Research project aggregating biodiversity data from checklists. Richness project aggregates data from studies that provided only average richness values at the alpha scale and a richness value at the gamma scale.
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. It is related to projects chase-lab/metacommunity-surveys and chase-lab/checklist_change.
Raw and aggregated data tables are provided. Aggregated data are in ./data/communities.csv and ./data/metadata.csv and column definitions are given in ./data/definitions_communities.txt and ./data/definitions_metadata.txt.
To ensure reproducibility, the working environment (R version and package version) were documented and isolated using the package renv (https://rstudio.github.io/renv/index.html). 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 and install them on your system.
After downloading or cloning this repository, run these scripts in order to wrangle raw data and merge all data sets into one long table.
renv::restore()
source('./R/1.0_wrangling_raw_data.r')
source('./R/2.0_merging_long-format_tables')