean", see details of <code>modCost</code>, or "tc" for the
+ two component error model of Rocke and Lorenzato.</p></td>
+ </tr>
+ <tr>
+ <th>tc</th>
+ <td><p>The two components of the Rocke and Lorenzato error model as used
+ for (initial) weighting</p></td>
</tr>
<tr>
<th>scaleVar</th>
@@ -321,12 +327,19 @@
<th>reweight.method</th>
<td><p>The method used for iteratively reweighting residuals, also known
as iteratively reweighted least squares (IRLS). Default is NULL,
- the other method implemented is called "obs", meaning that each
- observed variable is assumed to have its own variance, this is
- estimated from the fit and used for weighting the residuals
- in each iteration until convergence of this estimate up to
+ i.e. no iterative weighting.
+ The first reweighting method is called "obs", meaning that each
+ observed variable is assumed to have its own variance. This variance
+ is estimated from the fit (mean squared residuals) and used for weighting
+ the residuals in each iteration until convergence of this estimate up to
<code>reweight.tol</code> or up to the maximum number of iterations
- specified by <code>reweight.max.iter</code>.</p></td>
+ specified by <code>reweight.max.iter</code>.
+ The second reweighting method is called "tc" (two-component error model).
+ When using this method, the two components of the error model according
+ to Rocke and Lorenzato (1995) are estimated from the fit and the resulting
+ variances are used for weighting the residuals in each iteration until
+ convergence of these components or up to the maximum number of iterations
+ specified.</p></td>
</tr>
<tr>
<th>reweight.tol</th>
@@ -373,21 +386,26 @@
numerical ODE solver. In this situation it may help to switch off the
internal rate transformation.</p>
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
+ measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
+
<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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:18 2017
-#&gt; Date of summary: Sat Jul 29 15:14:18 2017
+<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.47.1
+#&gt; R version: 3.4.3
+#&gt; Date of fit: Tue Jan 30 10:05:48 2018
+#&gt; Date of summary: Tue Jan 30 10:05:48 2018
#&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 0.141 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.31 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -456,7 +474,7 @@
<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; 0.888 0.000 0.890 </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; 1.196 0.000 1.195 </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
@@ -535,7 +553,7 @@
#&gt; Model cost at call 153 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; user system elapsed
-#&gt; 0.728 0.000 0.729 </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; 1.008 0.000 1.006 </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
@@ -576,10 +594,10 @@
<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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:28 2017
-#&gt; Date of summary: Sat Jul 29 15:14:28 2017
+<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.47.1
+#&gt; R version: 3.4.3
+#&gt; Date of fit: Tue Jan 30 10:06:00 2018
+#&gt; Date of summary: Tue Jan 30 10:06:00 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -587,7 +605,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.746 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.739 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -653,54 +671,50 @@
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 9.960e+01 -1.385e-01
-#&gt; 0 parent 102.04 9.960e+01 2.442e+00
-#&gt; 1 parent 93.50 9.024e+01 3.262e+00
-#&gt; 1 parent 92.50 9.024e+01 2.262e+00
-#&gt; 3 parent 63.23 7.407e+01 -1.084e+01
-#&gt; 3 parent 68.99 7.407e+01 -5.083e+00
-#&gt; 7 parent 52.32 4.991e+01 2.408e+00
-#&gt; 7 parent 55.13 4.991e+01 5.218e+00
-#&gt; 14 parent 27.27 2.501e+01 2.257e+00
-#&gt; 14 parent 26.64 2.501e+01 1.627e+00
-#&gt; 21 parent 11.50 1.253e+01 -1.035e+00
-#&gt; 21 parent 11.64 1.253e+01 -8.946e-01
-#&gt; 35 parent 2.85 3.148e+00 -2.979e-01
-#&gt; 35 parent 2.91 3.148e+00 -2.379e-01
