abund {ecolottery} R Documentation

## Compute absolute and relative abundances in the local community and the reference pool

### 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)


[Package ecolottery version 1.0.0 Index]