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-rw-r--r--docs/reference/mkinfit.html226
1 files changed, 117 insertions, 109 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index d3a826b9..7693287e 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -151,6 +151,7 @@ Per default, parameters in the kinetic models are internally transformed in
<pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>,
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
<span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>],
<span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>),
@@ -210,6 +211,13 @@ Per default, parameters in the kinetic models are internally transformed in
If this variable has no time zero observations, its initial value is set to 100.</p></td>
</tr>
<tr>
+ <th>err.ini</th>
+ <td><p>A named vector of initial values for the error model parameters to be
+ optimised. If set to "auto", initial values are set to default values.
+ Otherwise, inital values for all error model parameters must be
+ given.</p></td>
+ </tr>
+ <tr>
<th>fixed_parms</th>
<td><p>The names of parameters that should not be optimised but rather kept at the
values specified in <code>parms.ini</code>.</p></td>
@@ -353,19 +361,19 @@ Per default, parameters in the kinetic models are internally transformed in
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
-#&gt; R version used for fitting: 3.5.3
-#&gt; Date of fit: Wed Apr 10 10:10:01 2019
-#&gt; Date of summary: Wed Apr 10 10:10:01 2019
+#&gt; R version used for fitting: 3.6.0
+#&gt; Date of fit: Thu May 2 12:38:56 2019
+#&gt; Date of summary: Thu May 2 12:38:56 2019
#&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 using 221 model solutions performed in 0.508 s
+#&gt; Fitted using 221 model solutions performed in 0.455 s
#&gt;
#&gt; Error model:
-#&gt; NULL
+#&gt; Constant variance
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -393,10 +401,10 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Parameter correlation:
#&gt; parent_0 log_alpha log_beta sigma
-#&gt; parent_0 1.000e+00 -1.565e-01 -3.142e-01 -1.313e-07
-#&gt; log_alpha -1.565e-01 1.000e+00 9.564e-01 -2.634e-07
-#&gt; log_beta -3.142e-01 9.564e-01 1.000e+00 -2.200e-07
-#&gt; sigma -1.313e-07 -2.634e-07 -2.200e-07 1.000e+00
+#&gt; parent_0 1.000e+00 -1.565e-01 -3.142e-01 -1.317e-07
+#&gt; log_alpha -1.565e-01 1.000e+00 9.564e-01 -2.640e-07
+#&gt; log_beta -3.142e-01 9.564e-01 1.000e+00 -2.205e-07
+#&gt; sigma -1.317e-07 -2.640e-07 -2.205e-07 1.000e+00
#&gt;
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -408,7 +416,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; beta 1.917 4.373 3.601e-03 1.0650 3.451
#&gt; sigma 1.857 4.243 4.074e-03 0.7320 2.983
#&gt;
-#&gt; Chi2 error levels in percent:
+#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
#&gt; All data 6.657 3 6
#&gt; parent 6.657 3 6
@@ -435,7 +443,7 @@ Per default, parameters in the kinetic models are internally transformed in
<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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.653 0.000 1.653 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</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; 1.551 0.000 1.552 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</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
#&gt;
@@ -448,71 +456,71 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; m1 131.760715 437.69962
#&gt; </div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit.deSolve</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'>"deSolve"</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; Negative log-likelihood at call 1: 18915.53
-#&gt; Negative log-likelihood at call 2: 18915.53
-#&gt; Negative log-likelihood at call 6: 11424.02
-#&gt; Negative log-likelihood at call 10: 11424
-#&gt; Negative log-likelihood at call 13: 2367.052
-#&gt; Negative log-likelihood at call 14: 2367.05
-#&gt; Negative log-likelihood at call 19: 1314.716
-#&gt; Negative log-likelihood at call 22: 1314.714
-#&gt; Negative log-likelihood at call 25: 991.8311
-#&gt; Negative log-likelihood at call 28: 991.8305
-#&gt; Negative log-likelihood at call 30: 893.6462
