diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 11:38:43 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 11:38:43 +0200 |
| commit | c4a35c0e141a4bb05ba508914bebdc2884109e76 (patch) | |
| tree | 81464f3e17e683dfc7614dadf0899850517954f7 /docs/reference/mccall81_245T.html | |
| parent | dd65f3503e9d091c82aedcf91635fcf40f778bf9 (diff) | |
Exclude more example code from CRAN checks
to avoid NOTES about long execution times.
Static documentation rebuilt by pkgdown with run_dont_run = TRUE
Diffstat (limited to 'docs/reference/mccall81_245T.html')
| -rw-r--r-- | docs/reference/mccall81_245T.html | 111 |
1 files changed, 96 insertions, 15 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index cea92155..ac2adf1e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -155,19 +155,11 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'> </div><span class='co'># NOT RUN {</span> - <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='co'># }</span><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span> - <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span> - <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), - <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), - <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.3 + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 06:39:07 2018 -#> Date of summary: Fri Sep 14 06:39:07 2018 +#> Date of fit: Fri Sep 14 11:34:50 2018 +#> Date of summary: Fri Sep 14 11:34:50 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -177,7 +169,96 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.423 s +#> Fitted with method Port using 574 model solutions performed in 3.33 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> T245_0 100.9000 state +#> k_T245_sink 0.1000 deparm +#> k_T245_phenol 0.1001 deparm +#> k_phenol_sink 0.1002 deparm +#> k_phenol_anisole 0.1003 deparm +#> k_anisole_sink 0.1004 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> T245_0 100.900000 -Inf Inf +#> log_k_T245_sink -2.302585 -Inf Inf +#> log_k_T245_phenol -2.301586 -Inf Inf +#> log_k_phenol_sink -2.300587 -Inf Inf +#> log_k_phenol_anisole -2.299590 -Inf Inf +#> log_k_anisole_sink -2.298593 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> phenol_0 0 state +#> anisole_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> T245_0 103.9000 NA NA NA +#> log_k_T245_sink -4.1130 NA NA NA +#> log_k_T245_phenol -3.6120 NA NA NA +#> log_k_phenol_sink -25.0800 NA NA NA +#> log_k_phenol_anisole -0.9037 NA NA NA +#> log_k_anisole_sink -5.0090 NA NA NA +#> +#> Parameter correlation:</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#> Could not estimate covariance matrix; singular system: +#> +#> Residual standard error: 2.78 on 18 degrees of freedom +#> +#> 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 +#> T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA +#> k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA +#> k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA +#> k_phenol_sink 1.286e-11 4.575e-11 5.000e-01 NA NA +#> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA +#> k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 10.070 6 16 +#> T245 7.908 3 5 +#> phenol 106.445 2 5 +#> anisole 5.379 1 6 +#> +#> Resulting formation fractions: +#> ff +#> T245_sink 3.772e-01 +#> T245_phenol 6.228e-01 +#> phenol_sink 3.175e-11 +#> phenol_anisole 1.000e+00 +#> anisole_sink 1.000e+00 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> T245 15.982 53.091 +#> phenol 1.711 5.685 +#> anisole 103.784 344.763</div><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span> + <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span> + <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:34:51 2018 +#> Date of summary: Fri Sep 14 11:34:51 2018 +#> +#> Equations: +#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 +#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - +#> k_phenol_anisole * phenol +#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 246 model solutions performed in 1.417 s #> #> Weighting: none #> @@ -257,7 +338,7 @@ #> DT50 DT90 #> T245 15.982 53.091 #> phenol 1.711 5.685 -#> anisole 103.784 344.763</div></pre> +#> anisole 103.784 344.763</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |