diff --git a/README.md b/README.md index f1efb2a..ea34876 100644 --- a/README.md +++ b/README.md @@ -6,17 +6,17 @@ A tool to check fungus names for the most up to date classification according to FungusNameCheck.R is an [R](https://www.r-project.org/) script (written in R v4.1.1) designed to run in the linux command line. -It requires the [**taxize**](https://github.com/ropensci/taxize) R package. - To download: ``` git clone https://github.com/Rowena-h/FungusNameCheck.git ``` +It requires the [**taxize**](https://github.com/ropensci/taxize) R package to run. + ## Usage -The only input needed is a file containing a list of names to check **without a header**. To see an example, refer to [example/list](example/list). +The only input needed is a file containing a list of names **without a header**. To see an example, refer to [example/list](example/list). To run the script: @@ -24,6 +24,8 @@ To run the script: 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](example/checked_names_PID333527.csv)). + To run the script and additionally produce a log file: ```