MetaCommunityMetrics is a collection of tools and utilities for analyzing meta-communities in Julia. The current version is compatible with julia version 1.9.3.
This package is a comprehensive toolkit designed to characterize the spatiotemporal structure and dynamics of a metacommunity—a network of communities linked by the dispersal of multiple, interacting species, each with unique niche breadths. It includes functions to calculate a range of specific metrics, which have been previously implemented in R and proven valuable for metacommunity analysis.
However, they come with high computational costs, especially for large species community datasets. To address this issue, MetaCommunityMetrics.jl was developed in Julia, a programming language known for its efficiency in handling computationally intensive tasks. This implementation significantly improves the efficiency of calculating these metrics, making it a powerful tool for metacommunity analysis.
These metrics include:
- Averaged beta diversity decomposition in space/time: total diversity, species replacement (turnover), and richness differences for both presence-absence and abundance data
- Dispersal-niche continuum index to evaluate the degree to which communities are influenced by dispersal processes and niche breadth
- Niche overlap indices to determine the extent of niche sharing among species within the metacommunity
- The proportion of habitat patches occupied by each species
- The variability of community composition across different spatial and temporal scales
To install MetaCommunityMetrics, use the following command:
using Pkg
Pkg.add("MetaCommunityMetrics")
using MetaCommunityMetricsTo assess the sample data, use the following command:
using MetaCommunityMetrics
load_sample_data()julia> using MetaCommunityMetrics
julia> load_sample_data()
48735×10 DataFrame
Row │ Year Month Day Sampling_date_order plot Species Abundance Presence Latitude Longitude
│ Int64 Int64 Int64 Int64 Int64 String3 Int64 Int64 Float64 Float64
───────┼────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ 2010 1 16 1 1 BA 0 0 35.0 -110.0
2 │ 2010 1 16 1 2 BA 0 0 35.0 -109.5
3 │ 2010 1 16 1 8 BA 0 0 35.5 -109.5
4 │ 2010 1 16 1 9 BA 0 0 35.5 -109.0
5 │ 2010 1 16 1 11 BA 0 0 35.5 -108.0
6 │ 2010 1 16 1 14 BA 0 0 36.0 -109.5
7 │ 2010 1 16 1 17 BA 0 0 36.0 -108.0
8 │ 2010 1 16 1 22 BA 0 0 36.5 -108.5
9 │ 2010 1 16 1 6 BA 0 0 35.0 -107.5
10 │ 2010 1 16 1 13 BA 0 0 36.0 -110.0
11 │ 2010 1 16 1 15 BA 0 0 36.0 -109.0
12 │ 2010 1 16 1 20 BA 0 0 36.5 -109.5
⋮ │ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮
48725 │ 2023 3 21 117 15 SH 1 1 36.0 -109.0
48726 │ 2023 3 21 117 19 SH 0 0 36.5 -110.0
48727 │ 2023 3 21 117 20 SH 0 0 36.5 -109.5
48728 │ 2023 3 21 117 21 SH 0 0 36.5 -109.0
48729 │ 2023 3 21 117 22 SH 0 0 36.5 -108.5
48730 │ 2023 3 21 117 1 SH 0 0 35.0 -110.0
48731 │ 2023 3 21 117 9 SH 0 0 35.5 -109.0
48732 │ 2023 3 21 117 10 SH 0 0 35.5 -108.5
48733 │ 2023 3 21 117 12 SH 1 1 35.5 -107.5
48734 │ 2023 3 21 117 16 SH 0 0 36.0 -108.5
48735 │ 2023 3 21 117 23 SH 0 0 36.5 -108.0
48712 rows omitted
