West_Africa_checklist

Data and code for the data analyses used in Piepenbring, Maciá-Vicente, Codjia, Glatthorn, Kirk, Meswaet, Minter, Olou, Reschke, Schmidt, Yorou (2020) Mapping mycological ignorance – checklists and diversity patterns of fungi known for West Africa. IMA Fungus 11:13.

Contents

R_process.R

R script with commands to run all the analyses.

Code/functions.R

Custom R functions called by the script R_process.R.

Data/

Files with raw data necessary for the analyses.

• checklist.csv: checklist data, including all fungal records for West Africa and their associated metadata.
• first_author_activity.csv: data on the origin of first authors of publications on West African fungi (for Figure 3c).
• GBIF records.csv: Fungal records for West Africa available in the Global Biodiversity Information Facility (GBIF) database.
• IMI_records.csv: Fungal records for West Africa available in the former International Mycological Institute (IMI) fungal reference collection.
• known_spp_numbers.csv: numbers of fungal species known worldwide for systematic groups of fungi and fungus-like organisms. Data from the Catalogue of Life.
• known_spp_numbers_selection.csv: subset of known_spp_numbers.csv with a selection of systematic groups (for Table 2).

Usage

Run the script R_process.R in R, using as working directory the same folder where all data and code files and folders are stored. The following R packages need to be installed: ggplot2, ggthemes, Hmisc, maps, RColorBrewer, rnaturalearth, sf, sp, vegan. Upon running the script, all results will be stored in a folder named Output that is automatically created.