abund {ecolottery} | R Documentation |
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.
abund(x)
x |
a list including the species pool composition ( |
pool |
species abundances and relative abundances in the reference pool |
com |
species abundances and relative abundances in the local community |
F. Munoz, P. Denelle and M. Grenie
# 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)