-#&gt; Negative log-likelihood at call 33: 893.6457
-#&gt; Negative log-likelihood at call 35: 569.4049
-#&gt; Negative log-likelihood at call 38: 569.4047
-#&gt; Negative log-likelihood at call 40: 565.0651
-#&gt; Negative log-likelihood at call 41: 565.065
-#&gt; Negative log-likelihood at call 42: 565.0637
-#&gt; Negative log-likelihood at call 45: 428.0188
-#&gt; Negative log-likelihood at call 46: 428.0185
-#&gt; Negative log-likelihood at call 50: 406.732
-#&gt; Negative log-likelihood at call 52: 406.732
-#&gt; Negative log-likelihood at call 55: 398.9115
-#&gt; Negative log-likelihood at call 57: 398.9113
-#&gt; Negative log-likelihood at call 60: 394.5943
-#&gt; Negative log-likelihood at call 62: 394.5943
-#&gt; Negative log-likelihood at call 66: 385.26
-#&gt; Negative log-likelihood at call 67: 385.2599
-#&gt; Negative log-likelihood at call 69: 385.2599
-#&gt; Negative log-likelihood at call 70: 385.2597
-#&gt; Negative log-likelihood at call 71: 374.7604
-#&gt; Negative log-likelihood at call 72: 374.7603
-#&gt; Negative log-likelihood at call 76: 373.199
-#&gt; Negative log-likelihood at call 79: 373.199
-#&gt; Negative log-likelihood at call 80: 373.199
-#&gt; Negative log-likelihood at call 81: 372.3772
-#&gt; Negative log-likelihood at call 84: 372.3772
-#&gt; Negative log-likelihood at call 86: 371.2615
-#&gt; Negative log-likelihood at call 89: 371.2615
-#&gt; Negative log-likelihood at call 90: 371.2615
-#&gt; Negative log-likelihood at call 92: 371.2439
-#&gt; Negative log-likelihood at call 93: 371.2439
-#&gt; Negative log-likelihood at call 94: 371.2439
-#&gt; Negative log-likelihood at call 97: 371.2198
-#&gt; Negative log-likelihood at call 98: 371.2198
-#&gt; Negative log-likelihood at call 102: 371.2174
-#&gt; Negative log-likelihood at call 104: 371.2174
-#&gt; Negative log-likelihood at call 107: 371.2147
-#&gt; Negative log-likelihood at call 110: 371.2147
-#&gt; Negative log-likelihood at call 111: 371.2147
-#&gt; Negative log-likelihood at call 112: 371.2145
-#&gt; Negative log-likelihood at call 113: 371.2145
-#&gt; Negative log-likelihood at call 116: 371.2145
-#&gt; Negative log-likelihood at call 119: 371.2135
-#&gt; Negative log-likelihood at call 121: 371.2135
-#&gt; Negative log-likelihood at call 124: 371.2135
-#&gt; Negative log-likelihood at call 126: 371.2135
-#&gt; Negative log-likelihood at call 127: 371.2135
-#&gt; Negative log-likelihood at call 133: 371.2134
-#&gt; Negative log-likelihood at call 135: 371.2134
-#&gt; Negative log-likelihood at call 138: 371.2134
-#&gt; Negative log-likelihood at call 142: 371.2134
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 18915.53
+#&gt; Sum of squared residuals at call 2: 18915.53
+#&gt; Sum of squared residuals at call 6: 11424.02
+#&gt; Sum of squared residuals at call 10: 11424
+#&gt; Sum of squared residuals at call 13: 2367.052
+#&gt; Sum of squared residuals at call 14: 2367.05
+#&gt; Sum of squared residuals at call 19: 1314.716
+#&gt; Sum of squared residuals at call 22: 1314.714
+#&gt; Sum of squared residuals at call 25: 991.8311
+#&gt; Sum of squared residuals at call 28: 991.8305
+#&gt; Sum of squared residuals at call 30: 893.6462
+#&gt; Sum of squared residuals at call 33: 893.6457
+#&gt; Sum of squared residuals at call 35: 569.4049
+#&gt; Sum of squared residuals at call 38: 569.4047
+#&gt; Sum of squared residuals at call 40: 565.0651
+#&gt; Sum of squared residuals at call 41: 565.065
+#&gt; Sum of squared residuals at call 42: 565.0637
+#&gt; Sum of squared residuals at call 45: 428.0188
+#&gt; Sum of squared residuals at call 46: 428.0185
+#&gt; Sum of squared residuals at call 50: 406.732
+#&gt; Sum of squared residuals at call 52: 406.732
+#&gt; Sum of squared residuals at call 55: 398.9115
+#&gt; Sum of squared residuals at call 57: 398.9113
+#&gt; Sum of squared residuals at call 60: 394.5943
+#&gt; Sum of squared residuals at call 62: 394.5943
+#&gt; Sum of squared residuals at call 66: 385.26
+#&gt; Sum of squared residuals at call 67: 385.2599
+#&gt; Sum of squared residuals at call 69: 385.2599
+#&gt; Sum of squared residuals at call 70: 385.2597
