calc1DCIs

This computes 1D confidence intervals from an inferred likelihood surface by profile likelihood ratio methods

inference

Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.

Franois Rousset

blackbox

Black Box Optimization and Exploration of Parameter Space

François Rousset

Raphaël Leblois

calc1DCIs function

<dl> <dt>oneDimCIvars</dt>
<dd>The names of parameters for which confidence intervals are computed</dd> <dt>FONKgNames</dt>
<dd>The names of &#8220;Fitted Or Not&#8221; parameters (see Details in <code>blackbox.options</code> for this concept)</dd> <dt>fittedNames</dt>
<dd>The names of fitted parameters (see Details in <code>blackbox.options</code> for this concept)</dd> <dt>CIlevel</dt>
<dd>Level (1-coverage) of the confidence intervals. Default is 0.05.</dd> <dt>nextBounds</dt>
<dd>For development purposes, not documented</dd> <dt>NextBoundsLevel</dt>
<dd>For development purposes, not documented</dd> <dt>boundsOutfile</dt>
<dd>For development purposes, not documented</dd> <dt>dataString</dt>
<dd>A prefix string in some outputs.</dd> <dt>cleanResu</dt>
<dd>A connection, or a character string naming a file for some nicely formated output. If <code>""</code> (the default), print to the standard output connection.</dd></dl>

Arguments

Compute 1D confidence intervals — calc1DCIs

<dl>

 <dt>oneDimCIvars</dt>
<dd>The names of parameters for which confidence intervals are computed</dd>

 <dt>FONKgNames</dt>
<dd>The names of &#8220;Fitted Or Not&#8221; parameters (see Details in <code>blackbox.options</code> for this concept)</dd>

 <dt>fittedNames</dt>
<dd>The names of fitted parameters (see Details in <code>blackbox.options</code> for this concept)</dd>

 <dt>CIlevel</dt>
<dd>Level (1-coverage) of the confidence intervals. Default is 0.05.</dd>

 <dt>nextBounds</dt>
<dd>For development purposes, not documented</dd>

 <dt>NextBoundsLevel</dt>
<dd>For development purposes, not documented</dd>

 <dt>boundsOutfile</dt>
<dd>For development purposes, not documented</dd>

 <dt>dataString</dt>
<dd>A prefix string in some outputs.</dd>

 <dt>cleanResu</dt>
<dd>A connection, or a character string naming a file for some nicely formated output. If <code>""</code> (the default), print to the standard output connection.</dd>

</dl>

calc1DCIs: Compute 1D confidence intervals

Description

Usage

Value

Arguments