MetaCommunityMetrics

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.

An Overview

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

Getting Started

Installation

To install MetaCommunityMetrics, use the following command:

using Pkg

Pkg.add("MetaCommunityMetrics")

using MetaCommunityMetrics

Sample Data

To assess the sample data, use the following command:

using MetaCommunityMetrics

load_sample_data()

Example

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

Acknowledgment

This package includes translations and adaptations of functions from the R packages adespatial (licensed under GPL-3), vegan (licensed under GPL-2 or later), and DNCImper (licensed under GPL-3). The original packages and their documentation are available at:

• adespatial: https://cran.r-project.org/web/packages/adespatial/index.html
• vegan: https://cran.r-project.org/web/packages/vegan/index.html
• DNCImper: https://github.com/Corentin-Gibert-Paleontology/DNCImper

Please refer to these sources for full details on the original implementations and licenses.

License

This project is licensed under the terms of the GNU General Public License v3.0. See the LICENSE file for more details.