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Joint Species Distribution Modelling of a Pollinator Community in Flanders

Langeraert, Ward[^aut][^cre][^inbo.be] Research Institute for Nature and Forest (INBO)^cph

[^cph]: copyright holder

[^cre]: contact person [^inbo.be]: Research Institute for Nature and Forest (INBO)

keywords: JSDM; species distribution modelling; pollinators; Flanders

Description

Explore Joint Species Distribution Modelling of a pollinator community in Flanders. <!-- description: end -->

This repo is made in preparation of the summer school 'Model-based multivariate analysis for ecologists' from 21st-25th of July 2025 in Hjerkinn, Norway (link).

Personal notes can be found in the docs folder.

Order of execution

Follow the steps below to run the scripts in a logical order.

Step 1: data_preparation.qmd

Load and prepare the observation data from data/raw folder. This includes merging of datasets and data filtering.

Step 2: preparetraitphylo.qmd

Load and prepare the trait and phylogenetic data from data/raw folder. Clean up trait dataset and create workflow to create taxonomical tree.

Step 3: calcenvironmentalvars.qmd

Filter observation data based on habitat layer and add environmental variables.

Step 4: trygllvmpackage.qmd

Test gllvm package.

Repo structure

├── source │ ├── quarto ├ quarto reports │ └── scripts ├ R scripts │ ├── data │ ├── raw ├ store raw data here │ ├── intermediate ├ intermediate datasets │ └── processed ├ finalised datasets │ ├── docs ├ notes │ ├── checklist.yml ├ options checklist package (https://github.com/inbo/checklist) ├── inst │ └── en_gb.dic ├ dictionary with words that should not be checked by checklist ├── .github │ │ ├── workflows │ │ │ └── checklist_project.yml ├ GitHub repo settings │ ├── CODE_OF_CONDUCT.md │ │ └── CONTRIBUTING.md │ ├── jsdm-pollinators-flanders.Rproj ├ R project ├── README.md ├ project description ├── LICENSE.md ├ license ├── CITATION.cff ├ citation info ├── .zenodo.json ├ zenodo metadata └── .gitignore ├ files to ignore