R: Plant Species Traits Data

plantTraits {cluster} | R Documentation

## Plant Species Traits Data

### Description

This dataset constitutes a description of 136 plant species according to biological attributes (morphological or reproductive)

### Usage

    data(plantTraits)

### Format

A data frame with 136 observations on the following 31 variables.

`pdias`

  Diaspore mass (mg)

`longindex`

  Seed bank longevity

`durflow`

  Flowering duration

`height`

  Plant height, an ordered factor with levels `1` < `2` < ... < `8`.

`begflow`

  Time of first flowering, an ordered factor with levels `1` < `2` < `3` < `4` < `5` < `6` < `7` < `8` < `9`

`mycor`

  Mycorrhizas, an ordered factor with levels `0`never < `1` sometimes< `2`always

`vegaer`

  aerial vegetative propagation, an ordered factor with levels `0`never < `1` present but limited< `2`important.

`vegsout`

  underground vegetative propagation, an ordered factor with 3 levels identical to `vegaer` above.

`autopoll`

  selfing pollination, an ordered factor with levels `0`never < `1`rare < `2` often< the rule`3`

`insects`

  insect pollination, an ordered factor with 5 levels `0` < ... < `4`.

`wind`

  wind pollination, an ordered factor with 5 levels `0` < ... < `4`.

`lign`

  a binary factor with levels `0:1`, indicating if plant is woody.

`piq`

  a binary factor indicating if plant is thorny.

`ros`

  a binary factor indicating if plant is rosette.

`semiros`

  semi-rosette plant, a binary factor (`0`: no; `1`: yes).

`leafy`

  leafy plant, a binary factor.

`suman`

  summer annual, a binary factor.

`winan`

  winter annual, a binary factor.

`monocarp`

  monocarpic perennial, a binary factor.

`polycarp`

  polycarpic perennial, a binary factor.

`seasaes`

  seasonal aestival leaves, a binary factor.

`seashiv`

  seasonal hibernal leaves, a binary factor.

`seasver`

  seasonal vernal leaves, a binary factor.

`everalw`

  leaves always evergreen, a binary factor.

`everparti`

  leaves partially evergreen, a binary factor.

`elaio`

  fruits with an elaiosome (dispersed by ants), a binary factor.

`endozoo`

  endozoochorous fruits, a binary factor.

`epizoo`

  epizoochorous fruits, a binary factor.

`aquat`

  aquatic dispersal fruits, a binary factor.

`windgl`

  wind dispersed fruits, a binary factor.

`unsp`

  unspecialized mechanism of seed dispersal, a binary factor.

### Details

Most of factor attributes are not disjunctive. For example, a plant can be usually pollinated by insects but sometimes self-pollination can occured.

### Source

Vallet, Jeanne (2005) Structuration de communautés végétales et analyse comparative de traits biologiques le long d'un gradient d'urbanisation. Mémoire de Master 2 'Ecologie-Biodiversité-Evolution'; Université Paris Sud XI, 30p.+ annexes (in french)

### Examples

    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)

[Package cluster version 1.14.2 Index]