R Packages from Conda Environment in Bash Scripting Job

If you are a data scientist or analyst, working with R programming language, you might have found it difficult to manage the packages that your project depends on. One way to manage the packages is to use conda environment. In this article, we will explore how you can use R packages from a Conda environment in a bash script.

What is Conda?

Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux. It is used to manage packages and environments in various programming languages such as Python, R, and C++. Conda is particularly useful for managing dependencies of software projects.

How to create a Conda environment?

Before we can use R packages from a Conda environment, we need to create one. Here is how you can create a Conda environment for R:

conda create -n my-r-env r-base

This will create a Conda environment named my-r-env with R installed in it.

How to activate a Conda environment?

Once you have created a Conda environment, you need to activate it to use it. Here is how you can activate the Conda environment we just created:

conda activate my-r-env

This will activate the my-r-env Conda environment and you will be able to use R packages installed in this environment.

How to use R packages from a Conda environment in a bash script?

Now that we have created and activated our Conda environment for R, we can use the packages installed in this environment in our bash script. Here is an example of a bash script that uses R packages from a Conda environment:

#!/bin/bash
conda activate my-r-env

# Install R package in Conda environment
conda install -c conda-forge r-tidyverse -y

# Use R package in bash script
Rscript -e "library(tidyverse); df <- read_csv('data.csv'); summary(df)"

In this script, we are activating the my-r-env Conda environment using conda activate my-r-env. Then we are installing the tidyverse R package in this environment using conda install -c conda-forge r-tidyverse -y. Finally, we are using this R package in the bash script using Rscript -e "library(tidyverse); df <- read_csv('data.csv'); summary(df)".

Conclusion

In conclusion, using Conda environment for managing R packages is a useful practice and using it in a bash script can make package management easier for data scientists and analysts. We hope this article has helped you understand how to use R packages from a Conda environment in a bash script.