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Moth trends and traits in Flanders (northern Belgium)

Maes, Dirk[^aut][^INBO] Langeraert, Ward[^aut][^cre][^INBO] Onkelinx, Thierry[^aut][^INBO] Van Calster, Hans[^aut][^INBO] Veraghtert, Wim[^aut][^Natuurpunt] Merckx, Thomas[^aut][^VUB] Research Institute for Nature and Forest (INBO)^cph

[^cph]: copyright holder

[^cre]: contact person [^INBO]: Research Institute for Nature and Forest (INBO), Herman Teirlinckgebouw, Havenlaan 88 PO Box 73, B-1000 Brussels, Belgium [^RIBES]: Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, PO Box 9010, NL-6500 GL Nijmegen, The Netherlands [^Natuurpunt]: Natuurpunt Studie, Coxiestraat 11, B-2800 Mechelen, Belgium [^VUB]: WILD, Biology Department, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium

keywords: Global change; Insect decline; Life-history traits; Multi-Species Change Index (MSCI); Nature management; Nature policy; Pollinators; Threatened species

Description

Investigation of species traits as a guidance for moth conservation in the highly anthropogenic European region of Flanders based on Multi-Species Change Indices (MSCIs). <!-- description: end -->

Order of execution

Follow the steps below to run the scripts in a logical order. You can skip any steps if desired, each script will create the necessary folders and download the necessary data from zenodo each time if required. Open the R project file macro-moths-msci.Rproj before opening any scripts such that the relative paths in the scripts work properly.

Step 1: data_preparation.Rmd

You can only run this script if you have the raw data at your disposal. If not, you can skip this step.

Create a folder data/raw where you store the raw data. By running this script, you will merge the raw datasets in a single intermediate dataset. This dataset is then stored in data/intermediate which is created by the script if it does not exist yet.

Step 2: data_exploration.Rmd

In this script, data exploration is performed. In the end, a final dataset is written out for further analyses. This dataset is then stored in data/processed which is created by the script if it does not exist yet.

Step 3: modelspecificationmsci.Rmd

Test script for model specification, model fit and figure creation.

Step 4: calculatemscitraits.Rmd

In this script, all models are fitted for the calculation of MSCIs. Models are cached in the folder source/brms_cache which is created in the script if it does not exist yet. In the end, a summary table is written out as well as an R object used to create figures in step 6. The script creates the folder output to store these if it does not exist yet.

Step 5: calculatescispecies.Rmd

In this script, the model is fitted for the calculation of SCIs. Model is cached in the folder source/brms_cache which is created in the script if it does not exist yet. In the end, a summary table is written out. The script creates the folder output to store this if it does not exist yet.

Step 6: create_figures.Rmd

In this script, final figures are created to be used in the conference and the research paper. The script creates the folder media to store these if it does not exist yet.

Repo structure

bash ├── source │ ├── ... ├ markdown and R files (see order of execution) │ └── brms_cache ├ store brms models (see order of execution) │ └── ... │ ├── data │ ├── raw ├ create this folder and store raw data if at your disposal │ ├── intermediate ├ will be created in step 1 or 2 (see order of execution) │ └── processed ├ will be created in step 2, 3, 4 or 5 (see order of execution) ├── output ├ folder to store outputs (will be created in step 4, 5 or 6) ├── media ├ folder to store media (will be created in step 6) ├── checklist.yml ├ options checklist package (https://github.com/inbo/checklist) ├── inst │ └── en_gb.dic ├ dictionary with words that should not be checked by the checklist package ├── .github │ │ ├── workflows │ │ │ └── checklist_project.yml ├ GitHub repo settings │ ├── CODE_OF_CONDUCT.md │ │ └── CONTRIBUTING.md │ ├── macro-moths-msci.Rproj ├ R project ├── README.md ├ project description ├── LICENSE.md ├ licence ├── CITATION.cff ├ citation info ├── .zenodo.json ├ zenodo metadata └── .gitignore ├ files to ignore