D4TAlink-common-args

Arguments used across the functions of the D4TAlink package.

Tools, methods and processes for the management
of analysis workflows. These lightweight solutions facilitate
structuring R&D activities. These solutions were developed to comply
with Good Documentation Practice (GDP),
with ALCOA+ principles as proposed by the U.S. FDA, and
with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>.

Gregoire Thomas

D4TAlink.light

GDP - Workflow Management

D4TAlink-common-args function

<dl><dt>project</dt>
<dd>Project name.</dd>
<dt>package</dt>
<dd>Package name.</dd>
<dt>taskname</dt>
<dd>Task name.</dd>
<dt>author</dt>
<dd>Author name, system username by default.</dd>
<dt>sponsor</dt>
<dd>Sponsor name, default set by <code>setTaskSponsor</code>.</dd>
<dt>rootpath</dt>
<dd>Path of the task repository, default set by <code>setTaskRoot</code>.</dd>
<dt>task</dt>
<dd>Object of class <code>D4TAlinkTask</code>, as created by <code>initTask</code>.</dd>
<dt>type</dt>
<dd>Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]</dd>
<dt>ext</dt>
<dd>Filename extension.</dd>
<dt>suffix</dt>
<dd>Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.</dd>
<dt>dirType</dt>
<dd>Directory type, e.g. 'bin' or 'data' or 'doc'.</dd>
<dt>subdir</dt>
<dd>(optional) Subdirectory.</dd>
<dt>dirCreate</dt>
<dd>Logical, if TRUE (by default) the directory is created.</dd>
<dt>pathgen</dt>
<dd>optional function returning a list of paths, currently <code>pathsGLPG</code> or <code>pathsPMS</code>.</dd></dl>

Arguments

Arguments used across the functions of the D4TAlink package. — D4TAlink-common-args

<dl>

<dt>project</dt>
<dd>Project name.</dd>


<dt>package</dt>
<dd>Package name.</dd>


<dt>taskname</dt>
<dd>Task name.</dd>


<dt>author</dt>
<dd>Author name, system username by default.</dd>


<dt>sponsor</dt>
<dd>Sponsor name, default set by <code>setTaskSponsor</code>.</dd>


<dt>rootpath</dt>
<dd>Path of the task repository, default set by <code>setTaskRoot</code>.</dd>


<dt>task</dt>
<dd>Object of class <code>D4TAlinkTask</code>, as created by <code>initTask</code>.</dd>


<dt>type</dt>
<dd>Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]</dd>


<dt>ext</dt>
<dd>Filename extension.</dd>


<dt>suffix</dt>
<dd>Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.</dd>


<dt>dirType</dt>
<dd>Directory type, e.g. 'bin' or 'data' or 'doc'.</dd>


<dt>subdir</dt>
<dd>(optional) Subdirectory.</dd>


<dt>dirCreate</dt>
<dd>Logical, if TRUE (by default) the directory is created.</dd>


<dt>pathgen</dt>
<dd>optional function returning a list of paths, currently <code>pathsGLPG</code> or <code>pathsPMS</code>.</dd>

</dl>

D4TAlink-common-args: Arguments used across the functions of the D4TAlink package.

Description

Value

Arguments