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dissmapr-test1

R package to analyse compositional dissimilarity and biodiversity turnover

https://github.com/macsands/dissmapr-test1

Science Score: 44.0%

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R package to analyse compositional dissimilarity and biodiversity turnover

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Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Code of conduct Citation Codemeta

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# dissMapR: A Novel Framework for Automated Compositional Dissimilarity and Biodiversity Turnover Analysis


[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![test-coverage](https://github.com/macSands/dissMapR/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/macSands/dissMapR/actions/workflows/test-coverage.yaml)
[![Codecov test coverage](https://codecov.io/gh/macSands/dissMapR/graph/badge.svg)](https://app.codecov.io/gh/macSands/dissMapR)


`dissMapR` is an R package designed to streamline the assessment, mapping, and prediction of compositional dissimilarity and biodiversity turnover. It integrates multi-site dissimilarity metrics - particularly zeta diversity - and advanced modelling approaches, such as Multi-Site Generalized Dissimilarity Modelling (MS-GDM), to evaluate how biodiversity patterns respond to environmental drivers at multiple spatial scales.

This project is part of the [B3 (B-Cubed) project](https://b-cubed.eu/), a Europe-wide collaboration dedicated to advancing robust biodiversity indicators for more effective policy and decision-making. In addition to this repository, `dissMapR` will be hosted on the [B-Cubed GitHub organization](https://github.com/b-cubed-eu).

## Features

- **Automated Data Integration**
  - Retrieve species occurrence data from
    [GBIF](https://www.gbif.org/)  
  - Access environmental variables from sources like
    [WorldClim](https://worldclim.org/) and
    [CHELSA](https://chelsa-climate.org/)
- **Compositional Turnover Metrics**
  - Calculate pairwise and multi-site dissimilarity (zeta diversity,
    Bray–Curtis, etc.)  
  - Model turnover using MS-GDM to link species composition with spatial
    and environmental gradients
- **Predictive Modeling & Visualization**
  - Project changes in community composition or “bioregions” under
    different environmental scenarios  
  - Generate interactive or static maps of turnover “hotspots” and
    emergent bioregions

## Why Use `dissMapR`?

1.  **Reproducible Workflows**  
    Automates data retrieval, cleaning, and modeling to reduce error and
    save time.

2.  **Beyond Alpha and Beta Diversity**  
    Emphasizes multi-site connectivity (zeta diversity), capturing
    compositional patterns often overlooked by simpler metrics.

3.  **Scalable and Flexible**  
    Adaptable to diverse datasets and spatial extents, from local to
    continental scales.

4.  **Decision-Support Ready**  
    Maps of predicted turnover and delineated bioregions can inform
    conservation priorities, climate adaptation plans, and biodiversity
    policies.

## Example Application

Below is a brief overview of how `dissMapR` can be applied to butterfly
occurrence data in southern Africa:

1.  **Data Access**
    - Automated retrieval of occurrence records via GBIF  
    - Environmental data (e.g., temperature, precipitation) from
      WorldClim
2.  **Multi-Site Metrics**
    - Computation of zeta diversity to assess the proportion of shared
      species across multiple sites  
    - Calculation of Bray–Curtis dissimilarity and others for broader
      context
3.  **MS-GDM**
    - Linking environmental gradients (e.g., climate variables) with
      biodiversity turnover  
    - Predicting compositional changes under future environmental
      scenarios
4.  **Visualization**
    - Mapping of high-turnover “hotspots” and distinct bioregional
      clusters  
    - Identifying potential zones of rapid community shift under climate
      change
      
## Installation

You can install the development version of dissMapR from [GitHub](https://github.com/) with:

``` r
# Coming soon:
# install.packages("devtools")
# devtools::install_github("b-cubed-eu/dissMapR")
```

## Example

This is a basic example which shows you how to solve a common problem:

```{r example}
library(dissMapR)
## basic example code
```

What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:

```{r cars}
summary(cars)
```

You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this.

You can also embed plots, for example:

```{r pressure, echo = FALSE}
plot(pressure)
```

In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN.

Owner

  • Name: Sandra MacFadyen
  • Login: macSands
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: "dissMapR: Analysing compositional dissimilarity and biodiversity turnover"
authors:
- given-names: Sandra
  family-names: MacFadyen
  affiliation: Stellenbosch University (SUN)
  orcid: 0000-0002-5316-440X
keywords:
- dissimilarity
- turnover
- B-Cubed
- biodiversity
- zeta diversity
contact:
- given-names: Sandra
  family-names: MacFadyen
  affiliation: Stellenbosch University (SUN)
  orcid: 0000-0002-5316-440X
doi: xxxxxxx
license: MIT
repository-code: https://github.com/macSands/dissMapR
type: software
abstract: "dissMapR is an R package designed to streamline the assessment, mapping, and prediction of compositional dissimilarity and biodiversity turnover. It integrates multi-site dissimilarity metrics - particularly zeta diversity - and advanced modelling approaches, such as Multi-Site Generalized Dissimilarity Modelling (MS-GDM), to evaluate how biodiversity patterns respond to environmental drivers at multiple spatial scales."
identifiers:
- type: doi
  value: xxxxxxx
- type: url
  value: https://macsands.github.io/dissMapR/
version: 0.0.1

CodeMeta (codemeta.json) 

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  "description": "dissMapR is an R package for analyzing compositional dissimilarity and biodiversity turnover, integrating multi-site zeta diversity, spatial mapping, and predictive modeling to assess community changes and bioregional shifts under environmental gradients, supporting evidence-based conservation planning",
  "name": "dissMapR: R package to analyse compositional dissimilarity and biodiversity turnover",
  "codeRepository": "https://github.com/macSands/dissMapR",
  "issueTracker": "https://github.com/macSands/dissMapR/issues",
  "license": "https://spdx.org/licenses/MIT",
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Dependencies

DESCRIPTION cran
  • data.table * imports
  • dplyr * imports
  • httr * imports
  • tidyr * imports
  • testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.5.0 composite
  • actions/checkout v4 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
  • codecov/codecov-action v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite