abund: Compute absolute and relative abundances in the local...

In ecolottery: Coalescent-Based Simulation of Ecological Communities

Description

Compute the abundances and relative abundances of species in simulated communities and in the corresponding species pools. The input must be an output of either coalesc or the forward functions.

Usage

abund(x)

Arguments

x	a list including the species pool composition (x$pool) and the local community composition (x$com)

Value

pool	species abundances and relative abundances in the reference pool
com	species abundances and relative abundances in the local community

Author(s)

F. Munoz, P. Denelle and M. Grenie

Examples

# Simulation of a neutral community including 500 individuals
J <- 500; theta <- 50; m <- 0.05;
comm1a <- coalesc(J, m, theta) 
abund1a <- abund(comm1a) 
  
# Log-series distribution of regional abundances
fit <- vegan::fisherfit(abund1a$pool$ab)
freq <- as.numeric(names(fit$fisher))
plot(log(freq), fit$fisher,
     xlab = "Frequency (log)",
     ylab = "Species", type = "n")
rect(log(freq - 0.5), 0, log(freq + 0.5), fit$fisher, col="skyblue")

alpha <- fit$estimate
k <- fit$nuisance

curve(alpha * k^exp(x) / exp(x), log(0.5), max(log(freq)),
      col = "red", lwd = 2, add = TRUE)

# Relationship between local and regional abundances
par(mfrow=c(1, 2))
plot(abund1a$pool[rownames(abund1a$com), "relab"],
  abund1a$com$relab,
  main = "m = 0.05",
  xlab = "Regional abundance",
  ylab = "Local abundance",
  log = "xy")
abline(0,1)

# With higher immigration rate
m <- 0.95
comm1b <- coalesc(J, m, theta) 
abund1b <- abund(comm1b) 
plot(abund1b$pool[rownames(abund1b$com),"relab"],
  abund1b$com$relab,
  main = "m = 0.95",
  xlab = "Regional abundance",
  ylab = "Local abundance",
  log = "xy")
abline(0,1)

ecolottery documentation built on May 2, 2019, 9:34 a.m.