R: Plant assemblages in woodlands of the conurbation of Angers...

woangers {ade4} | R Documentation

## Plant assemblages in woodlands of the conurbation of Angers (France)

### Description

This data set gives the presence of plant species in relevés of woodlands in the conurbation of Angers; and their biological traits.

### Usage

    data(woangers)

### Format

`woangers` is a list of 2 components.

1. flo: is a data frame that contains the presence/absence of species in each sample site. In the codes for the sample sites (first column of the data frame), the first three letters provide the code of the woodland and the numbers represent the 5 quadrats sampled in each site. Codes for the woodlands are based on either their local name when they have one or on the name of the nearest locality.

2. traits: is a data frame that contains the values of the 13 functional traits considered in the paper. One trait can be encoded by several columns. The codes are as follows:

   - Column 1: Species names;

   - Column 2: `li`, nominal variable that indicates the presence (y) or absence (n) of ligneous structures;

   - Column 3: `pr`, nominal variable that indicates the presence (y) or absence (n) of prickly structures;

   - Column 4: `fo`, circular variable that indicates the month when the flowering period starts (from 1 January to 9 September);

   - Column 5: `he`, ordinal variable that indicates the maximum height of the leaf canopy;

   - Column 6: `ae`, ordinal variable that indicates the degree of aerial vegetative multiplication;

   - Column 7: `un`, ordinal variable that indicates the degree of underground vegetative multiplication;

   - Column 8: `lp`, nominal variable that represents the leaf position by 3 levels (`ros` = rosette, `semiros` = semi-rosette and `leafy` = leafy stem);

   - Column 9: `le`, nominal variable that represents the mode of leaf persistence by 5 levels (`seasaes` = seasonal aestival, `seashib` = seasonal hibernal, `seasver` = seasonal vernal, `everalw` = always evergreen, `everparti` = partially evergreen);

   - Columns 10, 11 and 12: fuzzy variable that describes the modes of pollination with 3 levels (`auto` = autopollination, `insects` = pollination by insects, `wind` = pollination by wind); this fuzzy variable is expressed as proportions, i.e. for each row, the sum of the three columns equals 1;

   - Columns 13, 14 and 15: fuzzy variable that describes the life cycle with 3 levels (annual, monocarpic and polycarpic); this fuzzy variable is expressed as proportions, i.e. for each row, the sum of the three column equals 1;

   - Columns 16 to 20: fuzzy variable that describes the modes of dispersion with 5 levels (`elaio` = dispersion by ants, `endozoo` = injection by animals, `epizoo` = external transport by animals, `wind` = transport by wind, `unsp` = unspecialized transport); this fuzzy variable is expressed as proportions, i.e. for each row, the sum of the three columns equals 1;

   - Column 21: `lo`, quantitative variable that provides the seed bank longevity index;

   - Column 22: `lf`, quantitative variable that provides the length of the flowering period.

### Source

Pavoine, S., Vallet, J., Dufour, A.-B., Gachet, S. and Daniel, H. (2009) On the challenge of treating various types of variables: Application for improving the measurement of functional diversity. Oikos, 118, 391–402.

### Examples

    # Loading the data
    data(woangers)

    # Preparating of the traits
    traits <- woangers$traits
    # Nominal variables 'li', 'pr', 'lp' and 'le'
    # (see table 1 in the main text for the codes of the variables)
    tabN <- traits[, c(1:2, 7, 8)]
    # Circular variable 'fo'
    tabC <- traits[3]
    tabCp <- prep.circular(tabC, 1, 12)
    # The levels of the variable lie between 1 (January) and 12 (December).
    # Ordinal variables 'he', 'ae' and 'un'
    tabO <- traits[, 4:6]
    # Fuzzy variables 'mp', 'pe' and 'di'
    tabF <- traits[, 9:19]
    tabFp <- prep.fuzzy(tabF, c(3, 3, 5), labels = c("mp", "pe", "di"))
    # 'mp' has 3 levels, 'pe' has 3 levels and 'di' has 5 levels.
    # Quantitative variables 'lo' and 'lf'
    tabQ <- traits[, 20:21]

    # Combining the traits
    ktab1 <- ktab.list.df(list(tabN, tabCp, tabO, tabFp, tabQ))
    ## Not run:
    # Calculating the distances for all traits combined
    distrait <- dist.ktab(ktab1, c("N", "C", "O", "F", "Q"))
    is.euclid(distrait)

    # Calculating the contribution of each trait in the combined distances
    contrib <- kdist.cor(ktab1, type = c("N", "C", "O", "F", "Q"))
    contrib
    dotchart(sort(contrib$glocor), labels = rownames(contrib$glocor)[order(contrib$glocor[, 1])])

    ## End(Not run)

[Package ade4 version 1.7-16 Index]