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Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/confint.mkinfit.html | 31 |
1 files changed, 22 insertions, 9 deletions
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 64ea0d4c..ec8938c5 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -36,7 +36,9 @@ <meta property="og:title" content="Confidence intervals for parameters of mkinfit objects — confint.mkinfit" /> -<meta property="og:description" content="Confidence intervals for parameters of mkinfit objects" /> +<meta property="og:description" content="The default method 'profile' is based on the profile likelihood for each +parameter. The method uses two nested optimisations. The speed of the method +could likely be improved by using the method of Venzon and Moolgavkar (1988)." /> <meta name="twitter:card" content="summary" /> @@ -133,14 +135,16 @@ </div> <div class="ref-description"> - <p>Confidence intervals for parameters of mkinfit objects</p> + <p>The default method 'profile' is based on the profile likelihood for each +parameter. The method uses two nested optimisations. 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> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>object</span>, <span class='no'>parm</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> - - <span class='no'>level</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"profile"</span>, <span class='st'>"quadratic"</span>), <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distribution</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"student_t"</span>, <span class='st'>"normal"</span>), - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> + <span class='no'>level</span>, <span class='no'>cutoff</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"profile"</span>, <span class='st'>"quadratic"</span>), + <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>distribution</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"student_t"</span>, <span class='st'>"normal"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -163,6 +167,12 @@ confidence intervals. If missing, all parameters are considered.</p></td> <td><p>The allowed error probability, overrides 'level' if specified.</p></td> </tr> <tr> + <th>cutoff</th> + <td><p>Possibility to specify an alternative cutoff for the difference +in the log-likelihoods at the confidence boundary. Specifying an explicit +cutoff value overrides arguments 'level' and 'alpha'</p></td> + </tr> + <tr> <th>method</th> <td><p>The 'profile' method searches the parameter space for the cutoff of the confidence intervals by means of a likelihood ratio test. @@ -204,7 +214,10 @@ the parameter estimate</p></td> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>Pawitan Y (2013) In all likelihood - Statistical modelling and - inference using likelihood. Clarendon Press, Oxford.</p> + inference using likelihood. Clarendon Press, Oxford. + Venzon DJ and Moolgavkar SH (1988) A Method for Computing + Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, + 87–94.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -213,9 +226,9 @@ the parameter estimate</p></td> #> k_parent_sink 0.2109541 0.4440528 #> sigma 1.9778868 7.3681380</div><div class='input'><span class='co'># \dontrun{</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 71.3471007 93.9447024 -#> k_parent_sink 0.2030765 0.4491067 -#> sigma 2.9810656 8.8633278</div><div class='input'># } +#> parent_0 73.0641834 92.1392181 +#> k_parent_sink 0.2170293 0.4235348 +#> sigma 3.1307772 8.0628314</div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |