Routine production of population trends from citizen-science data: insights into the dynamics of common bird and plant species in hexagonal France

This repository has been made so that it contains a snapshot of the exact code used in the analyses presented in an article currently in review (this article will be attached to this repository as soon as it is accepted). 

More specifically, this repository is made of a folder indicatorRoutine that contains:

1) an updated version of the pipeline found here: https://outils-patrinat.mnhn.fr/gitlab/vigie-nature/tendances/indicatorroutine. This pipeline aims at estimating population temporal trends based on observations from biodiversity monitoring programs. It is a flexible tool, that allows the user to choose and specify multiple relevant parameters in the estimation process. In the end, it produces multiple outputs:

• models are stored in RData objects that are made available;
• all species trends are gathered within a table, that is also made available;
• figures are created for each species with these trends showing also, if required, non-linear patterns.

NB: see the guideline associated with the gitlab repository for more information on how to use the routine.

2) the data used in the article, that are three datasets:

• Two datasets of birds counts in hexagonal France from the Suivi Temporel des Oiseaux Communs (STOC) monitoring program. One covers the 2001 - 2023 period, the other the 1989 - 2023 period;
• One dataset of plants occurrence in hexagonal France covering the 2009 - 2023 period, from the Vigie-flore monitoring program.

It also contains an additional folder updatedPlotFunctions, which contains scripts to create additional figures or modify existing figures so that it is relevant and readable in the article. The script "alluvial_classification" allows the creation of an alluvial plot between trends obtained at two different time frames. The script "plot" updates species trends figures so that it is more readable in the article.