EVOLUTION-MANAGER
Edit File: plantTraits.html
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: Plant Species Traits Data</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <link rel="stylesheet" type="text/css" href="R.css" /> </head><body> <table width="100%" summary="page for plantTraits {cluster}"><tr><td>plantTraits {cluster}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plant Species Traits Data</h2> <h3>Description</h3> <p>This dataset constitutes a description of 136 plant species according to biological attributes (morphological or reproductive) </p> <h3>Usage</h3> <pre>data(plantTraits) </pre> <h3>Format</h3> <p>A data frame with 136 observations on the following 31 variables. </p> <dl> <dt><code>pdias</code></dt><dd><p>Diaspore mass (mg)</p> </dd> <dt><code>longindex</code></dt><dd><p>Seed bank longevity</p> </dd> <dt><code>durflow</code></dt><dd><p>Flowering duration</p> </dd> <dt><code>height</code></dt><dd><p>Plant height, an ordered factor with levels <code>1</code> < <code>2</code> < ... < <code>8</code>.</p> </dd> </dl> <dl> <dt><code>begflow</code></dt><dd><p>Time of first flowering, an ordered factor with levels <code>1</code> < <code>2</code> < <code>3</code> < <code>4</code> < <code>5</code> < <code>6</code> < <code>7</code> < <code>8</code> < <code>9</code></p> </dd> </dl> <dl> <dt><code>mycor</code></dt><dd><p>Mycorrhizas, an ordered factor with levels <code>0</code>never < <code>1</code> sometimes< <code>2</code>always</p> </dd> <dt><code>vegaer</code></dt><dd><p>aerial vegetative propagation, an ordered factor with levels <code>0</code>never < <code>1</code> present but limited< <code>2</code>important.</p> </dd> <dt><code>vegsout</code></dt><dd><p>underground vegetative propagation, an ordered factor with 3 levels identical to <code>vegaer</code> above.</p> </dd> <dt><code>autopoll</code></dt><dd><p>selfing pollination, an ordered factor with levels <code>0</code>never < <code>1</code>rare < <code>2</code> often< the rule<code>3</code></p> </dd> <dt><code>insects</code></dt><dd><p>insect pollination, an ordered factor with 5 levels <code>0</code> < ... < <code>4</code>.</p> </dd> <dt><code>wind</code></dt><dd><p>wind pollination, an ordered factor with 5 levels <code>0</code> < ... < <code>4</code>.</p> </dd> <dt><code>lign</code></dt><dd><p>a binary factor with levels <code>0:1</code>, indicating if plant is woody.</p> </dd> <dt><code>piq</code></dt><dd><p>a binary factor indicating if plant is thorny.</p> </dd> <dt><code>ros</code></dt><dd><p>a binary factor indicating if plant is rosette.</p> </dd> <dt><code>semiros</code></dt><dd><p>semi-rosette plant, a binary factor (<code>0</code>: no; <code>1</code>: yes).</p> </dd> <dt><code>leafy</code></dt><dd><p>leafy plant, a binary factor.</p> </dd> <dt><code>suman</code></dt><dd><p>summer annual, a binary factor.</p> </dd> <dt><code>winan</code></dt><dd><p>winter annual, a binary factor.</p> </dd> <dt><code>monocarp</code></dt><dd><p>monocarpic perennial, a binary factor.</p> </dd> <dt><code>polycarp</code></dt><dd><p>polycarpic perennial, a binary factor.</p> </dd> <dt><code>seasaes</code></dt><dd><p>seasonal aestival leaves, a binary factor.</p> </dd> <dt><code>seashiv</code></dt><dd><p>seasonal hibernal leaves, a binary factor.</p> </dd> <dt><code>seasver</code></dt><dd><p>seasonal vernal leaves, a binary factor.</p> </dd> <dt><code>everalw</code></dt><dd><p>leaves always evergreen, a binary factor.</p> </dd> <dt><code>everparti</code></dt><dd><p>leaves partially evergreen, a binary factor.</p> </dd> <dt><code>elaio</code></dt><dd><p>fruits with an elaiosome (dispersed by ants), a binary factor.</p> </dd> <dt><code>endozoo</code></dt><dd><p>endozoochorous fruits, a binary factor.</p> </dd> <dt><code>epizoo</code></dt><dd><p>epizoochorous fruits, a binary factor.</p> </dd> <dt><code>aquat</code></dt><dd><p>aquatic dispersal fruits, a binary factor.</p> </dd> <dt><code>windgl</code></dt><dd><p>wind dispersed fruits, a binary factor.</p> </dd> <dt><code>unsp</code></dt><dd><p>unspecialized mechanism of seed dispersal, a binary factor.</p> </dd> </dl> <h3>Details</h3> <p>Most of factor attributes are not disjunctive. For example, a plant can be usually pollinated by insects but sometimes self-pollination can occured. </p> <h3>Source</h3> <p>Vallet, Jeanne (2005) <em>Structuration de communautés végétales et analyse comparative de traits biologiques le long d'un gradient d'urbanisation</em>. Mémoire de Master 2 'Ecologie-Biodiversité-Evolution'; Université Paris Sud XI, 30p.+ annexes (in french) </p> <h3>Examples</h3> <pre> data(plantTraits) ## Calculation of a dissimilarity matrix library(cluster) dai.b <- daisy(plantTraits, type = list(ordratio = 4:11, symm = 12:13, asymm = 14:31)) ## Hierarchical classification agn.trts <- agnes(dai.b, method="ward") plot(agn.trts, which.plots = 2, cex= 0.6) plot(agn.trts, which.plots = 1) cutree6 <- cutree(agn.trts, k=6) cutree6 ## Principal Coordinate Analysis cmdsdai.b <- cmdscale(dai.b, k=6) plot(cmdsdai.b[, 1:2], asp = 1, col = cutree6) </pre> <hr /><div style="text-align: center;">[Package <em>cluster</em> version 2.0.8 <a href="00Index.html">Index</a>]</div> </body></html>