demo.samples

A samples database, for demonstrating the <code>TRAMPR</code> package.
 This is a subset of a full samples database, is not intended to
 represent any real data set, and should not be assumed to be
 accurate.
The data are stored as a <code><a rd-options="" href="/link/TRAMPsamples?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::TRAMPsamples">TRAMPsamples</a></code> object. Columns in
 the <code>info</code> and <code>data</code> components are described on the
 <code><a rd-options="" href="/link/TRAMPsamples?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::TRAMPsamples">TRAMPsamples</a></code> page, but with some additions:<ul>
<li><code>info</code>:<ul>
<li><code>soilcore.fk</code>: Key to the soil core from which a
 sample came. See <code>soilcore</code>, below.</li>
</ul></li>
<li><code>data</code>:<ul>
<li><code>sample.file.name</code>: Original <code>.fsa</code> file
 corresponding to the TRFLP run. This is included in all
 <code>TRAMPsamples</code> objects created by <code><a rd-options="" href="/link/load.abi?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::load.abi">load.abi</a></code>.</li>
</ul></li>
<li><code>soilcore</code>: A <code>data.frame</code> with information about
 the soilcore from which samples came.<ul>
<li><code>soilcore.pk</code>: Key, distinguishing soil cores.</li>
<li><code>plot</code>: Plot number (1 to 10).</li>
<li><code>elevation</code>: Height above mean sea level, in metres.</li>
<li><code>east</code>: Easting (New Zealand Map Grid/NZMG).</li>
<li><code>north</code>: Northing (NZMG).</li>
<li><code>vegetation</code>: Vegetation type (<code>Nothofagus
	solandri</code> or <code>Pinus contorta</code>).</li>
</ul></li>
</ul>

datasets

Matching terminal restriction fragment length
polymorphism ('TRFLP') profiles between unknown samples and a
database of known samples.  'TRAMPR' facilitates analysis of
many unknown profiles at once, and provides tools for working
directly with electrophoresis output through to generating
summaries suitable for community analyses with R's rich set of
statistical functions.  'TRAMPR' also resolves the issues of
multiple 'TRFLP' profiles within a species, and shared 'TRFLP'
profiles across species.

Rich FitzJohn

TRAMPR

'TRFLP' Analysis and Matching Package for R

Ian Dickie

demo.samples function

A <code><a rd-options="" href="/link/TRAMPsamples?package=TRAMPR&version=1.0-10" data-mini-rdoc="TRAMPR::TRAMPsamples">TRAMPsamples</a></code> object.

Format

This data set is provided under a Creative Commons
 &#8220;Attribution-NonCommercial-NoDerivs 2.5&#8221; licence. Please see
 <a href="https://creativecommons.org/licenses/by-nc-nd/2.5/">https://creativecommons.org/licenses/by-nc-nd/2.5/</a> for details.

Licence

A samples database, for demonstrating the <code>TRAMPR</code> package.
 This is a subset of a full samples database, is not intended to
 represent any real data set, and should not be assumed to be
 accurate.
The data are stored as a <code><a rd-options='' href='TRAMPsamples'>TRAMPsamples</a></code> object. Columns in
 the <code>info</code> and <code>data</code> components are described on the
 <code><a rd-options='' href='TRAMPsamples'>TRAMPsamples</a></code> page, but with some additions:<ul>
<li><code>info</code>:<ul>
<li><code>soilcore.fk</code>: Key to the soil core from which a
 sample came. See <code>soilcore</code>, below.</li>
</ul></li>
<li><code>data</code>:<ul>
<li><code>sample.file.name</code>: Original <code>.fsa</code> file
 corresponding to the TRFLP run. This is included in all
 <code>TRAMPsamples</code> objects created by <code><a rd-options='' href='load.abi'>load.abi</a></code>.</li>
</ul></li>
<li><code>soilcore</code>: A <code>data.frame</code> with information about
 the soilcore from which samples came.<ul>
<li><code>soilcore.pk</code>: Key, distinguishing soil cores.</li>
<li><code>plot</code>: Plot number (1 to 10).</li>
<li><code>elevation</code>: Height above mean sea level, in metres.</li>
<li><code>east</code>: Easting (New Zealand Map Grid/NZMG).</li>
<li><code>north</code>: Northing (NZMG).</li>
<li><code>vegetation</code>: Vegetation type (<code>Nothofagus
	solandri</code> or <code>Pinus contorta</code>).</li>
</ul></li>
</ul>

Demonstration Samples Database — demo.samples

A <code><a rd-options='' href='TRAMPsamples'>TRAMPsamples</a></code> object.

This data set is provided under a Creative Commons
 &#8220;Attribution-NonCommercial-NoDerivs 2.5&#8221; licence. Please see
 <a href='https://creativecommons.org/licenses/by-nc-nd/2.5/'>https://creativecommons.org/licenses/by-nc-nd/2.5/</a> for details.

demo.samples: Demonstration Samples Database

Description

Usage

Arguments

Format

Licence