MC Utilities: Manipulation of meta-communities

Description

Tools to manipulate meta-communities. From a list of meta-communities, MergeMC creates a metacommunity whose communities are each original metacommunity. MergeC creates a metacommunity whose communities are each original community. ShuffleMC randomly assigns original communities to a metacommunity, keeping original weights, and returns a list of meta-communities.

Usage

MergeMC(MClist, Weights = rep(1, length(MClist)), CheckArguments = TRUE)
MergeC(MClist, Weights = rep(1, length(MClist)), CheckArguments = TRUE)
ShuffleMC(MClist, Weights = rep(1, length(MClist)), CheckArguments = TRUE)

Arguments

MClist

A list of MetaCommunity objects.

Weights

A vector of numbers containing the weight of each metacommunity of the list. It does not have to be normalized to sum to 1.

CheckArguments

Logical; if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.

Value

MergeMC and MergeC return a MetaCommunity. ShuffleMC returns a list of MetaCommunity objects.

Details

MergeMC is used for hierarchical partitioning of diversity. The gamma diversity of communities of the list becomes alpha diversity of the merged meta-community. MergeC creates a new meta-community by mixing original ones. Original communities are kept, their new weight is the product of their original weight and the weight of their original meta-community. ShuffleMC is used for simulations of the null hypothesis that all metacommunities of the list are identical.

Examples

Run this code

# First meta-community
(df <- data.frame(C1 = c(10, 10, 10, 10), C2 = c(0, 20, 35, 5),
  C3 = c(25, 15, 0, 2), row.names = c("sp1", "sp2", "sp3", "sp4")))
w <- c(1, 2, 1)
MC1 <- MetaCommunity(Abundances = df, Weights = w)
# Second meta-community
(df <- data.frame(C1 = c(10, 4), C2 = c(3, 4), row.names = c("sp1", "sp5")))
w <- c(3, 2)
MC2 <- MetaCommunity(Abundances = df, Weights = w)

# Merge communities
plot(MergeC(list(MC1, MC2)), main="Merged communities")
# Merge metacommunities
plot(MergeMC(list(MC1, MC2)), main="Merged meta-communities")