-#&gt; 50 parent 0.69 7.162e-01 -2.624e-02
-#&gt; 50 parent 0.63 7.162e-01 -8.624e-02
-#&gt; 75 parent 0.05 6.074e-02 -1.074e-02
-#&gt; 75 parent 0.06 6.074e-02 -7.381e-04
-#&gt; 100 parent NA 5.151e-03 NA
-#&gt; 100 parent NA 5.151e-03 NA
-#&gt; 120 parent NA 7.155e-04 NA
-#&gt; 120 parent NA 7.155e-04 NA
-#&gt; 0 m1 0.00 0.000e+00 0.000e+00
-#&gt; 0 m1 0.00 0.000e+00 0.000e+00
-#&gt; 1 m1 4.84 4.803e+00 3.704e-02
-#&gt; 1 m1 5.64 4.803e+00 8.370e-01
-#&gt; 3 m1 12.91 1.302e+01 -1.140e-01
-#&gt; 3 m1 12.96 1.302e+01 -6.400e-02
-#&gt; 7 m1 22.97 2.504e+01 -2.075e+00
-#&gt; 7 m1 24.47 2.504e+01 -5.748e-01
-#&gt; 14 m1 41.69 3.669e+01 5.000e+00
-#&gt; 14 m1 33.21 3.669e+01 -3.480e+00
-#&gt; 21 m1 44.37 4.165e+01 2.717e+00
-#&gt; 21 m1 46.44 4.165e+01 4.787e+00
-#&gt; 35 m1 41.22 4.331e+01 -2.093e+00
-#&gt; 35 m1 37.95 4.331e+01 -5.363e+00
-#&gt; 50 m1 41.19 4.122e+01 -2.831e-02
-#&gt; 50 m1 40.01 4.122e+01 -1.208e+00
-#&gt; 75 m1 40.09 3.645e+01 3.643e+00
-#&gt; 75 m1 33.85 3.645e+01 -2.597e+00
-#&gt; 100 m1 31.04 3.198e+01 -9.416e-01
-#&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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:30 2017
-#&gt; Date of summary: Sat Jul 29 15:14:30 2017
+#&gt; 0 parent 99.46 99.59848 -1.385e-01
+#&gt; 0 parent 102.04 99.59848 2.442e+00
+#&gt; 1 parent 93.50 90.23787 3.262e+00
+#&gt; 1 parent 92.50 90.23787 2.262e+00
+#&gt; 3 parent 63.23 74.07319 -1.084e+01
+#&gt; 3 parent 68.99 74.07319 -5.083e+00
+#&gt; 7 parent 52.32 49.91206 2.408e+00
+#&gt; 7 parent 55.13 49.91206 5.218e+00
+#&gt; 14 parent 27.27 25.01257 2.257e+00
+#&gt; 14 parent 26.64 25.01257 1.627e+00
+#&gt; 21 parent 11.50 12.53462 -1.035e+00
+#&gt; 21 parent 11.64 12.53462 -8.946e-01
+#&gt; 35 parent 2.85 3.14787 -2.979e-01
+#&gt; 35 parent 2.91 3.14787 -2.379e-01
+#&gt; 50 parent 0.69 0.71624 -2.624e-02
+#&gt; 50 parent 0.63 0.71624 -8.624e-02
+#&gt; 75 parent 0.05 0.06074 -1.074e-02
+#&gt; 75 parent 0.06 0.06074 -7.381e-04
+#&gt; 0 m1 0.00 0.00000 0.000e+00
+#&gt; 0 m1 0.00 0.00000 0.000e+00
+#&gt; 1 m1 4.84 4.80296 3.704e-02
+#&gt; 1 m1 5.64 4.80296 8.370e-01
+#&gt; 3 m1 12.91 13.02400 -1.140e-01
+#&gt; 3 m1 12.96 13.02400 -6.400e-02
+#&gt; 7 m1 22.97 25.04476 -2.075e+00
+#&gt; 7 m1 24.47 25.04476 -5.748e-01
+#&gt; 14 m1 41.69 36.69002 5.000e+00
+#&gt; 14 m1 33.21 36.69002 -3.480e+00
+#&gt; 21 m1 44.37 41.65310 2.717e+00
+#&gt; 21 m1 46.44 41.65310 4.787e+00
+#&gt; 35 m1 41.22 43.31312 -2.093e+00
+#&gt; 35 m1 37.95 43.31312 -5.363e+00
+#&gt; 50 m1 41.19 41.21831 -2.831e-02
+#&gt; 50 m1 40.01 41.21831 -1.208e+00
+#&gt; 75 m1 40.09 36.44703 3.643e+00
+#&gt; 75 m1 33.85 36.44703 -2.597e+00
+#&gt; 100 m1 31.04 31.98163 -9.416e-01
+#&gt; 100 m1 33.13 31.98163 1.148e+00
+#&gt; 120 m1 25.15 28.78984 -3.640e+00
+#&gt; 120 m1 33.31 28.78984 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: 0.9.47.1
+#&gt; R version: 3.4.3
+#&gt; Date of fit: Tue Jan 30 10:06:02 2018
+#&gt; Date of summary: Tue Jan 30 10:06:02 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -708,9 +722,14 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 468 model solutions performed in 1.914 s
+#&gt; Fitted with method Port using 523 model solutions performed in 2.151 s
+#&gt;
+#&gt; Weighting: none
#&gt;
-#&gt; Weighting: none then iterative reweighting method obs
+#&gt; Iterative reweighting with method obs
+#&gt; Final mean squared residuals of observed variables:
+#&gt; parent m1
+#&gt; 11.573408 7.407845
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -739,10 +758,10 @@
#&gt;
#&gt; Parameter correlation:
#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
-#&gt; parent_0 1.0000 0.5083 -0.1979 -0.6147
+#&gt; parent_0 1.0000 0.5083 -0.1979 -0.6148
#&gt; log_k_parent 0.5083 1.0000 -0.3894 -0.6062
#&gt; log_k_m1 -0.1979 -0.3894 1.0000 0.7417
-#&gt; f_parent_ilr_1 -0.6147 -0.6062 0.7417 1.0000
+#&gt; f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000
#&gt;
#&gt; Residual standard error: 1.054 on 36 degrees of freedom
#&gt;
@@ -751,9 +770,9 @@
#&gt; t-test (unrealistically) based on the assumption of normal distribution
#&gt; for estimators of untransformed parameters.
