ecospace (version 1.0.0)

ecospace-package: ecospace: Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks

Description

ecospace is an R package that implements stochastic simulations of community assembly (ecological diversification) using customizable ecospace frameworks (functional trait spaces). Simulations model the 'neutral', 'redundancy', 'partitioning", and "expansion" models of Bush and Novack-Gottshall (2012). It provides a wrapper to calculate common ecological disparity and functional ecology statistical dynamics as a function of species richness. Functions are written so they will work in a parallel-computing environment.

Details

The package also contains a sample data set, functional traits for Late Ordovician (Type Cincinnatian) fossil species from the Kope and Waynesville formations, from Novack-Gottshall (In pressB).

References

Bush, A. and P.M. Novack-Gottshall. 2012. Modelling the ecological-functional diversification of marine Metazoa on geological time scales. Biology Letters 8: 151-155.

Novack-Gottshall, P.M. In review at Paleobiology, submitted Oct. 5, 2015. General models of ecological diversification. I. Conceptual synthesis.

Novack-Gottshall, P.M. In review at Paleobiology, submitted Oct. 5, 2015. General models of ecological diversification. II. Simulations and empirical applications.

See Also

The 'calc_metrics' function relies extensively on the functional diversity package FD, and hence lists this package as a depends, so it is loaded simultaneously.

Examples

# Get the package version and citation of ecospace
packageVersion("ecospace")
citation("ecospace")

# Create an ecospace framework (functional-trait space) with 15 characters
#    (functional traits) of mixed types
nchar <- 15
ecospace <- create_ecospace(nchar=nchar, char.state=rep(3, nchar),
  char.type=rep(c("factor", "ord.fac", "ord.num"), nchar / 3))

# Use to assemble a stochastic "neutral" sample of 20 species (from
#    initial seeding by 5 species)
x <- neutral(Sseed=5, Smax=20, ecospace=ecospace)
head(x, 10)

# Calculate ecological disparity (functional diversity) dynamics as a
#    function of species richness
# Statistic 'V' [total variance] not calculated because there are factors
#    in the sample
metrics <- calc_metrics(samples=x, Smax=20, Model="Neutral", Param="NA")
metrics

# Plot statistical dynamics as function of species richness
op <- par()
par(mfrow=c(2,4), mar=c(4, 4, 1, .3))
attach(metrics)
plot(S, H, type="l", cex=.5)
plot(S, D, type="l", cex=.5)
plot(S, M, type="l", cex=.5)
plot(S, V, type="l", cex=.5)
plot(S, FRic, type="l", cex=.5)
plot(S, FEve, type="l", cex=.5)
plot(S, FDiv, type="l", cex=.5)
plot(S, FDis, type="l", cex=.5)

par(op)