+#&gt; Sum of squared residuals at call 71: 374.7604
+#&gt; Sum of squared residuals at call 72: 374.7603
+#&gt; Sum of squared residuals at call 76: 373.199
+#&gt; Sum of squared residuals at call 79: 373.199
+#&gt; Sum of squared residuals at call 80: 373.199
+#&gt; Sum of squared residuals at call 81: 372.3772
+#&gt; Sum of squared residuals at call 84: 372.3772
+#&gt; Sum of squared residuals at call 86: 371.2615
+#&gt; Sum of squared residuals at call 89: 371.2615
+#&gt; Sum of squared residuals at call 90: 371.2615
+#&gt; Sum of squared residuals at call 92: 371.2439
+#&gt; Sum of squared residuals at call 93: 371.2439
+#&gt; Sum of squared residuals at call 94: 371.2439
+#&gt; Sum of squared residuals at call 97: 371.2198
+#&gt; Sum of squared residuals at call 98: 371.2198
+#&gt; Sum of squared residuals at call 102: 371.2174
+#&gt; Sum of squared residuals at call 104: 371.2174
+#&gt; Sum of squared residuals at call 107: 371.2147
+#&gt; Sum of squared residuals at call 110: 371.2147
+#&gt; Sum of squared residuals at call 111: 371.2147
+#&gt; Sum of squared residuals at call 112: 371.2145
+#&gt; Sum of squared residuals at call 113: 371.2145
+#&gt; Sum of squared residuals at call 116: 371.2145
+#&gt; Sum of squared residuals at call 119: 371.2135
+#&gt; Sum of squared residuals at call 121: 371.2135
+#&gt; Sum of squared residuals at call 124: 371.2135
+#&gt; Sum of squared residuals at call 126: 371.2135
+#&gt; Sum of squared residuals at call 127: 371.2135
+#&gt; Sum of squared residuals at call 133: 371.2134
+#&gt; Sum of squared residuals at call 135: 371.2134
+#&gt; Sum of squared residuals at call 138: 371.2134
+#&gt; Sum of squared residuals at call 142: 371.2134
#&gt; Negative log-likelihood at call 152: 97.22429
#&gt; Optimisation successfully terminated.
#&gt; User System verstrichen
-#&gt; 1.136 0.000 1.135 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</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; 1.152 0.000 1.153 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</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
#&gt;
@@ -543,9 +551,9 @@ Per default, parameters in the kinetic models are internally transformed in
</div><div class='input'><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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
-#&gt; R version used for fitting: 3.5.3
-#&gt; Date of fit: Wed Apr 10 10:10:17 2019
-#&gt; Date of summary: Wed Apr 10 10:10:17 2019
+#&gt; R version used for fitting: 3.6.0
+#&gt; Date of fit: Thu May 2 12:39:13 2019
+#&gt; Date of summary: Thu May 2 12:39:13 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -553,10 +561,10 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method using 404 model solutions performed in 1.105 s
+#&gt; Fitted using 404 model solutions performed in 1.178 s
#&gt;
#&gt; Error model:
-#&gt; NULL
+#&gt; Constant variance
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -605,7 +613,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
#&gt; sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
#&gt;
-#&gt; Chi2 error levels in percent:
+#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
#&gt; All data 6.398 4 15
#&gt; parent 6.459 2 7
@@ -661,9 +669,9 @@ Per default, parameters in the kinetic models are internally transformed in
#&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.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</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: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
-#&gt; R version used for fitting: 3.5.3
-#&gt; Date of fit: Wed Apr 10 10:10:19 2019
-#&gt; Date of summary: Wed Apr 10 10:10:19 2019
+#&gt; R version used for fitting: 3.6.0
+#&gt; Date of fit: Thu May 2 12:39:14 2019
+#&gt; Date of summary: Thu May 2 12:39:14 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -671,10 +679,10 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method using 558 model solutions performed in 1.602 s
+#&gt; Fitted using 558 model solutions performed in 1.518 s
#&gt;
#&gt; Error model:
-#&gt; NULL
+#&gt; Variance unique to each observed variable
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -735,7 +743,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00
