geochem

Geochemistry pipeline for processing and visualising data from IRMS, IC and ICP-MS.

Installation

Installation of the package and its dependencies can be done either using a conda environment or directly in R.

Option 1: Install using R

devtools::install_github("giovannellilab/geochem", dependencies=TRUE, build_vignettes=TRUE)

Option 2: Install using a conda environment

Creating a conda environment simplifies having different R and packages versions. It is strongly recommended to create an environment and install all required packages in there.

conda create -n geochem -y

# NOTE: for Macs with M1/M2 chips
CONDA_SUBDIR=osx-64 conda create -n geochem -y

Installation of dependencies:

conda activate geochem
conda install r-base r-essentials r-ggtern r-rio r-devtools r-svglite -y

IMPORTANT: if you use RStudio you need to launch it from the terminal with the activated conda environment:

conda activate geochem
rstudio

Installation of the geochem package can then be done by running the following code in R:

devtools::install_github("giovannellilab/geochem", build_vignettes=TRUE)

Usage

For a detailed pipeline, please refer to the geochem vignette. You can display it after installation via:

vignette("geochem")

Processing ICP-MS data

Refer to the ICP-MS section in the geochem vignette, in which the process is detailed.