diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-03-30 21:43:10 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-03-30 21:43:10 +0200 |
| commit | 575fcacaa33076de97f41a79afb37efb97ca82e0 (patch) | |
| tree | 0ad2a40da65e7026f22566ed41c3b53d21fe9e64 /docs/reference/mkinfit.html | |
| parent | cfa1340c41fe77117c3c2481ddbb25579f196bdd (diff) | |
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 109 |
1 files changed, 62 insertions, 47 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7ee73f15..ffc8d52b 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -75,7 +75,7 @@ likelihood function." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -148,18 +148,33 @@ degradation model parameters, as both of them are arguments of the likelihood function.</p> </div> - <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <pre class="usage"><span class='fu'>mkinfit</span>( + <span class='no'>mkinmod</span>, + <span class='no'>observed</span>, + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], + <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>), - <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, + <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>eval.max</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>iter.max</span> <span class='kw'>=</span> <span class='fl'>200</span>), - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, + <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"const"</span>, <span class='st'>"obs"</span>, <span class='st'>"tc"</span>), - <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, - <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, - <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> + <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, + <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), + <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, + <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, + <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -400,17 +415,17 @@ estimators.</p> <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'><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 Nov 1 10:08:21 2019 -#> Date of summary: Fri Nov 1 10:08:21 2019 +<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: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:41:20 2020 +#> Date of summary: Mon Mar 30 21:41:20 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.456 s +#> Fitted using 222 model solutions performed in 0.463 s #> #> Error model: Constant variance #> @@ -440,10 +455,10 @@ estimators.</p> #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08 -#> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.758e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.007e-07 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.568e-08 +#> sigma 4.758e-08 1.007e-07 8.568e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -482,7 +497,7 @@ 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 -#> 1.488 0.000 1.491 </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 +#> 1.526 0.000 1.530 </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 #> @@ -533,9 +548,9 @@ estimators.</p> #> Sum of squared residuals at call 82: 373.1711 #> Sum of squared residuals at call 84: 373.1711 #> Sum of squared residuals at call 87: 372.6445 -#> Sum of squared residuals at call 88: 372.1615 -#> Sum of squared residuals at call 90: 372.1615 -#> Sum of squared residuals at call 91: 372.1615 +#> Sum of squared residuals at call 88: 372.1614 +#> Sum of squared residuals at call 90: 372.1614 +#> Sum of squared residuals at call 91: 372.1614 #> Sum of squared residuals at call 94: 371.6464 #> Sum of squared residuals at call 99: 371.4299 #> Sum of squared residuals at call 101: 371.4299 @@ -555,7 +570,7 @@ 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 -#> 1.058 0.000 1.059 </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 +#> 1.083 0.000 1.084 </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 #> @@ -589,10 +604,10 @@ estimators.</p> <span class='co'># \dontrun{</span> <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>)</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 Nov 1 10:08:36 2019 -#> Date of summary: Fri Nov 1 10:08:36 2019 + <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: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:41:36 2020 +#> Date of summary: Mon Mar 30 21:41:36 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -600,7 +615,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.083 s +#> Fitted using 422 model solutions performed in 1.144 s #> #> Error model: Constant variance #> @@ -634,11 +649,11 @@ estimators.</p> #> #> Parameter correlation: #> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma -#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -2.265e-07 -#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.785e-07 -#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.386e-07 -#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -3.641e-08 -#> sigma -2.265e-07 3.785e-07 -1.386e-07 -3.641e-08 1.000e+00 +#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -2.443e-07 +#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.181e-07 +#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.369e-07 +#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -2.287e-08 +#> sigma -2.443e-07 3.181e-07 -1.369e-07 -2.287e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -706,10 +721,10 @@ estimators.</p> #> 100 m1 31.04 31.98163 -9.416e-01 #> 100 m1 33.13 31.98163 1.148e+00 #> 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 Nov 1 10:08:39 2019 -#> Date of summary: Fri Nov 1 10:08:39 2019 +#> 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: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:41:39 2020 +#> Date of summary: Mon Mar 30 21:41:39 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -717,7 +732,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 978 model solutions performed in 2.553 s +#> Fitted using 979 model solutions performed in 2.576 s #> #> Error model: Variance unique to each observed variable #> @@ -838,10 +853,10 @@ estimators.</p> #> 100 m1 31.04 31.98773 -9.477e-01 #> 100 m1 33.13 31.98773 1.142e+00 #> 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 Nov 1 10:08:48 2019 -#> Date of summary: Fri Nov 1 10:08:48 2019 +#> 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: 0.9.49.9 +#> R version used for fitting: 3.6.3 +#> Date of fit: Mon Mar 30 21:41:50 2020 +#> Date of summary: Mon Mar 30 21:41:50 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -849,12 +864,12 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.253 s +#> Fitted using 2552 model solutions performed in 10.593 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Direct fitting and three-step fitting yield approximately the same likelihood +#> Three-step fitting yielded a higher likelihood than direct fitting #> #> Starting values for parameters to be optimised: #> value type @@ -960,8 +975,8 @@ estimators.</p> #> 50 m1 40.01 41.34199 -1.331985 #> 75 m1 40.09 36.61471 3.475295 #> 75 m1 33.85 36.61471 -2.764705 -#> 100 m1 31.04 32.20082 -1.160823 -#> 100 m1 33.13 32.20082 0.929177 +#> 100 m1 31.04 32.20082 -1.160824 +#> 100 m1 33.13 32.20082 0.929176 #> 120 m1 25.15 29.04130 -3.891304 #> 120 m1 33.31 29.04130 4.268696</div><div class='input'># } |