A short tutorial on Tax4Fun2

• Tax4Fun2 was developed by Wemheuer et al. (2020) (https://doi.org/10.1186/s40793-020-00358-7). This is only a short tutorial on how it could be used for functional prediction.
• I am a former colleague of the Tax4Fun2 developers, this tutorial was prepared with the hope that it might be helpful.
• Error reports and suggestions can be posted on the issue page.

Installation

Files needed

• Source code: Tax4Fun2_1.1.5.tar.gz

• Database file: Tax4Fun2_ReferenceData_v2.tar.gz

  # You'll need to decompress it before performing functional prediction
  $ tar xzvf Tax4Fun2_ReferenceData_v2.tar.gz
  

• Example input files: example_input_files

In Rstudio

• open RStudio > Tools > install packages > from "Install from" select "Package Archive File" > choose "Tax4Fun2_1.1.5.tar.gz" > click "Install"

In Terminal (Linux and Mac)

$ R
$ install.packages(pkgs="Tax4Fun2_1.1.5.tar.gz", repos=NULL, source=TRUE)

• If you're running Tax4Fun2 on Windows, you might found this helpful.

Example commands

1. Making functional predictions using the default database

2. Making functional predictions using the default database + a user-generated database