diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-08 20:57:48 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-08 20:57:48 +0200 |
| commit | c6079a807e2b400fe0c772603392aeacd887da2f (patch) | |
| tree | 5b590e06de87ce9cd5c776fccfabc8a629a10cad /docs/reference/mkinfit.html | |
| parent | c322a8102a399cbb1fe38c4c4ca4485cea8bc4e8 (diff) | |
Add functionality to plot the error model
by plotting squared residuals against predicted values, and
showing the variance function used in the fitted error model.
Rebuild docs
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 28 |
1 files changed, 14 insertions, 14 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 09329a86..bfca44fc 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -362,15 +362,15 @@ Per default, parameters in the kinetic models are internally transformed in <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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue May 7 08:36:16 2019 -#> Date of summary: Tue May 7 08:36:16 2019 +#> Date of fit: Wed May 8 20:50:50 2019 +#> Date of summary: Wed May 8 20:50:50 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 0.89 s +#> Fitted using 222 model solutions performed in 0.456 s #> #> Error model: #> Constant variance @@ -443,7 +443,7 @@ Per default, parameters in the kinetic models are internally transformed in <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://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>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 -#> 2.251 0.000 2.253 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>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 +#> 1.488 0.000 1.488 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>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 #> @@ -515,7 +515,7 @@ Per default, parameters in the kinetic models are internally transformed in #> 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 -#> 1.151 0.000 1.152 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>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 +#> 1.086 0.000 1.087 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>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 #> @@ -547,8 +547,8 @@ Per default, parameters in the kinetic models are internally transformed in <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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue May 7 08:36:33 2019 -#> Date of summary: Tue May 7 08:36:33 2019 +#> Date of fit: Wed May 8 20:51:06 2019 +#> Date of summary: Wed May 8 20:51:06 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -556,7 +556,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.1 s +#> Fitted using 421 model solutions performed in 1.082 s #> #> Error model: #> Constant variance @@ -665,8 +665,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue May 7 08:36:35 2019 -#> Date of summary: Tue May 7 08:36:35 2019 +#> Date of fit: Wed May 8 20:51:08 2019 +#> Date of summary: Wed May 8 20:51:08 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -674,7 +674,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 758 model solutions performed in 1.991 s +#> Fitted using 758 model solutions performed in 1.971 s #> #> Error model: #> Variance unique to each observed variable @@ -795,8 +795,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.80430 -3.654e+00 #> 120 m1 33.31 28.80430 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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue May 7 08:36:39 2019 -#> Date of summary: Tue May 7 08:36:39 2019 +#> Date of fit: Wed May 8 20:51:11 2019 +#> Date of summary: Wed May 8 20:51:11 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -804,7 +804,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 821 model solutions performed in 3.304 s +#> Fitted using 821 model solutions performed in 3.29 s #> #> Error model: #> Two-component variance function |