plot_mv: Plot mean-variance relationship

In seananderson/ecofolio: Tools to quantify metapopulation portfolio effects

Description

Creates a scatter plot of the time series log(variance) vs. log(mean). Shows a model fit to the mean-variance data and an extrapolation to the size of the metapopulation. The linear version of this model is referred to as Taylor's power law.

Usage

plot_mv(x, show = c("linear", "quadratic", "robust"), col = c("#D95F02",
  "#1B9E77", "#E7298A"), lty = c(1, 1, 1), pch_sa = c(1, 5, 6),
  ci = FALSE, pch_subpops = 21, pch_port = 4, add_z = TRUE,
  xlab = "log(mean)", ylab = "log(variance)", ...)

Arguments

x	A matrix or dataframe of abundance or biomass data. The columns should represent different subpopulations or species. The rows should represent the values through time.
show	A vector of character objects indicating which mean-variance models to show.
col	Colour for the mean-variance model fit. A vector of length 3 with the three values corresponding to linear, quadratic, robust.
lty	Line type for the mean-variance model fit. A vector of length 3 with the three values corresponding to linear, quadratic, robust.
pch_sa	Point type for the extrapolated "single-asset" portfolio. A vector of length 3 with the three values corresponding to linear, quadratic, robust.
ci	Add a confidence interval around the model fit? Only appears for the linear fit option.
pch_subpops	Point type for the subpopulations.
pch_port	Point type for the portfolio.
add_z	Logical. Add Taylor's power law z value (based on a linear model)?
xlab	Label for x-axis.
ylab	Label for y-axis.
...	Other values to pass to plot.

References

Anderson, S.C., A.B. Cooper, N.K. Dulvy. 2013. Ecological prophets: Quantifying metapopulation portfolio effects. Methods in Ecology and Evolution. In Press.

Doak, D., D. Bigger, E. Harding, M. Marvier, R. O'Malley, and D. Thomson. 1998. The Statistical Inevitability of Stability-Diversity Relationships in Community Ecology. Amer. Nat. 151:264-276.

Tilman, D., C. Lehman, and C. Bristow. 1998. Diversity-Stability Relationships: Statistical Inevitability or Ecological Consequence? Amer. Nat. 151:277-282.

Tilman, D. 1999. The Ecological Consequences of Changes in Biodiversity: A Search for General Principles. Ecology 80:1455-1474.

Taylor, L. 1961. Aggregation, Variance and the Mean. Nature 189:732-735. doi: 10.1038/189732a0.

Taylor, L., I. Woiwod, and J. Perry. 1978. The Density-Dependence of Spatial Behaviour and the Rarity of Randomness. J. Anim. Ecol. 47:383-406.

Examples

data(pinkbr)
par(mfrow = c(1,3))
plot_mv(pinkbr[,-1], show = "linear")
mtext("Linear")
plot_mv(pinkbr[,-1], show = "quadratic", add_z = FALSE)
mtext("Quadratic")
plot_mv(pinkbr[,-1], show = "robust", add_z = FALSE)
mtext("Robust linear")

seananderson/ecofolio documentation built on May 29, 2019, 4:25 p.m.