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authorJohannes Ranke <jranke@uni-bremen.de>2020-04-20 18:52:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-04-20 18:52:52 +0200
commit3a62211d9211cd0aedecec055226d66b55a17958 (patch)
tree23ec36c38f7a17c800c7004610550230bd7e39a5 /docs/reference/mkinfit.html
parent5526bf5ba6b003c6dae842f7f03f33c1648c9551 (diff)
Prepare release to address failed CRAN check
Diffstat (limited to 'docs/reference/mkinfit.html')
-rw-r--r--docs/reference/mkinfit.html44
1 files changed, 19 insertions, 25 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index ffc8d52b..09837505 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -75,7 +75,7 @@ likelihood function." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
@@ -415,17 +415,17 @@ estimators.</p>
<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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.9
+<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.11
#&gt; R version used for fitting: 3.6.3
-#&gt; Date of fit: Mon Mar 30 21:41:20 2020
-#&gt; Date of summary: Mon Mar 30 21:41:20 2020
+#&gt; Date of fit: Mon Apr 20 18:52:22 2020
+#&gt; Date of summary: Mon Apr 20 18:52:22 2020
#&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 using 222 model solutions performed in 0.463 s
+#&gt; Fitted using 222 model solutions performed in 0.473 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -497,13 +497,10 @@ estimators.</p>
<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://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>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; 1.526 0.000 1.530 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>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; 1.465 0.003 1.474 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>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;
-#&gt; $SFORB
-#&gt; logical(0)
-#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 7.022929 23.32967
@@ -570,13 +567,10 @@ estimators.</p>
#&gt; Sum of squared residuals at call 126: 371.2134
#&gt; Sum of squared residuals at call 135: 371.2134
#&gt; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.083 0.000 1.084 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>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; 1.052 0.000 1.068 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>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;
-#&gt; $SFORB
-#&gt; logical(0)
-#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 7.022929 23.32967
@@ -604,10 +598,10 @@ estimators.</p>
<span class='co'># \dontrun{</span>
<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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.9
+ <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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.11
#&gt; R version used for fitting: 3.6.3
-#&gt; Date of fit: Mon Mar 30 21:41:36 2020
-#&gt; Date of summary: Mon Mar 30 21:41:36 2020
+#&gt; Date of fit: Mon Apr 20 18:52:37 2020
+#&gt; Date of summary: Mon Apr 20 18:52:37 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -615,7 +609,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 422 model solutions performed in 1.144 s
+#&gt; Fitted using 422 model solutions performed in 1.087 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -721,10 +715,10 @@ estimators.</p>
#&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.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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.9
+#&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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.11
#&gt; R version used for fitting: 3.6.3
-#&gt; Date of fit: Mon Mar 30 21:41:39 2020
-#&gt; Date of summary: Mon Mar 30 21:41:39 2020
+#&gt; Date of fit: Mon Apr 20 18:52:40 2020
+#&gt; Date of summary: Mon Apr 20 18:52:40 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -732,7 +726,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 979 model solutions performed in 2.576 s
+#&gt; Fitted using 979 model solutions performed in 2.518 s
#&gt;
#&gt; Error model: Variance unique to each observed variable
#&gt;
@@ -853,10 +847,10 @@ estimators.</p>
#&gt; 100 m1 31.04 31.98773 -9.477e-01
#&gt; 100 m1 33.13 31.98773 1.142e+00
#&gt; 120 m1 25.15 28.80429 -3.654e+00
-#&gt; 120 m1 33.31 28.80429 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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.9
+#&gt; 120 m1 33.31 28.80429 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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.11
#&gt; R version used for fitting: 3.6.3
-#&gt; Date of fit: Mon Mar 30 21:41:50 2020
-#&gt; Date of summary: Mon Mar 30 21:41:50 2020
+#&gt; Date of fit: Mon Apr 20 18:52:50 2020
+#&gt; Date of summary: Mon Apr 20 18:52:50 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -864,7 +858,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 2552 model solutions performed in 10.593 s
+#&gt; Fitted using 2552 model solutions performed in 10.186 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;

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