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/transform_odeparms.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/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 82 |
1 files changed, 43 insertions, 39 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index fbc792f1..7e05480e 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -71,7 +71,7 @@ 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="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> @@ -202,30 +202,32 @@ The transformation of sets of formation fractions is fragile, as it supposes <pre class="examples"><div class='input'><span class='no'>SFO_SFO</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='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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='no'>fit.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</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>)</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='no'>fit.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>) <span class='co'># Transformed and backtransformed parameters</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.60 1.6137 96.33 102.87 -#> log_k_parent_sink -3.04 0.0783 -3.20 -2.88 -#> log_k_parent_m1 -2.98 0.0412 -3.06 -2.90 -#> log_k_m1_sink -5.25 0.1361 -5.52 -4.97</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.613712 61.72 2.02e-38 96.32572 1.03e+02 -#> k_parent_sink 0.04792 0.003750 12.78 3.05e-15 0.04089 5.62e-02 -#> k_parent_m1 0.05078 0.002094 24.25 3.41e-24 0.04670 5.52e-02 -#> k_m1_sink 0.00526 0.000716 7.35 5.76e-09 0.00399 6.93e-03</div><div class='input'> +#> parent_0 99.60 1.5702 96.40 102.79 +#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 +#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 +#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 +#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 +#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 +#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 +#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> </div><div class='input'><span class='co'># Compare to the version without transforming rate parameters</span> -<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>) +<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.59848 1.613710 96.32573 1.03e+02 -#> k_parent_sink 0.04792 0.003750 0.04031 5.55e-02 -#> k_parent_m1 0.05078 0.002094 0.04653 5.50e-02 -#> k_m1_sink 0.00526 0.000716 0.00381 6.71e-03</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.613710 61.72 2.02e-38 96.32573 1.03e+02 -#> k_parent_sink 0.04792 0.003750 12.78 3.05e-15 0.04031 5.55e-02 -#> k_parent_m1 0.05078 0.002094 24.25 3.41e-24 0.04653 5.50e-02 -#> k_m1_sink 0.00526 0.000716 7.35 5.76e-09 0.00381 6.71e-03</div><div class='input'> +#> parent_0 99.59848 1.57022 96.40384 1.03e+02 +#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 +#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 +#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 +#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 +#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 +#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 +#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</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'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></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> @@ -238,17 +240,18 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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>)</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='no'>fit.ff.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>) +<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>)</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='no'>fit.ff.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.598 1.6137 96.3257 102.871 -#> log_k_parent -2.316 0.0419 -2.4006 -2.231 -#> log_k_m1 -5.248 0.1361 -5.5235 -4.972 -#> f_parent_ilr_1 0.041 0.0648 -0.0904 0.172</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.613712 61.72 2.02e-38 96.32574 1.03e+02 -#> k_parent 0.09870 0.004132 23.88 5.70e-24 0.09066 1.07e-01 -#> k_m1 0.00526 0.000716 7.35 5.76e-09 0.00399 6.93e-03 -#> f_parent_to_m1 0.51448 0.022880 22.49 4.37e-23 0.46808 5.61e-01</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) +#> parent_0 99.598 1.5702 96.4038 102.793 +#> log_k_parent -2.316 0.0409 -2.3988 -2.233 +#> log_k_m1 -5.248 0.1332 -5.5184 -4.977 +#> f_parent_ilr_1 0.041 0.0631 -0.0875 0.169 +#> sigma 3.126 0.3585 2.3961 3.855</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 +#> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 +#> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 +#> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>)</div><div class='output co'>#> f_parent_to_m1 #> 0.5 </div><div class='input'> @@ -258,15 +261,16 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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>)</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='no'>fit.ff.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>) +<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>)</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='no'>fit.ff.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 84.79 2.9651 78.78 90.80 -#> log_k_parent -2.76 0.0809 -2.92 -2.59 -#> log_k_m1 -4.21 0.1115 -4.44 -3.99</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 84.7916 2.96505 28.60 3.94e-27 78.7838 90.7994 -#> k_parent 0.0635 0.00514 12.36 5.24e-15 0.0539 0.0748 -#> k_m1 0.0148 0.00165 8.97 4.11e-11 0.0118 0.0185</div></pre> +#> parent_0 84.79 3.012 78.67 90.91 +#> log_k_parent -2.76 0.082 -2.92 -2.59 +#> log_k_m1 -4.21 0.123 -4.46 -3.96 +#> sigma 8.22 0.943 6.31 10.14</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913 +#> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075 +#> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019 +#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |