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| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-07-29 15:15:41 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-07-29 15:15:41 +0200 |
| commit | 20d7834a633d32b663c6bcc1a7f7b0300aa65d5b (patch) | |
| tree | 77338f14ecaf26a4059ada9933ffde1fb5c19072 /docs/reference/mkinfit.html | |
| parent | 5447af959b2a9b0dc52695bf6a309f346ced085a (diff) | |
Bump version, update NEWS and rebuild pkdown docsv0.9.46
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 72 |
1 files changed, 36 insertions, 36 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 875bd1dd..cdf7c7ef 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -377,17 +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'><-</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'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:06 2017 -#> Date of summary: Fri May 5 12:45:06 2017 +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:18 2017 +#> Date of summary: Sat Jul 29 15:14:18 2017 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.206 s +#> Fitted with method Port using 64 model solutions performed in 0.141 s #> #> Weighting: none #> @@ -456,7 +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'>#> <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'><-</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'>#> user system elapsed -#> 0.912 0.000 0.915 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -535,7 +535,7 @@ #> Model cost at call 153 : 371.2134 #> Optimisation by method Port successfully terminated. #> user system elapsed -#> 0.792 0.000 0.793 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -576,10 +576,10 @@ <span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</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'>#> <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'><-</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'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:17 2017 -#> Date of summary: Fri May 5 12:45:17 2017 +<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:28 2017 +#> Date of summary: Sat Jul 29 15:14:28 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -697,10 +697,10 @@ #> 100 m1 33.13 3.198e+01 1.148e+00 #> 120 m1 25.15 2.879e+01 -3.640e+00 #> 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</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'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:19 2017 -#> Date of summary: Fri May 5 12:45:19 2017 +<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:30 2017 +#> Date of summary: Sat Jul 29 15:14:30 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -708,7 +708,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 468 model solutions performed in 1.925 s +#> Fitted with method Port using 468 model solutions performed in 1.914 s #> #> Weighting: none then iterative reweighting method obs #> @@ -818,10 +818,10 @@ #> 100 m1 33.13 3.199e+01 1.140e+00 2.722 #> 120 m1 25.15 2.881e+01 -3.659e+00 2.722 #> 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'><-</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'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:20 2017 -#> Date of summary: Fri May 5 12:45:20 2017 +<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:31 2017 +#> Date of summary: Sat Jul 29 15:14:31 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -829,7 +829,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.699 s +#> Fitted with method Port using 155 model solutions performed in 0.692 s #> #> Weighting: mean #> @@ -940,10 +940,10 @@ #> 120 m1 25.15 28.824128 -3.674128 #> 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</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'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:21 2017 -#> Date of summary: Fri May 5 12:45:21 2017 +<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:32 2017 +#> Date of summary: Sat Jul 29 15:14:32 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -951,7 +951,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.767 s +#> Fitted with method Port using 174 model solutions performed in 0.701 s #> #> Weighting: manual #> @@ -1062,10 +1062,10 @@ <span class='no'>errors</span> <span class='kw'><-</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'><-</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'><-</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'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:22 2017 -#> Date of summary: Fri May 5 12:45:22 2017 +<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:33 2017 +#> Date of summary: Sat Jul 29 15:14:33 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1073,7 +1073,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 297 model solutions performed in 1.276 s +#> Fitted with method Port using 297 model solutions performed in 1.223 s #> #> Weighting: manual #> @@ -1184,10 +1184,10 @@ #> 120 m1 25.15 28.760616 -3.610616 2 #> 120 m1 33.31 28.760616 4.549384 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</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'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:25 2017 -#> Date of summary: Fri May 5 12:45:25 2017 +<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:36 2017 +#> Date of summary: Sat Jul 29 15:14:36 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1195,7 +1195,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 628 model solutions performed in 2.626 s +#> Fitted with method Port using 628 model solutions performed in 2.578 s #> #> Weighting: manual then iterative reweighting method obs #> |