#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.67000 55.630 8.181e-37 96.040000 1.033e+02
+#&gt; parent_0 99.67000 55.630 8.184e-37 96.040000 1.033e+02
#&gt; k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01
-#&gt; k_m1 0.00524 7.996 8.487e-10 0.004066 6.753e-03
+#&gt; k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03
#&gt; f_parent_to_m1 0.51340 23.000 2.038e-23 0.468100 5.584e-01
#&gt;
#&gt; Chi2 error levels in percent:
@@ -774,54 +793,50 @@
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual err
-#&gt; 0 parent 99.46 9.967e+01 -2.122e-01 3.402
-#&gt; 0 parent 102.04 9.967e+01 2.368e+00 3.402
-#&gt; 1 parent 93.50 9.027e+01 3.228e+00 3.402
-#&gt; 1 parent 92.50 9.027e+01 2.228e+00 3.402
-#&gt; 3 parent 63.23 7.405e+01 -1.082e+01 3.402
-#&gt; 3 parent 68.99 7.405e+01 -5.056e+00 3.402
-#&gt; 7 parent 52.32 4.982e+01 2.499e+00 3.402
-#&gt; 7 parent 55.13 4.982e+01 5.309e+00 3.402
-#&gt; 14 parent 27.27 2.490e+01 2.367e+00 3.402
-#&gt; 14 parent 26.64 2.490e+01 1.737e+00 3.402
-#&gt; 21 parent 11.50 1.245e+01 -9.476e-01 3.402
-#&gt; 21 parent 11.64 1.245e+01 -8.076e-01 3.402
-#&gt; 35 parent 2.85 3.110e+00 -2.600e-01 3.402
-#&gt; 35 parent 2.91 3.110e+00 -2.000e-01 3.402
-#&gt; 50 parent 0.69 7.037e-01 -1.374e-02 3.402
-#&gt; 50 parent 0.63 7.037e-01 -7.374e-02 3.402
-#&gt; 75 parent 0.05 5.913e-02 -9.133e-03 3.402
-#&gt; 75 parent 0.06 5.913e-02 8.666e-04 3.402
-#&gt; 100 parent NA 4.969e-03 NA 3.402
-#&gt; 100 parent NA 4.969e-03 NA 3.402
-#&gt; 120 parent NA 6.852e-04 NA 3.402
-#&gt; 120 parent NA 6.852e-04 NA 3.402
-#&gt; 0 m1 0.00 0.000e+00 0.000e+00 2.722
-#&gt; 0 m1 0.00 0.000e+00 0.000e+00 2.722
-#&gt; 1 m1 4.84 4.813e+00 2.672e-02 2.722
-#&gt; 1 m1 5.64 4.813e+00 8.267e-01 2.722
-#&gt; 3 m1 12.91 1.305e+01 -1.378e-01 2.722
-#&gt; 3 m1 12.96 1.305e+01 -8.779e-02 2.722
-#&gt; 7 m1 22.97 2.508e+01 -2.106e+00 2.722
-#&gt; 7 m1 24.47 2.508e+01 -6.062e-01 2.722
-#&gt; 14 m1 41.69 3.671e+01 4.983e+00 2.722
-#&gt; 14 m1 33.21 3.671e+01 -3.497e+00 2.722
-#&gt; 21 m1 44.37 4.165e+01 2.720e+00 2.722
-#&gt; 21 m1 46.44 4.165e+01 4.790e+00 2.722
-#&gt; 35 m1 41.22 4.329e+01 -2.069e+00 2.722
-#&gt; 35 m1 37.95 4.329e+01 -5.339e+00 2.722
-#&gt; 50 m1 41.19 4.119e+01 -3.376e-03 2.722
-#&gt; 50 m1 40.01 4.119e+01 -1.183e+00 2.722
-#&gt; 75 m1 40.09 3.644e+01 3.652e+00 2.722
-#&gt; 75 m1 33.85 3.644e+01 -2.588e+00 2.722
-#&gt; 100 m1 31.04 3.199e+01 -9.497e-01 2.722
-#&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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:31 2017
-#&gt; Date of summary: Sat Jul 29 15:14:31 2017
+#&gt; 0 parent 99.46 99.67218 -2.122e-01 3.402
+#&gt; 0 parent 102.04 99.67218 2.368e+00 3.402
+#&gt; 1 parent 93.50 90.27153 3.228e+00 3.402
+#&gt; 1 parent 92.50 90.27153 2.228e+00 3.402
+#&gt; 3 parent 63.23 74.04648 -1.082e+01 3.402
+#&gt; 3 parent 68.99 74.04648 -5.056e+00 3.402
+#&gt; 7 parent 52.32 49.82092 2.499e+00 3.402
+#&gt; 7 parent 55.13 49.82092 5.309e+00 3.402
+#&gt; 14 parent 27.27 24.90287 2.367e+00 3.402
+#&gt; 14 parent 26.64 24.90287 1.737e+00 3.402
+#&gt; 21 parent 11.50 12.44764 -9.476e-01 3.402
+#&gt; 21 parent 11.64 12.44764 -8.076e-01 3.402
+#&gt; 35 parent 2.85 3.11002 -2.600e-01 3.402
+#&gt; 35 parent 2.91 3.11002 -2.000e-01 3.402
+#&gt; 50 parent 0.69 0.70374 -1.374e-02 3.402
+#&gt; 50 parent 0.63 0.70374 -7.374e-02 3.402
+#&gt; 75 parent 0.05 0.05913 -9.134e-03 3.402
+#&gt; 75 parent 0.06 0.05913 8.662e-04 3.402
+#&gt; 0 m1 0.00 0.00000 0.000e+00 2.722
+#&gt; 0 m1 0.00 0.00000 0.000e+00 2.722
+#&gt; 1 m1 4.84 4.81328 2.672e-02 2.722
+#&gt; 1 m1 5.64 4.81328 8.267e-01 2.722
