diff options
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 50 |
1 files changed, 26 insertions, 24 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3c8442b6..9bbe3900 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -326,7 +326,7 @@ <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>, or "tc" for the - two component error model. The option "manual" is available for + two component error model. The option "manual" is available for the case that <code>err</code>!=<code>NULL</code>, but it is not necessary to specify it.</p></td> </tr> <tr> @@ -406,6 +406,8 @@ <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> +<p>Comparisons of models fitted to the same data can be made using <code>AIC</code> + by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p> <p>Fitting of several models to several datasets in a single call to <code><a href='mmkin.html'>mmkin</a></code>.</p></div> @@ -434,15 +436,15 @@ <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 used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:16:52 2018 -#> Date of summary: Tue Sep 18 15:16:52 2018 +#> Date of fit: Fri Nov 23 19:57:22 2018 +#> Date of summary: Fri Nov 23 19:57:22 2018 #> #> 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 0.158 s +#> Fitted with method Port using 64 model solutions performed in 0.155 s #> #> Weighting: none #> @@ -511,7 +513,7 @@ <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 verstrichen -#> 1.011 0.000 1.012 </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 +#> 0.995 0.000 0.995 </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 @@ -586,7 +588,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.755 0.000 0.755 </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 +#> 0.789 0.000 0.790 </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 @@ -624,8 +626,8 @@ <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 used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:04 2018 -#> Date of summary: Tue Sep 18 15:17:04 2018 +#> Date of fit: Fri Nov 23 19:57:34 2018 +#> Date of summary: Fri Nov 23 19:57:34 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -633,7 +635,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.823 s +#> Fitted with method Port using 186 model solutions performed in 0.825 s #> #> Weighting: none #> @@ -741,8 +743,8 @@ #> 120 m1 33.31 28.78984 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 used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:06 2018 -#> Date of summary: Tue Sep 18 15:17:06 2018 +#> Date of fit: Fri Nov 23 19:57:36 2018 +#> Date of summary: Fri Nov 23 19:57:36 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -750,7 +752,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.374 s +#> Fitted with method Port using 551 model solutions performed in 2.528 s #> #> Weighting: none #> @@ -863,8 +865,8 @@ #> 120 m1 33.31 28.80898 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 used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:07 2018 -#> Date of summary: Tue Sep 18 15:17:07 2018 +#> Date of fit: Fri Nov 23 19:57:37 2018 +#> Date of summary: Fri Nov 23 19:57:37 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -872,7 +874,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.636 s +#> Fitted with method Port using 155 model solutions performed in 0.687 s #> #> Weighting: mean #> @@ -981,8 +983,8 @@ <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 used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:08 2018 -#> Date of summary: Tue Sep 18 15:17:08 2018 +#> Date of fit: Fri Nov 23 19:57:38 2018 +#> Date of summary: Fri Nov 23 19:57:38 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -990,7 +992,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.717 s +#> Fitted with method Port using 174 model solutions performed in 0.781 s #> #> Weighting: manual #> @@ -1101,8 +1103,8 @@ <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 used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:09 2018 -#> Date of summary: Tue Sep 18 15:17:09 2018 +#> Date of fit: Fri Nov 23 19:57:39 2018 +#> Date of summary: Fri Nov 23 19:57:39 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1110,7 +1112,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.181 s +#> Fitted with method Port using 270 model solutions performed in 1.201 s #> #> Weighting: manual #> @@ -1219,8 +1221,8 @@ <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 used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:13 2018 -#> Date of summary: Tue Sep 18 15:17:13 2018 +#> Date of fit: Fri Nov 23 19:57:43 2018 +#> Date of summary: Fri Nov 23 19:57:43 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1228,7 +1230,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.077 s +#> Fitted with method Port using 692 model solutions performed in 3.087 s #> #> Weighting: manual #> |