Direct Gradient Analysis
Direct gradient analysis is a graphical representation of the abundance distribution of (typically) species along opposing environmental gradients
dga(z,x,y,step=50,pres="+",abs="-",labcex=1,
xlab = deparse(substitute(x)), ylab = deparse(substitute(y)),
pch = 1, title = "", ...)z |
the variable (typically a species abundance) to be plotted |
x |
the variable to use as the x axis |
y |
the variable to use as the y axis |
step |
controls the grid density fed to the GAM surface fitter |
pres |
the symbol to print when a species is present (presence/absence mode) |
abs |
the symbol to print when a species is absent (presence/absence mode) |
labcex |
the character size for contour labels |
xlab |
the x axis legend |
ylab |
the y axis legend |
pch |
the symbol to print in continuous abundance plots |
title |
the title to print |
... |
miscellaneous arguments to pass to par |
‘dga’ interpolates a grid of x,y values from the supplied data
and fits a GAM (from mgcv) of the z variable to the grid.
For presence/absence data (enterd as a logical) it employs a binomial family, for
species abundances a negative binomial is employed.
The GAM surface is then represented by a contour map and abundance
symbols as described above.
a graph of the distribution of the z variable on a grid of x and y is displayed on the current active device.
Direct gradient analysis was promoted by Robert Whittaker and followers as a preferred method of vegetation analysis.
data(bryceveg) # returns a data.frame called bryceveg x <- c(0.2,0.5,1.0,2.0,3.0,4.0,5.0,6.0) y <- c(0.2,0.5,3.0,15.0,37.5,62.5,85.0,97.5) cover <- abundtrans(bryceveg,x,y) data(brycesite) dga(round(cover$arcpat),brycesite$elev,brycesite$av)
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