+#&gt; 3 m1 12.91 13.04779 -1.378e-01 2.722
+#&gt; 3 m1 12.96 13.04779 -8.779e-02 2.722
+#&gt; 7 m1 22.97 25.07615 -2.106e+00 2.722
+#&gt; 7 m1 24.47 25.07615 -6.062e-01 2.722
+#&gt; 14 m1 41.69 36.70729 4.983e+00 2.722
+#&gt; 14 m1 33.21 36.70729 -3.497e+00 2.722
+#&gt; 21 m1 44.37 41.65050 2.720e+00 2.722
+#&gt; 21 m1 46.44 41.65050 4.790e+00 2.722
+#&gt; 35 m1 41.22 43.28866 -2.069e+00 2.722
+#&gt; 35 m1 37.95 43.28866 -5.339e+00 2.722
+#&gt; 50 m1 41.19 41.19338 -3.383e-03 2.722
+#&gt; 50 m1 40.01 41.19338 -1.183e+00 2.722
+#&gt; 75 m1 40.09 36.43820 3.652e+00 2.722
+#&gt; 75 m1 33.85 36.43820 -2.588e+00 2.722
+#&gt; 100 m1 31.04 31.98971 -9.497e-01 2.722
+#&gt; 100 m1 33.13 31.98971 1.140e+00 2.722
+#&gt; 120 m1 25.15 28.80897 -3.659e+00 2.722
+#&gt; 120 m1 33.31 28.80897 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: 0.9.47.1
+#&gt; R version: 3.4.3
+#&gt; Date of fit: Tue Jan 30 10:06:03 2018
+#&gt; Date of summary: Tue Jan 30 10:06:03 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -829,7 +844,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.692 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.675 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -895,55 +910,51 @@
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 99.730570 -0.270570
-#&gt; 0 parent 102.04 99.730570 2.309430
-#&gt; 1 parent 93.50 90.298055 3.201945
-#&gt; 1 parent 92.50 90.298055 2.201945
-#&gt; 3 parent 63.23 74.025028 -10.795028
-#&gt; 3 parent 68.99 74.025028 -5.035028
-#&gt; 7 parent 52.32 49.748382 2.571618
-#&gt; 7 parent 55.13 49.748382 5.381618
-#&gt; 14 parent 27.27 24.815876 2.454124
-#&gt; 14 parent 26.64 24.815876 1.824124
-#&gt; 21 parent 11.50 12.378849 -0.878849
-#&gt; 21 parent 11.64 12.378849 -0.738849
-#&gt; 35 parent 2.85 3.080219 -0.230219
-#&gt; 35 parent 2.91 3.080219 -0.170219
-#&gt; 50 parent 0.69 0.693958 -0.003958
-#&gt; 50 parent 0.63 0.693958 -0.063958
-#&gt; 75 parent 0.05 0.057888 -0.007888
-#&gt; 75 parent 0.06 0.057888 0.002112
-#&gt; 100 parent NA 0.004829 NA
-#&gt; 100 parent NA 0.004829 NA
-#&gt; 120 parent NA 0.000662 NA
-#&gt; 120 parent NA 0.000662 NA
-#&gt; 0 m1 0.00 0.000000 0.000000
-#&gt; 0 m1 0.00 0.000000 0.000000
-#&gt; 1 m1 4.84 4.821488 0.018512
-#&gt; 1 m1 5.64 4.821488 0.818512
-#&gt; 3 m1 12.91 13.066692 -0.156692
-#&gt; 3 m1 12.96 13.066692 -0.106692
-#&gt; 7 m1 22.97 25.101058 -2.131058
-#&gt; 7 m1 24.47 25.101058 -0.631058
-#&gt; 14 m1 41.69 36.720923 4.969077
-#&gt; 14 m1 33.21 36.720923 -3.510923
-#&gt; 21 m1 44.37 41.648353 2.721647
-#&gt; 21 m1 46.44 41.648353 4.791647
-#&gt; 35 m1 41.22 43.269225 -2.049225
-#&gt; 35 m1 37.95 43.269225 -5.319225
-#&gt; 50 m1 41.19 41.173639 0.016361
-#&gt; 50 m1 40.01 41.173639 -1.163639
-#&gt; 75 m1 40.09 36.431224 3.658776
-#&gt; 75 m1 33.85 36.431224 -2.581224
-#&gt; 100 m1 31.04 31.996124 -0.956124
-#&gt; 100 m1 33.13 31.996124 1.133876
-#&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>,
+#&gt; 0 parent 99.46 99.73057 -0.270570
+#&gt; 0 parent 102.04 99.73057 2.309430
+#&gt; 1 parent 93.50 90.29805 3.201945
+#&gt; 1 parent 92.50 90.29805 2.201945
+#&gt; 3 parent 63.23 74.02503 -10.795028
+#&gt; 3 parent 68.99 74.02503 -5.035028
+#&gt; 7 parent 52.32 49.74838 2.571618
+#&gt; 7 parent 55.13 49.74838 5.381618
+#&gt; 14 parent 27.27 24.81588 2.454124
+#&gt; 14 parent 26.64 24.81588 1.824124
+#&gt; 21 parent 11.50 12.37885 -0.878849
+#&gt; 21 parent 11.64 12.37885 -0.738849
+#&gt; 35 parent 2.85 3.08022 -0.230219
+#&gt; 35 parent 2.91 3.08022 -0.170219
+#&gt; 50 parent 0.69 0.69396 -0.003958
+#&gt; 50 parent 0.63 0.69396 -0.063958
