diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-04-10 10:17:35 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-04-10 10:17:35 +0200 |
| commit | 194659fcaccdd1ee37851725b8c72e99daa3a8cf (patch) | |
| tree | edbbebe8956000b9eb725ca425b91e051571ec02 /docs/reference/summary.mkinfit.html | |
| parent | 5814be02f286ce96d6cff8d698aea6844e4025f1 (diff) | |
Adapt tests, vignettes and examples
- Write the NEWS
- Static documentation rebuilt by pkgdown
- Adapt mkinerrmin
- Fix (hopefully all) remaining problems in mkinfit
Diffstat (limited to 'docs/reference/summary.mkinfit.html')
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 64 |
1 files changed, 34 insertions, 30 deletions
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f561e258..e5565990 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -32,10 +32,10 @@ <meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" /> -<meta property="og:description" content="Lists model equations, the summary as returned by summary.modFit, - the chi2 error levels calculated according to FOCUS guidance (2006) as far - as defined therein, and optionally the data, consisting of observed, predicted - and residual values." /> +<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with some + uncertainty statistics, the chi2 error levels calculated according to FOCUS + guidance (2006) as defined therein, formation fractions, DT50 values and + optionally the data, consisting of observed, predicted and residual values." /> <meta name="twitter:card" content="summary" /> @@ -66,7 +66,7 @@ </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">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -131,10 +131,10 @@ <div class="ref-description"> - <p>Lists model equations, the summary as returned by <code>summary.modFit</code>, - the chi2 error levels calculated according to FOCUS guidance (2006) as far - as defined therein, and optionally the data, consisting of observed, predicted - and residual values.</p> + <p>Lists model equations, initial parameter values, optimised parameters with some + uncertainty statistics, the chi2 error levels calculated according to FOCUS + guidance (2006) as defined therein, formation fractions, DT50 values and + optionally the data, consisting of observed, predicted and residual values.</p> </div> @@ -178,8 +178,7 @@ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The summary function returns a list derived from - <code>summary.modFit</code>, with components, among others</p> + <p>The summary function returns a list with components, among others</p> <dt>version, Rversion</dt><dd><p>The mkin and R versions used</p></dd> <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were produced</p></dd> <dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd> @@ -193,6 +192,7 @@ <dt>errmin </dt><dd><p>The chi2 error levels for each observed variable.</p></dd> <dt>bparms.ode </dt><dd><p>All backtransformed ODE parameters, for use as starting parameters for related models.</p></dd> + <dt>errparms </dt><dd><p>Error model parameters.</p></dd> <dt>ff </dt><dd><p>The estimated formation fractions derived from the fitted model.</p></dd> <dt>distimes </dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> <dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> @@ -209,52 +209,56 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></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='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 -#> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 14:06:25 2019 -#> Date of summary: Mon Mar 4 14:06:25 2019 + <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></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='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 +#> R version used for fitting: 3.5.3 +#> Date of fit: Wed Apr 10 10:11:15 2019 +#> Date of summary: Wed Apr 10 10:11:15 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.085 s +#> Fitted with method using 131 model solutions performed in 0.284 s #> -#> Weighting: none +#> Error model: +#> NULL #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 101.24 state -#> k_parent_sink 0.10 deparm +#> value type +#> parent_0 101.240000 state +#> k_parent_sink 0.100000 deparm +#> sigma 5.265546 error #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> parent_0 101.240000 -Inf Inf #> log_k_parent_sink -2.302585 -Inf Inf +#> sigma 5.265546 0 Inf #> #> Fixed parameter values: #> None #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper -#> parent_0 109.200 4.3910 98.410 119.900 -#> log_k_parent_sink -3.291 0.1152 -3.573 -3.009 +#> parent_0 109.200 3.70400 99.630 118.700 +#> log_k_parent_sink -3.291 0.09176 -3.527 -3.055 +#> sigma 5.266 1.31600 1.882 8.649 #> #> Parameter correlation: -#> parent_0 log_k_parent_sink -#> parent_0 1.000 0.575 -#> log_k_parent_sink 0.575 1.000 -#> -#> Residual standard error: 6.08 on 6 degrees of freedom +#> parent_0 log_k_parent_sink sigma +#> parent_0 1.000e+00 5.428e-01 1.642e-07 +#> log_k_parent_sink 5.428e-01 1.000e+00 2.507e-07 +#> sigma 1.642e-07 2.507e-07 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 109.20000 24.860 1.394e-07 98.41000 119.90000 -#> k_parent_sink 0.03722 8.679 6.457e-05 0.02807 0.04934 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 109.20000 29.47 4.218e-07 99.6300 118.70000 +#> k_parent_sink 0.03722 10.90 5.650e-05 0.0294 0.04712 +#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 #> #> Chi2 error levels in percent: #> err.min n.optim df |