RedModRphree

This package serves as test bed for the developments about surrogate models and reactive transport in the framework of the RedMod project. It includes a number of utility functions to efficiently work with PHREEQC, for which we use the phreeqc R package from USGS, trying to keep at minimum the external dependencies.

Installation

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

## if you need to install devtools, just type in the R command line:
## install.packages("devtools")
library(devtools)
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:

devtools::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")