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Diffstat (limited to 'docs')
| -rw-r--r-- | docs/news/index.html | 5 | ||||
| -rw-r--r-- | docs/reference/confint.mkinfit.html | 20 | ||||
| -rw-r--r-- | docs/reference/lrtest.mkinfit.html | 30 |
3 files changed, 37 insertions, 18 deletions
diff --git a/docs/news/index.html b/docs/news/index.html index baddfc96..5aef06f9 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -134,12 +134,13 @@ <a href="#mkin-0-9-49-8-unreleased" class="anchor"></a>mkin 0.9.49.8 (unreleased)<small> Unreleased </small> </h1> <ul> -<li>‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes too much time for any with more than three parameters</li> +<li><p>‘lrtest.mkinfit’: Improve naming of the compared fits in the case of fixed parameters</p></li> +<li><p>‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes a lot of time, especially if the fit has more than three parameters</p></li> </ul> </div> <div id="mkin-0-9-49-7-2019-11-01" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-49-7-2019-11-01" class="anchor"></a>mkin 0.9.49.7 (2019-11-01)<small> Unreleased </small> +<a href="#mkin-0-9-49-7-2019-11-01" class="anchor"></a>mkin 0.9.49.7 (2019-11-01)<small> 2019-11-02 </small> </h1> <ul> <li><p>Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation</p></li> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 13662adf..ea69c3bb 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -40,10 +40,10 @@ the curvature of the likelihood function at the maximum likelihood parameter estimates. The alternative method 'profile' is based on the profile likelihood for each -parameter. The method uses two nested optimisations and can take a very long -time, even if parallelized by specifying 'cores' on unixoid platforms. The -speed of the method could likely be improved by using the method of Venzon -and Moolgavkar (1988)." /> +parameter. The 'profile' method uses two nested optimisations and can take a +very long time, even if parallelized by specifying 'cores' on unixoid +platforms. The speed of the method could likely be improved by using the +method of Venzon and Moolgavkar (1988)." /> <meta name="twitter:card" content="summary" /> @@ -144,10 +144,10 @@ and Moolgavkar (1988)." /> the curvature of the likelihood function at the maximum likelihood parameter estimates. The alternative method 'profile' is based on the profile likelihood for each -parameter. The method uses two nested optimisations and can take a very long -time, even if parallelized by specifying 'cores' on unixoid platforms. The -speed of the method could likely be improved by using the method of Venzon -and Moolgavkar (1988).</p> +parameter. The 'profile' method uses two nested optimisations and can take a +very long time, even if parallelized by specifying 'cores' on unixoid +platforms. The speed of the method could likely be improved by using the +method of Venzon and Moolgavkar (1988).</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> @@ -254,13 +254,13 @@ On Windows machines, cores > 1 is currently not supported.</p></td> <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>f_d_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</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/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> User System verstrichen -#> 51.341 0.000 51.370 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> +#> 51.058 0.000 51.088 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> <span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> <span class='co'># minor interest), we get a nice performance improvement from about 50</span> <span class='co'># seconds to about 12 seconds if we use at least four cores</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile_no_parent_0</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> User System verstrichen -#> 0.001 0.007 11.432 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#> 2.5% 97.5% +#> 0.005 0.004 11.349 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#> 2.5% 97.5% #> parent_0 96.456003650 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 #> k_parent_m1 0.046786482 5.500879e-02 diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index fae471fc..1d82eb74 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -73,7 +73,7 @@ and can be expressed by fixing the parameters of the other." /> </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">0.9.49.8</span> </span> </div> @@ -196,11 +196,29 @@ lower number of fitted parameters (null hypothesis).</p> #> 2 3 -63.954 -2 43.002 4.594e-10 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'> -# The following two examples are commented out as they fail during -# generation of the static help pages by pkgdown -# lrtest(dfop_fit, error_model = "tc") -# lrtest(dfop_fit, fixed_parms = c(k2 = 0)) -# } +<span class='co'># The following two examples are commented out as they fail during</span> +<span class='co'># generation of the static help pages by pkgdown</span> +<span class='co'>#lrtest(dfop_fit, error_model = "tc")</span> +<span class='co'>#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span> + +<span class='co'># However, this equivalent syntax works for static help pages</span> +<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>dfop_fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>))</div><div class='output co'>#> Likelihood ratio test +#> +#> Model 1: DFOP with error model tc +#> Model 2: DFOP with error model const +#> #Df LogLik Df Chisq Pr(>Chisq) +#> 1 6 -34.587 +#> 2 5 -42.453 -1 15.731 7.302e-05 *** +#> --- +#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>dfop_fit</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0</span>)))</div><div class='output co'>#> Likelihood ratio test +#> +#> Model 1: DFOP with error model const +#> Model 2: DFOP with error model const and fixed parameter(s) k2 +#> #Df LogLik Df Chisq Pr(>Chisq) +#> 1 5 -42.453 +#> 2 4 -57.340 -1 29.776 4.851e-08 *** +#> --- +#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |