1d:T701,# Compute absolute and relative abundances in the local community and the reference pool 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. ```r abund(x) ``` ## Arguments - `x`: a list including the species pool composition (`x$pool`) and the local community composition (`x$com`) ## Returns - **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 ```r # 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) ```1e:T49a,M7.49933 0.25C3.49635 0.25 0.25 3.49593 0.25 7.50024C0.25 10.703 2.32715 13.4206 5.2081 14.3797C5.57084 14.446 5.70302 14.2222 5.70302 14.0299C5.70302 13.8576 5.69679 13.4019 5.69323 12.797C3.67661 13.235 3.25112 11.825 3.25112 11.825C2.92

abund function