+#&gt; 75 parent 0.05 0.05789 -0.007888
+#&gt; 75 parent 0.06 0.05789 0.002112
+#&gt; 0 m1 0.00 0.00000 0.000000
+#&gt; 0 m1 0.00 0.00000 0.000000
+#&gt; 1 m1 4.84 4.82149 0.018512
+#&gt; 1 m1 5.64 4.82149 0.818512
+#&gt; 3 m1 12.91 13.06669 -0.156692
+#&gt; 3 m1 12.96 13.06669 -0.106692
+#&gt; 7 m1 22.97 25.10106 -2.131058
+#&gt; 7 m1 24.47 25.10106 -0.631058
+#&gt; 14 m1 41.69 36.72092 4.969077
+#&gt; 14 m1 33.21 36.72092 -3.510923
+#&gt; 21 m1 44.37 41.64835 2.721647
+#&gt; 21 m1 46.44 41.64835 4.791647
+#&gt; 35 m1 41.22 43.26923 -2.049225
+#&gt; 35 m1 37.95 43.26923 -5.319225
+#&gt; 50 m1 41.19 41.17364 0.016361
+#&gt; 50 m1 40.01 41.17364 -1.163639
+#&gt; 75 m1 40.09 36.43122 3.658776
+#&gt; 75 m1 33.85 36.43122 -2.581224
+#&gt; 100 m1 31.04 31.99612 -0.956124
+#&gt; 100 m1 33.13 31.99612 1.133876
+#&gt; 120 m1 25.15 28.82413 -3.674128
+#&gt; 120 m1 33.31 28.82413 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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:32 2017
-#&gt; Date of summary: Sat Jul 29 15:14:32 2017
+<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.47.1
+#&gt; R version: 3.4.3
+#&gt; Date of fit: Tue Jan 30 10:06:04 2018
+#&gt; Date of summary: Tue Jan 30 10:06:04 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -951,7 +962,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.701 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.68 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1062,10 +1073,10 @@
<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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:33 2017
-#&gt; Date of summary: Sat Jul 29 15:14:33 2017
+<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.47.1
+#&gt; R version: 3.4.3
+#&gt; Date of fit: Tue Jan 30 10:06:05 2018
+#&gt; Date of summary: Tue Jan 30 10:06:05 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1073,7 +1084,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 297 model solutions performed in 1.223 s
+#&gt; Fitted with method Port using 297 model solutions performed in 1.178 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1139,55 +1150,51 @@
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual err
-#&gt; 0 parent 99.46 99.485976 -0.025976 1
-#&gt; 0 parent 102.04 99.485976 2.554024 1
-#&gt; 1 parent 93.50 90.186117 3.313883 1
-#&gt; 1 parent 92.50 90.186117 2.313883 1
-#&gt; 3 parent 63.23 74.113162 -10.883162 1
-#&gt; 3 parent 68.99 74.113162 -5.123162 1
-#&gt; 7 parent 52.32 50.050295 2.269705 1
-#&gt; 7 parent 55.13 50.050295 5.079705 1
-#&gt; 14 parent 27.27 25.179750 2.090250 1
-#&gt; 14 parent 26.64 25.179750 1.460250 1
-#&gt; 21 parent 11.50 12.667654 -1.167654 1
-#&gt; 21 parent 11.64 12.667654 -1.027654 1
-#&gt; 35 parent 2.85 3.206164 -0.356164 1
-#&gt; 35 parent 2.91 3.206164 -0.296164 1
-#&gt; 50 parent 0.69 0.735619 -0.045619 1
-#&gt; 50 parent 0.63 0.735619 -0.105619 1
-#&gt; 75 parent 0.05 0.063256 -0.013256 1
-#&gt; 75 parent 0.06 0.063256 -0.003256 1
-#&gt; 100 parent NA 0.005439 NA 1
-#&gt; 100 parent NA 0.005439 NA 1
-#&gt; 120 parent NA 0.000764 NA 1
-#&gt; 120 parent NA 0.000764 NA 1
-#&gt; 0 m1 0.00 0.000000 0.000000 2
-#&gt; 0 m1 0.00 0.000000 0.000000 2
-#&gt; 1 m1 4.84 4.787287 0.052713 2
-#&gt; 1 m1 5.64 4.787287 0.852713 2
-#&gt; 3 m1 12.91 12.987848 -0.077848 2
-#&gt; 3 m1 12.96 12.987848 -0.027848 2
-#&gt; 7 m1 22.97 24.996945 -2.026945 2
-#&gt; 7 m1 24.47 24.996945 -0.526945 2
-#&gt; 14 m1 41.69 36.663527 5.026473 2
-#&gt; 14 m1 33.21 36.663527 -3.453527 2
-#&gt; 21 m1 44.37 41.656813 2.713187 2
-#&gt; 21 m1 46.44 41.656813 4.783187 2