#&gt; sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00
#&gt;
-#&gt; Chi2 error levels in percent:
+#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
#&gt; All data 6.398 4 15
#&gt; parent 6.464 2 7
@@ -791,9 +799,9 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 100 m1 33.13 31.98774 1.142e+00
#&gt; 120 m1 25.15 28.80430 -3.654e+00
#&gt; 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
-#&gt; R version used for fitting: 3.5.3
-#&gt; Date of fit: Wed Apr 10 10:10:22 2019
-#&gt; Date of summary: Wed Apr 10 10:10:22 2019
+#&gt; R version used for fitting: 3.6.0
+#&gt; Date of fit: Thu May 2 12:39:18 2019
+#&gt; Date of summary: Thu May 2 12:39:18 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -801,10 +809,10 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method using 756 model solutions performed in 3.222 s
+#&gt; Fitted using 844 model solutions performed in 3.501 s
#&gt;
#&gt; Error model:
-#&gt; NULL
+#&gt; Two-component variance function
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -812,8 +820,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; k_parent 0.1000 deparm
#&gt; k_m1 0.1001 deparm
#&gt; f_parent_to_m1 0.5000 deparm
-#&gt; sigma_low 0.5000 error
-#&gt; rsd_high 0.0700 error
+#&gt; sigma_low 3.0000 error
+#&gt; rsd_high 0.0100 error
#&gt;
#&gt; Starting values for the transformed parameters actually optimised:
#&gt; value lower upper
@@ -821,8 +829,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; log_k_parent -2.302585 -Inf Inf
#&gt; log_k_m1 -2.301586 -Inf Inf
#&gt; f_parent_ilr_1 0.000000 -Inf Inf
-#&gt; sigma_low 0.500000 0 Inf
-#&gt; rsd_high 0.070000 0 Inf
+#&gt; sigma_low 3.000000 0 Inf
+#&gt; rsd_high 0.010000 0 Inf
#&gt;
#&gt; Fixed parameter values:
#&gt; value type
@@ -858,7 +866,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; sigma_low 3.050e-03 0.6314 2.661e-01 -0.006786 1.289e-02
#&gt; rsd_high 7.928e-02 8.4170 6.418e-10 0.060100 9.847e-02
#&gt;
-#&gt; Chi2 error levels in percent:
+#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
#&gt; All data 6.475 4 15
#&gt; parent 6.573 2 7
@@ -876,18 +884,18 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 100.73434 -1.274340
-#&gt; 0 parent 102.04 100.73434 1.305660
+#&gt; 0 parent 99.46 100.73434 -1.274339
+#&gt; 0 parent 102.04 100.73434 1.305661
#&gt; 1 parent 93.50 91.09751 2.402486
#&gt; 1 parent 92.50 91.09751 1.402486
#&gt; 3 parent 63.23 74.50141 -11.271410
#&gt; 3 parent 68.99 74.50141 -5.511410
-#&gt; 7 parent 52.32 49.82880 2.491200
-#&gt; 7 parent 55.13 49.82880 5.301200
+#&gt; 7 parent 52.32 49.82880 2.491201
+#&gt; 7 parent 55.13 49.82880 5.301201
#&gt; 14 parent 27.27 24.64809 2.621908
#&gt; 14 parent 26.64 24.64809 1.991908
-#&gt; 21 parent 11.50 12.19232 -0.692316
-#&gt; 21 parent 11.64 12.19232 -0.552316
+#&gt; 21 parent 11.50 12.19232 -0.692315
+#&gt; 21 parent 11.64 12.19232 -0.552315
#&gt; 35 parent 2.85 2.98327 -0.133266
#&gt; 35 parent 2.91 2.98327 -0.073266
#&gt; 50 parent 0.69 0.66013 0.029874
@@ -900,20 +908,20 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 3 m1 12.96 13.22867 -0.268669
#&gt; 7 m1 22.97 25.36417 -2.394167
#&gt; 7 m1 24.47 25.36417 -0.894167
-#&gt; 14 m1 41.69 37.00974 4.680262
-#&gt; 14 m1 33.21 37.00974 -3.799738
+#&gt; 14 m1 41.69 37.00974 4.680263
+#&gt; 14 m1 33.21 37.00974 -3.799737
#&gt; 21 m1 44.37 41.90133 2.468668
#&gt; 21 m1 46.44 41.90133 4.538668
#&gt; 35 m1 41.22 43.45691 -2.236914
#&gt; 35 m1 37.95 43.45691 -5.506914
#&gt; 50 m1 41.19 41.34199 -0.151986
#&gt; 50 m1 40.01 41.34199 -1.331986
-#&gt; 75 m1 40.09 36.61470 3.475295
-#&gt; 75 m1 33.85 36.61470 -2.764705
-#&gt; 100 m1 31.04 32.20082 -1.160823
-#&gt; 100 m1 33.13 32.20082 0.929177
-#&gt; 120 m1 25.15 29.04130 -3.891303
-#&gt; 120 m1 33.31 29.04130 4.268697</div><div class='input'>
+#&gt; 75 m1 40.09 36.61471 3.475294
+#&gt; 75 m1 33.85 36.61471 -2.764706
+#&gt; 100 m1 31.04 32.20082 -1.160824
+#&gt; 100 m1 33.13 32.20082 0.929176
+#&gt; 120 m1 25.15 29.04130 -3.891305
+#&gt; 120 m1 33.31 29.04130 4.268695</div><div class='input'>
</div></pre>
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