RedModRphree

This package includes a number of utility functions to efficiently work with PHREEQC, for which we use the phreeqc R package from USGS, available from CRAN, trying to keep at minimum the external dependencies.

Recommended citation

More informations about the package and a nice way to acknowledge this software is by citing the following paper:

De Lucia, M., Kühn, M. (2021): Geochemical and reactive transport modelling in R with the RedModRphree package - Advances in Geosciences, 56, 33-43, https://doi.org/10.5194/adgeo-56-33-2021

Installation

In R, the quickest way is to install RedModRphree directly from this repository (git must be installed already on your system) using packages devtools or remotes:

## if you need to install devtools or remotes, just type in the R command line, e.g.:
## install.packages("remotes")
remotes::install_gitlab("delucia/RedModRphree", host="https://git.gfz-potsdam.de")

Optional: to install the package in a specific directory (which R must know about, e.g., specifying the variable R_LIBS_USER in the file $HOME/.Renviron:

R_LIBS_USER="~/MyRPackageDir"

then, in R:

remotes::install_gitlab("delucia/RedModRphree", host="https://git.gfz-potsdam.de", lib="~/MyRPackageDir")

This should (hopefully) take care of all dependencies.

Usage

library(RedModRphree) ## loads package and dependencies

There are a bunch of demo scripts and datasets provided by the package:

demo(package="RedModRphree") ## displays a list of available demo scripts

## A simple Pourbaix diagram 
demo("demo-Pourbaix",package="RedModRphree") 

## CAUTION: these take 1-2 minutes each
## some platform-independent parallelization is activated by default
demo("demo-equilibrium",package="RedModRphree") 
demo("demo-kinetics",package="RedModRphree") 

## CAUTION: these take 2-3 minutes each!
demo("demo-eq-surr-RF",package="RedModRphree") 
demo("demo-kin-surr",package="RedModRphree") 

## Instructions to obtain the code to the gmd2020-445 paper submitted to Geoscientific Model Development
demo("demo-gmd2020-445",package="RedModRphree")