-#&gt; 35 m1 41.22 43.350312 -2.130312 2
-#&gt; 35 m1 37.95 43.350312 -5.400312 2
-#&gt; 50 m1 41.19 41.256365 -0.066365 2
-#&gt; 50 m1 40.01 41.256365 -1.246365 2
-#&gt; 75 m1 40.09 36.460567 3.629433 2
-#&gt; 75 m1 33.85 36.460567 -2.610567 2
-#&gt; 100 m1 31.04 31.969288 -0.929288 2
-#&gt; 100 m1 33.13 31.969288 1.160712 2
-#&gt; 120 m1 25.15 28.760616 -3.610616 2
-#&gt; 120 m1 33.31 28.760616 4.549384 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>,
+#&gt; 0 parent 99.46 99.48598 -0.025976 1
+#&gt; 0 parent 102.04 99.48598 2.554024 1
+#&gt; 1 parent 93.50 90.18612 3.313883 1
+#&gt; 1 parent 92.50 90.18612 2.313883 1
+#&gt; 3 parent 63.23 74.11316 -10.883162 1
+#&gt; 3 parent 68.99 74.11316 -5.123162 1
+#&gt; 7 parent 52.32 50.05029 2.269705 1
+#&gt; 7 parent 55.13 50.05029 5.079705 1
+#&gt; 14 parent 27.27 25.17975 2.090250 1
+#&gt; 14 parent 26.64 25.17975 1.460250 1
+#&gt; 21 parent 11.50 12.66765 -1.167654 1
+#&gt; 21 parent 11.64 12.66765 -1.027654 1
+#&gt; 35 parent 2.85 3.20616 -0.356164 1
+#&gt; 35 parent 2.91 3.20616 -0.296164 1
+#&gt; 50 parent 0.69 0.73562 -0.045619 1
+#&gt; 50 parent 0.63 0.73562 -0.105619 1
+#&gt; 75 parent 0.05 0.06326 -0.013256 1
+#&gt; 75 parent 0.06 0.06326 -0.003256 1
+#&gt; 0 m1 0.00 0.00000 0.000000 2
+#&gt; 0 m1 0.00 0.00000 0.000000 2
+#&gt; 1 m1 4.84 4.78729 0.052713 2
+#&gt; 1 m1 5.64 4.78729 0.852713 2
+#&gt; 3 m1 12.91 12.98785 -0.077848 2
+#&gt; 3 m1 12.96 12.98785 -0.027848 2
+#&gt; 7 m1 22.97 24.99695 -2.026945 2
+#&gt; 7 m1 24.47 24.99695 -0.526945 2
+#&gt; 14 m1 41.69 36.66353 5.026473 2
+#&gt; 14 m1 33.21 36.66353 -3.453527 2
+#&gt; 21 m1 44.37 41.65681 2.713187 2
+#&gt; 21 m1 46.44 41.65681 4.783187 2
+#&gt; 35 m1 41.22 43.35031 -2.130312 2
+#&gt; 35 m1 37.95 43.35031 -5.400312 2
+#&gt; 50 m1 41.19 41.25637 -0.066365 2
+#&gt; 50 m1 40.01 41.25637 -1.246365 2
+#&gt; 75 m1 40.09 36.46057 3.629433 2
+#&gt; 75 m1 33.85 36.46057 -2.610567 2
+#&gt; 100 m1 31.04 31.96929 -0.929288 2
+#&gt; 100 m1 33.13 31.96929 1.160712 2
+#&gt; 120 m1 25.15 28.76062 -3.610616 2
+#&gt; 120 m1 33.31 28.76062 4.549384 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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:36 2017
-#&gt; Date of summary: Sat Jul 29 15:14:36 2017
+<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.47.1
+#&gt; R version: 3.4.3
+#&gt; Date of fit: Tue Jan 30 10:06:08 2018
+#&gt; Date of summary: Tue Jan 30 10:06:08 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1195,9 +1202,14 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 628 model solutions performed in 2.578 s
+#&gt; Fitted with method Port using 692 model solutions performed in 2.733 s
+#&gt;
+#&gt; Weighting: manual
#&gt;
-#&gt; Weighting: manual then iterative reweighting method obs
+#&gt; Iterative reweighting with method obs
+#&gt; Final mean squared residuals of observed variables:
+#&gt; parent m1
+#&gt; 11.573407 7.407845
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -1226,10 +1238,10 @@
#&gt;
#&gt; Parameter correlation:
#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
-#&gt; parent_0 1.0000 0.5083 -0.1979 -0.6147
+#&gt; parent_0 1.0000 0.5083 -0.1979 -0.6148
#&gt; log_k_parent 0.5083 1.0000 -0.3894 -0.6062
#&gt; log_k_m1 -0.1979 -0.3894 1.0000 0.7417
-#&gt; f_parent_ilr_1 -0.6147 -0.6062 0.7417 1.0000
+#&gt; f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000
#&gt;
#&gt; Residual standard error: 1.054 on 36 degrees of freedom
#&gt;
@@ -1238,10 +1250,10 @@
#&gt; t-test (unrealistically) based on the assumption of normal distribution
#&gt; for estimators of untransformed parameters.
