R scripts for the analysis of shifts in phenology of plants and their pollinators in Germany. The artcile is now published in Proceedings of the Royal Society B (DOI:10.1098/rspb.2021.2142).
- R 4.0 +
- RStudio (for running notebooks, any other way will do)
The models were run with about 24GB of physical memory and 100GB of swap memory.
- Ensure
renvis installed (Should be given if you are using Rstudio) - to install all necessary packages, simply call
renv::restore() - To run the analysis some additional data sets need to be downloaded and placed in the
static_datafolder:- Plant pollinator interaction data set from: https://doi.org/10.5285/6d8d5cb5-bd54-4da7-903a-15bd4bbd531b (login required, account creation should be possible for everyone)
- Plant trait data from bioflor. This should be done automatically, but the script attempts to resolve the current accepted name for each species. Therefore running this script at a later date might result in different species being included in the analysis. The original data set used in the analysis is available on request.
Everything necessary for obtaining the results from the paper is done from within analysis.Rmd. Some data, for
example the averaged climate datasets and the dataset keys for the gbif datasets used, is already provided in the
static_data folder. We also included the scripts we used to obtain plant trait data (get_bioflor_traits.R),
and the script used to compile that data from GBIF (start_gbif_downloads.R). They are located in the Scripts
folder, along with additional scripts run from within the main analysis notebook.