Metacommunity surveys

Description

This research compendium regroups scripts used to download, re-structure and aggregate data sets to constitute a large meta-analysis of communities sampled at least twice, 10 years apart or more.

As of 2.4, data are provided in a raw and standardised states. Raw data were restructured to fit a common template and few modifications were made, see rulebook.md. Standardised data were restructured to fit a common template and the effort was standardised to be consistent between localities and years of the same region.

Variable definitions are in files: r /data/definitions_communities.txt /data/definitions_metadata_raw.txt /data/definitions_metadata_standardised.txt

Availability

Latest version

The latest version can always be found on the dev branch but scripts there did not yet receive all the curation that the script getting to the main branch received.

Release v2.5-BlowesetalScience_Advances

• Code archived on Zenodo: https://zenodo.org/doi/10.5281/zenodo.7785286
• Data are also available in this repository in the following files:

r /data/communities_raw.rds /data/metadata_raw.rds /data/communities_standardised.rds /data/metadata_standardised.rds - Used by Dr Shane Blowes in the manuscript 'Synthesis reveals approximately balanced biotic differentiation and homogenization' published in Science Advances.

Release v1.0.0

• Code archived on Zenodo: https://doi.org/10.5281/zenodo.7785287
• Used by Dr Wubing Xu in his manuscript 'Regional occupancy increases for widespread species but decreases for narrowly distributed species in metacommunity time series' published in Nature Communication in March 2023: https://doi.org/10.1038/s41467-023-37127-2
• Data archived on iDiv Data Portal: https://doi.org/10.25829/idiv.3503-jevu6s

Reproducibility and R environment

R Packages

To ensure that the working environment (R version and packages version) are documented and isolated, the package renv (https://rstudio.github.io/renv/index.html) was used. By running renv::restore(), renv will install all missing packages at once. This function will use the renv.lock file to download the same versions of packages that we used.

Execution

After downloading or cloning this repository, run renv::restore() and these scripts in order to download raw data, wrangle raw data and merge all data sets into one long table. ``` r renv::restore()

The raw data were stored in the project so users would not need to download them

source('/R/1.0downloadingraw_data.r')

source('/R/2.0wranglingrawdata.r') source('/R/3.1merginglong-formattablesraw.r') source('/R/3.2merginglong-formattables_standardised.r') ```

Additional installations

You might need to install the 64-bit version of Java to run the Tabulizer package.