biplots function

Biplots of co-correspondence analysis models

Produces biplots of the response and predictor from the results of a co-correspondence analysis models.

## S3 method for class 'symcoca'
biplot(x,
    which = "y1",
    choices = 1:2,
    benzecri = TRUE,
    type = NULL,
    xlim = NULL,
    ylim = NULL,
    col.species = "red",
    col.sites = "black",
    pch.species = 3,
    pch.sites = 1,
    cex = 0.7,
    main = "",
    sub = "",
    ylab, xlab,
    ann = par("ann"),
    axes = TRUE,
    ...)

## S3 method for class 'predcoca'
biplot(x,
    which = "response",
    choices = 1:2,
    type = NULL,
    xlim = NULL,
    ylim = NULL,
    col.species = "red",
    col.sites = "black",
    pch.species = 3,
    pch.sites = 1,
    cex = 0.7,
    main = "",
    sub = "",
    ylab, xlab,
    ann = par("ann"),
    axes = TRUE,
    ...)

Arguments

• x: an object of class "symcoca", the result of a call to symcoca.

• which: character; should the response or predictor scores be plotted. Can be specified in several ways: response choices are one from c("y", "Y", "y1", "response"); predictor

  choices are one from c("x", "X", "y2", "predictor").

• choices: a vector of length 2 indicating which predictive CoCA axes to plot.

• benzecri: logical, should a Benzecri plot be drawn? Such plots draw species scores, scaled by the quarter root of the respective eigenvalues, with unscaled site scores. A Benzecri plot is the recommended biplot for symmetric CoCA. See scores.symcoca.

• type: one of "points", or "text". Determines how the site and species scores are displayed. If type = "points", scores are plotted as points. If type = "text", then the row names of the scores matrices are plotted.

• xlim, ylim: limits for the x and y axes. If non supplied, suitable limits will be determined from the data.

• col.species, col.sites, pch.species, pch.sites: colours and plotting characters used when plotting the species and sites scores.

• cex: numeric; scaling factor when drawing points or text labels.

• xlab, ylab: labels for the x and y axes. If non supplied suitable labels are formed from the result object.

• main, sub: the main and sub titles for the plot.

• ann: logical, if TRUE plots are annotated and not if FALSE, currently ignored.

• axes: a logical value indicating whether axes and plot border should be drawn on the plot.

• ...: other graphical parameters as in 'par' may also be passed as arguments.

References

Ter Braak, C.J.F and Schaffers, A.P. (2004) Co-Correspondence Analysis: a new ordination method to relate two community compositions. Ecology 85(3) , 834--846

Author(s)

Gavin L. Simpson.

See Also

coca, plot.default

Examples

## symmetric CoCA
data(beetles)
data(plants)

## log transform the beetle data
beetles <- log(beetles + 1)

## fit the model
bp.sym <- coca(beetles ~ ., data = plants, method = "symmetric")

## draw a biplot of the beetle results
biplot(bp.sym)

## biplot of both - Fig 1 in ter Braak & Schaffers (2004)
layout(matrix(1:2, ncol = 2))
biplot(bp.sym, which = "y1", main = "Beetles")
biplot(bp.sym, which = "y2", main = "Plants")
layout(1)

## predictive CoCA
bp.pred <- coca(beetles ~ ., data = plants)

## draw a biplot of the response
biplot(bp.pred)

## recreate Fig 3 in ter Braak & Schaffers (2004)
layout(matrix(1:2, ncol = 2))
biplot(bp.pred, which = "response", main = "Beetles")
biplot(bp.pred, which = "predictor", main = "Plants")
layout(1)