plotGradientKDE {paleoAM}R Documentation

Plot Kernel Density Estimates of Species Abundance Across a Focal Gradient

Description

This function plots each rescaled KDE fit to each specific-specific rise-and-fall in abundance across some ecological gradient variable.

Usage

plotGradientKDE(
  speciesKDEs,
  fullGradientRange,
  xlim = NULL,
  ylim = c(0, 1),
  logY = FALSE
)

Arguments

speciesKDEs

A list of rescaled-KDE data, where each element is a different species, such as that output by getSpeciesSpecificRescaledKDE.

fullGradientRange

The minimum and maximum value of the ecological gradient variable at which ecological assemblage data was observed. If xlim isn't given, this defines the horizontal axis limits for resulting plot.

xlim, ylim

Vectors of two elements, defining the minimum and maximum values for the horizontal (x) axis and vertical (y) axis, respectively. The default for xlim is NULL and only needs to be defined if different axis limits than fullGradientRange is desired. The default for ylim is c(0,1) which likely leaves considerable empty white space above the KDEs, which can be reduced by adjusting this argument.

logY

Should the vertical axis (the relative height of rescaled KDEs) be portrayed with logarithmic scaling?

Details

In many ways, this is an attempt to create empirical versions of the the hypothetical figures portraying abundance response curves relative to an environmental gradient in Patzkowsky & Holland (2012).

The ecological gradient variable is often an environmental characteristic, such as depth, oxygenation, altitude, precipitation, but this is not necessarily so.

Value

Nothing is returned, just a plot is made.

References

Patzkowsky, M.E. and Holland, S.M., 2012. Stratigraphic Paleobiology: Understanding the Distribution of Fossil Taxa in Time and Space. University of Chicago Press. 259 pages.

See Also

This function mainly exists to look at the output from getSpeciesSpecificRescaledKDE for a fossil assemblage.


[Package paleoAM version 1.0.1 Index]