goeveg (version 0.2.0)

specresponses: Multiple species response curves

Description

This function draws multiple species response curves for rough interpretation of species responses to environmental gradients or ordination axes. It is based on smooth.spline which fits a cubic smoothing spline to the supplied data. In contrast to specresponse this function can draw multiple curves into one plot, but will not draw points.

Usage

specresponses(matrix, var, main, xlab, method = "env", axis = 1, df = 5, bw = FALSE)

Arguments

matrix

Community data, a matrix-like object with samples in rows and species in columns. Response curves are drawn for all selected columns (species).

var

Vector containing environmental variable (per plot) OR vegan ordination result object if method = "ord".

main

Optional: Main title.

xlab

Optional: Label of x-axis.

method

Method defining the type of variable. Default method = "env" fits a response curve to environmental variables. Alternatively method = "ord" fits a response along ordination axes.

axis

Ordination axis (only if method = "ord").

df

Desired equivalent number of degrees of freedom (trace of the smoother matrix).

bw

If set on TRUE the lines will be drawn in black/white with different line types instead of colours.

Details

For response curves based on environmental gradients the argument var takes a single vector containing the variable corresponding to the species abundances. For a response to ordination axis (method = "ord") the argument var requires a vegan ordination result object (e.g. from decorana, cca, rda or metaMDS). First axis is used as default. A minimum of 10 occurences is recommenced to use response curves. Curves for species with less than 5 occurences are not drawn. It is recommended to filter the vegetation matrix for species with a minimum frequency of 10 before using this function. If you plot a response curve for only one species the use of specresponse is recommended for correct labels and the display of points.

See Also

specresponse

Examples

## Species (columns) need to be selected; call names() to get column numbers
names(schedenveg)
## Draw multiple species response curves on variable in black/white
specresponses(schedenveg[ ,c(9,18,14,19)], schedenenv$height_herb, bw = TRUE)

## Draw multiple species response curves on variable with
## custom x-axis label and lower df
specresponses(schedenveg[ ,c(9,18,14,19)], schedenenv$height_herb, df = 3,
    xlab = "Height of herb layer (cm)")

## Draw multiple species response curves on ordination axes
## First calculate DCA
library(vegan)
scheden.dca <- decorana(schedenveg)
specresponses(schedenveg[ ,c(9,18,14,19)], scheden.dca, method = "ord")
specresponses(schedenveg[ ,c(9,18,14,19)], scheden.dca, method = "ord", axis = 2)

## Plot with manually log-transformed abundances
specresponses(log(schedenveg[ ,c(9,18,14,19)]+1), schedenenv$height_herb)