Plant Species Traits Data

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

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.

% Plant height}{an ordered factor with levels \code{1} <10cm < \code{2} 10-30cm< \code{3} 30-60cm< \code{4}60-100cm < \code{5}1-3m < \code{6}3-6m < \code{7}:6-15m < \code{8}>15m}

begflow

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

% {\code{begflow}}{an ordered factor with levels \code{1} january< \code{2} february< \code{3} march< \code{4}april < \code{5} may< \code{6} june< \code{7} july< \code{8}august < \code{9}september}

mycor

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

vegaer

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

vegsout

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

autopoll

selfing pollination, an ordered factor with levels 0never < 1rare < 2 often< the rule3

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
#>   [1] 1 1 2 2 3 4 4 2 3 5 5 2 2 1 5 4 6 2 6 1 5 4 3 2 2 3 2 1 4 6 6 6 6 2 5 6 3
#>  [38] 5 4 3 5 2 2 6 1 6 1 1 3 4 4 3 3 3 6 2 5 2 2 2 6 5 5 4 4 6 2 6 2 6 3 6 2 2
#>  [75] 4 2 4 2 5 4 5 4 5 5 5 4 2 2 1 2 3 3 6 6 6 6 2 6 6 3 3 6 6 6 6 6 6 5 5 4 5
#> [112] 6 6 2 6 4 6 6 2 3 4 6 6 3 6 2 3 6 1 5 2 4 2 3 3 3

## Principal Coordinate Analysis
cmdsdai.b <- cmdscale(dai.b, k=6)
plot(cmdsdai.b[, 1:2], asp = 1, col = cutree6)