Added README.md stub and tracked some missed files

README.md

+# RedModRphree #
+
+This package serves as test bed for the developments about surrogate
+models and reactive transport in the framework of the RedMod project.
+
+### Installation ###
+
+In R, the quickest way is to install the package `devtools` and
+install RedModRphree directly from this repository:
+
+```R
+library(devtools)
+devtools::install_git("https://gitext.gfz-potsdam.de/delucia/RedModRphree.git")
+```R
+
+
+To install in a specific directory (which R must know about, e.g.,
+specifying the variable R_LIBS_USER in the file `$HOME/.Renviron`: 
+
+```shell
+R_LIBS_USER="~/MyRPackageDir"
+```
+then:
+```R
+devtools::install_git("https://gitext.gfz-potsdam.de/delucia/RedModRphree.git", lib="~/MyRPackageDir")
+```
+This should take care of (mostly) all dependencies.
+

man/DistributeMatrix.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Rphree_Kinetics.R
+\name{DistributeMatrix}
+\alias{DistributeMatrix}
+\title{Distribute all values from a matrix into a buffer, EQUILIBRIUM case}
+\usage{
+DistributeMatrix(input, prop, values, minerals, SI = FALSE)
+}
+\arguments{
+\item{input}{The input buffer to manipulate}
+
+\item{prop}{The names of properties to distribute}
+
+\item{values}{matrix or data.frame containing the values to distribute}
+
+\item{minerals}{indeces of the EQUILIBRIUM minerals}
+
+\item{SI}{logical, defaults to FALSE. Should we paste SI before value of a mineral?}
+}
+\value{
+input buffer with the values in correct places
+}
+\author{
+MDL
+}

man/ReactTranspBalanceEq.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Rphree_ReactTrans.R
+\name{ReactTranspBalanceEq}
+\alias{ReactTranspBalanceEq}
+\title{1D Reactive transport simulations using phreeqc or a
+    surrogate, equilibrium simulations}
+\usage{
+ReactTranspBalanceEq(setup, init, maxtime, step = c("time", "iter", "fix_dt"),
+  db = "phreeqc.dat", procs = 1, maxsim = 150, reduce = TRUE,
+  ebreak = FALSE, writeout = FALSE, surrogate = FALSE, surrogate.FUN,
+  model, baleq, tol = 1e-09, call_pqc = TRUE)
+}
+\arguments{
+\item{setup}{a list with several input parameters}
+
+\item{init}{optional, initial state of the simulation}
+
+\item{maxtime}{depending on \code{step}, the simulation time}
+
+\item{step}{one of c("time","iter","fix_dt"), defines the time
+stepping}
+
+\item{db}{the chemical database}
+
+\item{procs}{number of processors to be used in parallel execution}
+
+\item{maxsim}{number of simulations above which parallelization is
+triggered}
+
+\item{reduce}{logical, defaults to TRUE. Should we find the unique
+occurences of a geochemical problem?}
+
+\item{ebreak}{logical, defaults to FALSE. If TRUE, an early break
+is invoked}
+
+\item{writeout}{logical, defaults to FALSE.}
+
+\item{surrogate}{logical, defaults to FALSE. Should we use
+surrogates instead of phreeqc?}
+
+\item{surrogate.FUN}{The function which calls the surrogate}
+
+\item{model}{The list of surrogate models, one element per
+variable}
+
+\item{baleq}{data structure containing the balance equations}
+
+\item{tol}{absolute tolerance on the mass balance}
+
+\item{call_pqc}{logical, defaults to TRUE: if TRUE, calls phreeqc
+on the surrogate simulations which trespass the tolerance}
+}
+\value{
+a list containing lots of stuff
+}
+\description{
+TODO
+}
+\author{
+MDL
+}