diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 23:08:45 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 23:08:45 +0100 |
| commit | d852e9e000f57f280deb84611ae1af58daa883cc (patch) | |
| tree | 10d71ca9fd557ead9c15025d2050f977e08de14e /docs/reference/mkinfit.html | |
| parent | 30f55769fe2f042c7753144051dd34eec3596adc (diff) | |
Fix links in README, configure navbar, rebuild docs
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 48 |
1 files changed, 24 insertions, 24 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index a912b065..2f32348e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -49,7 +49,7 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Function reference</a> + <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> @@ -374,15 +374,15 @@ <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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 16:45:39 2016 -#> Date of summary: Fri Nov 18 16:45:39 2016 +#> Date of fit: Fri Nov 18 22:52:19 2016 +#> Date of summary: Fri Nov 18 22:52:19 2016 #> #> 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 0.146 s +#> Fitted with method Port using 64 model solutions performed in 0.145 s #> #> Weighting: none #> @@ -451,7 +451,7 @@ <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 -#> 1.220 1.216 0.920 </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 +#> 1.244 1.176 0.911 </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 @@ -528,7 +528,7 @@ #> Model cost at call 152 : 371.2134 #> Optimisation by method Port successfully terminated. #> user system elapsed -#> 0.724 0.048 0.722 </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 +#> 0.724 0.040 0.713 </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 @@ -571,8 +571,8 @@ <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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 16:45:50 2016 -#> Date of summary: Fri Nov 18 16:45:50 2016 +#> Date of fit: Fri Nov 18 22:52:29 2016 +#> Date of summary: Fri Nov 18 22:52:29 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -580,7 +580,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.872 s +#> Fitted with method Port using 185 model solutions performed in 0.757 s #> #> Weighting: none #> @@ -692,8 +692,8 @@ #> 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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 16:45:52 2016 -#> Date of summary: Fri Nov 18 16:45:52 2016 +#> Date of fit: Fri Nov 18 22:52:31 2016 +#> Date of summary: Fri Nov 18 22:52:31 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -701,7 +701,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 486 model solutions performed in 2.009 s +#> Fitted with method Port using 486 model solutions performed in 2.046 s #> #> Weighting: none then iterative reweighting method obs #> @@ -813,8 +813,8 @@ #> 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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 16:45:53 2016 -#> Date of summary: Fri Nov 18 16:45:53 2016 +#> Date of fit: Fri Nov 18 22:52:32 2016 +#> Date of summary: Fri Nov 18 22:52:32 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -822,7 +822,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.647 s +#> Fitted with method Port using 155 model solutions performed in 0.64 s #> #> Weighting: mean #> @@ -935,8 +935,8 @@ <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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 16:45:54 2016 -#> Date of summary: Fri Nov 18 16:45:54 2016 +#> Date of fit: Fri Nov 18 22:52:33 2016 +#> Date of summary: Fri Nov 18 22:52:33 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -944,7 +944,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.749 s +#> Fitted with method Port using 174 model solutions performed in 0.752 s #> #> Weighting: manual #> @@ -1057,8 +1057,8 @@ <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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 16:45:55 2016 -#> Date of summary: Fri Nov 18 16:45:55 2016 +#> Date of fit: Fri Nov 18 22:52:34 2016 +#> Date of summary: Fri Nov 18 22:52:34 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1066,7 +1066,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 316 model solutions performed in 1.288 s +#> Fitted with method Port using 316 model solutions performed in 1.28 s #> #> Weighting: manual #> @@ -1179,8 +1179,8 @@ <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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 16:45:58 2016 -#> Date of summary: Fri Nov 18 16:45:58 2016 +#> Date of fit: Fri Nov 18 22:52:37 2016 +#> Date of summary: Fri Nov 18 22:52:37 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1188,7 +1188,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 648 model solutions performed in 2.738 s +#> Fitted with method Port using 648 model solutions performed in 2.631 s #> #> Weighting: manual then iterative reweighting method obs #> |