carolus

R package for analysis of insect metabarcoding data

Installation

The carolus package can be install with devtools - if devtools is not installed on your machine please run install.packages("devtools") before proceeding. To install the carolus package simply run

devtools::install_github("station-linne/carolus")

in your R REPL (interactive prompt). This will install the carolus package and its dependencies.

Usage

At the moment, only a single function is supported: taxon_search. To test it out, you need to have the ensure that you have the IBA data available locally. In the case that you have not downloaded it yet, the data is available on Figshare and is split between a raw dataset containing raw amplicon sequence variants and a processed dataset containing processed data. For more details on the data see the Nature data paper.

With the data available and carolus installed, run

library(carolus)
configure_carolus()

This command will help you create a config file which contain the paths of the downloaded data. This config file is used by carolus to locate files in the datasets.

Next, run

configure_python()

to install the Python dependencies of the package (only pandas at the moment).

At the moment, carolus only supports a single function: taxon_search. Test it out with

taxon_search("Astata boops", "Species")

This will search for records of Astata boops in the Swedish IBA dataset. Type ?taxon_search to see further configuration options.