#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.67000 55.630 8.179e-37 96.040000 1.033e+02
-#&gt; k_parent 0.09906 21.930 1.015e-22 0.090310 1.087e-01
-#&gt; k_m1 0.00524 7.996 8.488e-10 0.004066 6.753e-03
-#&gt; f_parent_to_m1 0.51340 23.000 2.039e-23 0.468100 5.584e-01
+#&gt; parent_0 99.67000 55.630 8.184e-37 96.040000 1.033e+02
+#&gt; k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01
+#&gt; k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03
+#&gt; f_parent_to_m1 0.51340 23.000 2.038e-23 0.468100 5.584e-01
#&gt;
#&gt; Chi2 error levels in percent:
#&gt; err.min n.optim df
@@ -1257,54 +1269,50 @@
#&gt; Estimated disappearance times:
#&gt; DT50 DT90
#&gt; parent 6.997 23.24
-#&gt; m1 132.281 439.43
+#&gt; m1 132.282 439.43
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual err.ini err
-#&gt; 0 parent 99.46 9.967e+01 -2.122e-01 1 3.402
-#&gt; 0 parent 102.04 9.967e+01 2.368e+00 1 3.402
-#&gt; 1 parent 93.50 9.027e+01 3.228e+00 1 3.402
-#&gt; 1 parent 92.50 9.027e+01 2.228e+00 1 3.402
-#&gt; 3 parent 63.23 7.405e+01 -1.082e+01 1 3.402
-#&gt; 3 parent 68.99 7.405e+01 -5.056e+00 1 3.402
-#&gt; 7 parent 52.32 4.982e+01 2.499e+00 1 3.402
-#&gt; 7 parent 55.13 4.982e+01 5.309e+00 1 3.402
-#&gt; 14 parent 27.27 2.490e+01 2.367e+00 1 3.402
-#&gt; 14 parent 26.64 2.490e+01 1.737e+00 1 3.402
-#&gt; 21 parent 11.50 1.245e+01 -9.477e-01 1 3.402
-#&gt; 21 parent 11.64 1.245e+01 -8.077e-01 1 3.402
-#&gt; 35 parent 2.85 3.110e+00 -2.600e-01 1 3.402
-#&gt; 35 parent 2.91 3.110e+00 -2.000e-01 1 3.402
-#&gt; 50 parent 0.69 7.037e-01 -1.375e-02 1 3.402
-#&gt; 50 parent 0.63 7.037e-01 -7.375e-02 1 3.402
-#&gt; 75 parent 0.05 5.913e-02 -9.134e-03 1 3.402
-#&gt; 75 parent 0.06 5.913e-02 8.659e-04 1 3.402
-#&gt; 100 parent NA 4.969e-03 NA 1 3.402
-#&gt; 100 parent NA 4.969e-03 NA 1 3.402
-#&gt; 120 parent NA 6.852e-04 NA 1 3.402
-#&gt; 120 parent NA 6.852e-04 NA 1 3.402
-#&gt; 0 m1 0.00 0.000e+00 0.000e+00 2 2.722
-#&gt; 0 m1 0.00 0.000e+00 0.000e+00 2 2.722
-#&gt; 1 m1 4.84 4.813e+00 2.672e-02 2 2.722
-#&gt; 1 m1 5.64 4.813e+00 8.267e-01 2 2.722
-#&gt; 3 m1 12.91 1.305e+01 -1.378e-01 2 2.722
-#&gt; 3 m1 12.96 1.305e+01 -8.778e-02 2 2.722
-#&gt; 7 m1 22.97 2.508e+01 -2.106e+00 2 2.722
-#&gt; 7 m1 24.47 2.508e+01 -6.061e-01 2 2.722
-#&gt; 14 m1 41.69 3.671e+01 4.983e+00 2 2.722
-#&gt; 14 m1 33.21 3.671e+01 -3.497e+00 2 2.722
-#&gt; 21 m1 44.37 4.165e+01 2.719e+00 2 2.722
-#&gt; 21 m1 46.44 4.165e+01 4.789e+00 2 2.722
-#&gt; 35 m1 41.22 4.329e+01 -2.069e+00 2 2.722
-#&gt; 35 m1 37.95 4.329e+01 -5.339e+00 2 2.722
-#&gt; 50 m1 41.19 4.119e+01 -3.394e-03 2 2.722
-#&gt; 50 m1 40.01 4.119e+01 -1.183e+00 2 2.722
-#&gt; 75 m1 40.09 3.644e+01 3.652e+00 2 2.722
-#&gt; 75 m1 33.85 3.644e+01 -2.588e+00 2 2.722
-#&gt; 100 m1 31.04 3.199e+01 -9.497e-01 2 2.722
-#&gt; 100 m1 33.13 3.199e+01 1.140e+00 2 2.722
-#&gt; 120 m1 25.15 2.881e+01 -3.659e+00 2 2.722
-#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2 2.722</div><div class='input'>
+#&gt; 0 parent 99.46 99.67218 -2.122e-01 1 3.402
+#&gt; 0 parent 102.04 99.67218 2.368e+00 1 3.402
+#&gt; 1 parent 93.50 90.27153 3.228e+00 1 3.402
+#&gt; 1 parent 92.50 90.27153 2.228e+00 1 3.402
