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/transform_odeparms.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/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 245 |
1 files changed, 224 insertions, 21 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index a31b075e..c0ca534c 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes </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> @@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>parent</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'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</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'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.47.3 +<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</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 06:39:25 2018 -#> Date of summary: Fri Sep 14 06:39:25 2018 +#> Date of fit: Fri Sep 14 11:36:07 2018 +#> Date of summary: Fri Sep 14 11:36:07 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.642 s +#> Fitted with method Port using 153 model solutions performed in 0.627 s #> #> Weighting: none #> @@ -273,10 +273,82 @@ The transformation of sets of formation fractions is fragile, as it supposes #> DT50 DT90 #> parent 7.023 23.33 #> m1 131.761 437.70</div><div class='input'> -</div><span class='co'># NOT RUN {</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</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>) -<span class='co'># }</span><div class='input'> +</div><div class='input'><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</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 11:36:08 2018 +#> Date of summary: Fri Sep 14 11:36:08 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 350 model solutions performed in 1.437 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent_sink 0.1000 deparm +#> k_parent_m1 0.1001 deparm +#> k_m1_sink 0.1002 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.7500 -Inf Inf +#> k_parent_sink 0.1000 0 Inf +#> k_parent_m1 0.1001 0 Inf +#> k_m1_sink 0.1002 0 Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.600000 1.6140000 96.330000 1.029e+02 +#> k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02 +#> k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02 +#> k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03 +#> +#> Parameter correlation: +#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> parent_0 1.00000 0.6075 -0.06625 -0.1701 +#> k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +#> k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +#> k_m1_sink -0.17006 -0.6253 0.47164 1.0000 +#> +#> Residual standard error: 3.211 on 36 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 +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02 +#> k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02 +#> k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.827 3 6 +#> m1 4.490 1 9 +#> +#> Resulting formation fractions: +#> ff +#> parent_sink 0.4855 +#> parent_m1 0.5145 +#> m1_sink 1.0000 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70</div><div class='input'> <span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> <span class='fu'>names</span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start</span>) <span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> @@ -284,29 +356,160 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink #> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> -</div><span class='co'># NOT RUN {</span> -<span class='co'># The case of formation fractions</span> +</div><div class='input'><span class='co'># The case of formation fractions</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'>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'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>) -<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) -<span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) +<span class='fu'>summary</span>(<span class='no'>fit.ff</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 11:36:09 2018 +#> Date of summary: Fri Sep 14 11:36:09 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 186 model solutions performed in 0.773 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000 +#> +#> Residual standard error: 3.211 on 36 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 +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.459 2 7 +#> m1 4.690 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5145 +#> parent_sink 0.4855 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) <span class='no'>transformed</span> <span class='kw'><-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>) -<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>) - +<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#> f_parent_to_m1 +#> 0.5 </div><div class='input'> <span class='co'># And without sink</span> <span class='no'>SFO_SFO.ff.2</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'>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'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>m1</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) -<span class='co'># }</span></pre> +<span class='fu'>summary</span>(<span class='no'>fit.ff.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 11:36:10 2018 +#> Date of summary: Fri Sep 14 11:36:10 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 104 model solutions performed in 0.424 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 84.790 2.96500 78.78 90.800 +#> log_k_parent -2.756 0.08088 -2.92 -2.593 +#> log_k_m1 -4.214 0.11150 -4.44 -3.988 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 +#> parent_0 1.0000 0.11058 0.46156 +#> log_k_parent 0.1106 1.00000 0.06274 +#> log_k_m1 0.4616 0.06274 1.00000 +#> +#> Residual standard error: 8.333 on 37 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 +#> parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000 +#> k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483 +#> k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 19.66 3 16 +#> parent 17.56 2 7 +#> m1 18.71 1 9 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 10.91 36.25 +#> m1 46.89 155.75</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |