A script to check fungi names for the most up to date nomenclature according to Species Fungorum.
FungusNameCheck.R is an R script (written in R v4.1.1) designed to run in the linux command line.
To download:
git clone https://github.com/Rowena-h/FungusNameCheck.git
It requires the taxize R package to run.
The only input needed is a file containing a list of names without a header. To see an example, refer to example/list.
To run the script in the command line:
Rscript FungusNameCheck.R example/list
This will produce a csv file with two columns, where the first is the provided name and the second is the current name (see example/checked_names_PID333527.csv).
To run the script and additionally produce a log file:
Rscript FungusNameCheck.R example/list 2>&1 | tee log
If there is an NA in the current name column it means that the provided name can't be found anywhere in Species Fungorum, but as the script can't cope with typos, it's probably worth double-checking for that before anything else.