setupDirStructure

Convenience function to set up the directory structure used for storing data and results.

The provided benchmark suite enables the automated evaluation and comparison of any existing and novel indirect method for reference interval ('RI') estimation in a systematic way.
Indirect methods take routine measurements of diagnostic tests, containing pathological and non-pathological samples as input and use sophisticated
statistical methods to derive a model describing the distribution of the non-pathological samples, which can then be
used to derive reference intervals. The benchmark suite contains 5,760 simulated test sets with varying difficulty.
To include any indirect method, a custom wrapper function needs to be provided.
The package offers functions for generating the test sets, executing the indirect method and evaluating the results.
See ?RIbench or vignette("RIbench_package") for a more comprehensive description of the features.
A detailed description and application is described in Ammer T., Schuetzenmeister A., Prokosch H.-U., Zierk J., Rank C.M., Rauh M. "RIbench: A Proposed Benchmark for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation". Clinical Chemistry (2022) <doi:10.1093/clinchem/hvac142>.

Tatjana Ammer

RIbench

Benchmark Suite for Indirect Methods for RI Estimation

Christopher Rank

Andre Schuetzenmeister

setupDirStructure function

<dl><dt>outputDir</dt>
<dd>(character) specifying the base output directory. From here, Data/biomarker and Result/algoName/biomarker directories are generated</dd>
<dt>onlyData</dt>
<dd>(logical) if set to TRUE, only the biomarker subdirectories are generated, name of output directory is used as it is (default:FALSE)</dd>
<dt>onlyResults</dt>
<dd>(logical) if set to TRUE, only the algoName/biomarker subdirectories are generated, name of output directory is used as it is (default:FALSE)</dd>
<dt>tableTCs</dt>
<dd>(data frame) containing the pre-defined parameter combinations to generate the simulations</dd>
<dt>algoName</dt>
<dd>(character) specifying the name of the algorithm used for creating the subdirectory</dd></dl>

Arguments

Tatjana Ammer <a href="/link/tatjana.ammer%40roche.com?package=RIbench&version=1.0.2" data-mini-rdoc="RIbench::tatjana.ammer@roche.com">tatjana.ammer@roche.com</a>

Author

Convenience function to set up the directory structure used for storing data and results. — setupDirStructure

<dl>

<dt>outputDir</dt>
<dd>(character) specifying the base output directory. From here, Data/biomarker and Result/algoName/biomarker directories are generated</dd>


<dt>onlyData</dt>
<dd>(logical) if set to TRUE, only the biomarker subdirectories are generated, name of output directory is used as it is (default:FALSE)</dd>


<dt>onlyResults</dt>
<dd>(logical) if set to TRUE, only the algoName/biomarker subdirectories are generated, name of output directory is used as it is (default:FALSE)</dd>


<dt>tableTCs</dt>
<dd>(data frame) containing the pre-defined parameter combinations to generate the simulations</dd>


<dt>algoName</dt>
<dd>(character) specifying the name of the algorithm used for creating the subdirectory</dd>

</dl>

Tatjana Ammer <a href='mailto:tatjana.ammer@roche.com'>tatjana.ammer@roche.com</a>

setupDirStructure: Convenience function to set up the directory structure used for storing data and results.

Description

Usage

Value

Arguments

Author