+#&gt; 3 parent 63.23 74.04648 -1.082e+01 1 3.402
+#&gt; 3 parent 68.99 74.04648 -5.056e+00 1 3.402
+#&gt; 7 parent 52.32 49.82092 2.499e+00 1 3.402
+#&gt; 7 parent 55.13 49.82092 5.309e+00 1 3.402
+#&gt; 14 parent 27.27 24.90288 2.367e+00 1 3.402
+#&gt; 14 parent 26.64 24.90288 1.737e+00 1 3.402
+#&gt; 21 parent 11.50 12.44765 -9.476e-01 1 3.402
+#&gt; 21 parent 11.64 12.44765 -8.076e-01 1 3.402
+#&gt; 35 parent 2.85 3.11002 -2.600e-01 1 3.402
+#&gt; 35 parent 2.91 3.11002 -2.000e-01 1 3.402
+#&gt; 50 parent 0.69 0.70375 -1.375e-02 1 3.402
+#&gt; 50 parent 0.63 0.70375 -7.375e-02 1 3.402
+#&gt; 75 parent 0.05 0.05913 -9.134e-03 1 3.402
+#&gt; 75 parent 0.06 0.05913 8.662e-04 1 3.402
+#&gt; 0 m1 0.00 0.00000 0.000e+00 2 2.722
+#&gt; 0 m1 0.00 0.00000 0.000e+00 2 2.722
+#&gt; 1 m1 4.84 4.81328 2.672e-02 2 2.722
+#&gt; 1 m1 5.64 4.81328 8.267e-01 2 2.722
+#&gt; 3 m1 12.91 13.04779 -1.378e-01 2 2.722
+#&gt; 3 m1 12.96 13.04779 -8.779e-02 2 2.722
+#&gt; 7 m1 22.97 25.07615 -2.106e+00 2 2.722
+#&gt; 7 m1 24.47 25.07615 -6.062e-01 2 2.722
+#&gt; 14 m1 41.69 36.70729 4.983e+00 2 2.722
+#&gt; 14 m1 33.21 36.70729 -3.497e+00 2 2.722
+#&gt; 21 m1 44.37 41.65050 2.720e+00 2 2.722
+#&gt; 21 m1 46.44 41.65050 4.790e+00 2 2.722
+#&gt; 35 m1 41.22 43.28866 -2.069e+00 2 2.722
+#&gt; 35 m1 37.95 43.28866 -5.339e+00 2 2.722
+#&gt; 50 m1 41.19 41.19339 -3.386e-03 2 2.722
+#&gt; 50 m1 40.01 41.19339 -1.183e+00 2 2.722
+#&gt; 75 m1 40.09 36.43820 3.652e+00 2 2.722
+#&gt; 75 m1 33.85 36.43820 -2.588e+00 2 2.722
+#&gt; 100 m1 31.04 31.98971 -9.497e-01 2 2.722
+#&gt; 100 m1 33.13 31.98971 1.140e+00 2 2.722
+#&gt; 120 m1 25.15 28.80897 -3.659e+00 2 2.722
+#&gt; 120 m1 33.31 28.80897 4.501e+00 2 2.722</div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -1319,6 +1327,8 @@
<li><a href="#note">Note</a></li>
<li><a href="#note">Note</a></li>
+
+ <li><a href="#source">Source</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html
new file mode 100644
index 00000000..36f2a0c1
--- /dev/null
+++ b/docs/reference/sigma_rl.html
@@ -0,0 +1,167 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+ <h1>Two component error model of Rocke and Lorenzato</h1>
+ </div>
+
+
+ <p>Function describing the standard deviation of the measurement error
+ in dependence of the measured value:</p>
+<p>\(sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2)\)</p>
+
+
+ <pre class="usage"><span class='fu'>sigma_rl</span>(<span class='no'>y</span>, <span class='no'>sigma_low</span>, <span class='no'>rsd_high</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>y</th>
+ <td><p>The magnitude of the observed value</p></td>
+ </tr>
+ <tr>
+ <th>sigma_low</th>
+ <td><p>The asymptotic minimum of the standard deviation for low observed values</p></td>
+ </tr>
+ <tr>
+ <th>rsd_high</th>
+ <td><p>The coefficient describing the increase of the standard deviation with
+ the magnitude of the observed value</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The standard deviation of the response variable.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
+ measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#references">References</a></li>
+ </ul>
+
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