diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-10-31 01:55:01 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-10-31 01:59:05 +0100 |
| commit | 7091d3738e7e55acb20edb88772b228f6f5b6c98 (patch) | |
| tree | b6e31700074605c702662e5238162c57de330453 /docs/reference/mkinfit.html | |
| parent | 5e4ea59a41e00b05ea6664c08c7922e892e8ab77 (diff) | |
Add likelihood ratio test and other methods, fixes
The likelihood ratio test method is lrtest, in addition,
methods for update and residuals were added.
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 32 |
1 files changed, 17 insertions, 15 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 6c98bc38..c72d1cd0 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -218,7 +218,9 @@ must be given.</p></td> <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> +rather kept at the values specified in <code>parms.ini</code>. Alternatively, +a named numeric vector of parameters to be fixed, regardless of the values +in parms.ini.</p></td> </tr> <tr> <th>fixed_initials</th> @@ -400,15 +402,15 @@ estimators.</p> <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'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:07 2019 -#> Date of summary: Fri Oct 25 02:08:07 2019 +#> Date of fit: Thu Oct 31 01:48:29 2019 +#> Date of summary: Thu Oct 31 01:48:29 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.453 s +#> Fitted using 222 model solutions performed in 0.455 s #> #> Error model: Constant variance #> @@ -480,7 +482,7 @@ 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'>#> <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'><-</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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.447 0.000 1.448 </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'>#> 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'>#> $ff +#> 1.464 0.000 1.465 </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'>#> 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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -553,7 +555,7 @@ estimators.</p> #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 1.032 0.000 1.032 </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'>#> 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'>#> $ff +#> 1.047 0.000 1.047 </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'>#> 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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -589,8 +591,8 @@ estimators.</p> <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>)</div><div class='output co'>#> <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'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:22 2019 -#> Date of summary: Fri Oct 25 02:08:22 2019 +#> Date of fit: Thu Oct 31 01:48:44 2019 +#> Date of summary: Thu Oct 31 01:48:44 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -598,7 +600,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.062 s +#> Fitted using 421 model solutions performed in 1.136 s #> #> Error model: Constant variance #> @@ -706,8 +708,8 @@ estimators.</p> #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</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'>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'>#> <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'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:25 2019 -#> Date of summary: Fri Oct 25 02:08:25 2019 +#> Date of fit: Thu Oct 31 01:48:47 2019 +#> Date of summary: Thu Oct 31 01:48:47 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -715,7 +717,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 978 model solutions performed in 2.523 s +#> Fitted using 978 model solutions performed in 2.512 s #> #> Error model: Variance unique to each observed variable #> @@ -838,8 +840,8 @@ estimators.</p> #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>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'>#> <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'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:34 2019 -#> Date of summary: Fri Oct 25 02:08:34 2019 +#> Date of fit: Thu Oct 31 01:48:56 2019 +#> Date of summary: Thu Oct 31 01:48:56 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -847,7 +849,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.136 s +#> Fitted using 2289 model solutions performed in 9.124 s #> #> Error model: Two-component variance function #> |