cluster: plantTraits – R documentation

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plantTraits

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 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

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

cluster

"Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.

v2.1.2

GPL (>= 2)

Authors

Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Peter Rousseeuw [aut] (Fortran original, <https://orcid.org/0000-0002-3807-5353>), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, <https://orcid.org/0000-0001-6398-4850>), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), <https://orcid.org/0000-0003-4198-9911>), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), <https://orcid.org/0000-0001-9143-4880>), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))

Initial release

2021-04-16