MDL: fixes for CRAN submission

NAMESPACE

@@ -11,6 +11,7 @@ export(DistributeKin)
 export(DistributeKinMatrix)
 export(DistributeMatrix)
 export(ElementalBalanceMin)
+export(ExtractPphases)
 export(ExtractSamples)
 export(ExtractSpecies)
 export(ExtractTotals)

R/Rphree_Kinetics.R

 ##  Functions for dealing with simulations with kinetics
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
-### Time-stamp: "Last modified 2021-04-28 15:19:27 delucia"
+### Time-stamp: "Last modified 2021-04-28 16:06:07 delucia"
 
 ##' This function runs the generated input buffer (or a list thereof)
 ##' through \code{phreeqc}, which has been already loaded as
@@ -119,22 +119,26 @@ DistributeKin <- function(input, prop=NULL, values, ident="-m0")
     return(newinp)  
 }
 
-##' TODO
-##'
-##' TODO
-##' @title Splits a named matrix of data (a column is a variable) in n simulations to run in parallel
-##' @param data The matrix or data.frame containing the values to be splitted
+
+##' @title Splits a named matrix of data (a column is a variable) in n
+##'     simulations to run in parallel
+##' @param data The matrix or data.frame containing the values to be
+##'     splitted
 ##' @param procs How many processors?
 ##' @param base The base script SOLUTION block
-##' @param first The first block to be prepended to each generated input
+##' @param first The first block to be prepended to each generated
+##'     input
 ##' @param prop The names of the properties
-##' @param minerals vector containing the indeces of the EQUILIBRIUM minerals
+##' @param minerals vector containing the indeces of the EQUILIBRIUM
+##'     minerals
 ##' @param kin vector containing indeces of KINETICS minerals
 ##' @param dt time step
 ##' @param ann optional annotation to be postponed to the values
 ##' @param nmax minimum number of simulations in one "split"
-##' @param verbose logical, defaulting to FALSE. If TRUE, some message are displayed
-##' @return a list of length "procs" with the inputs, ready to be run in parallel
+##' @param verbose logical, defaulting to FALSE. If TRUE, some message
+##'     are displayed
+##' @return a list of length "procs" with the inputs, ready to be run
+##'     in parallel
 ##' @author MDL
 ##' @export
 splitMultiKin <- function(data, procs, base, first, prop, minerals, kin, dt, ann, nmax=200, verbose=FALSE)
@@ -274,8 +278,6 @@ DistributeMatrix <- function(input, prop, values, minerals, SI=FALSE)
 }
 
 ##' This function \link{DistributeKin} a matrix of properties values into a buffer
-##'
-##' TODO
 ##' @title Distribute all values from a matrix into a buffer, KINETICS case
 ##' @param input The input buffer to manipulate
 ##' @param prop The names of properties to distribute
@@ -357,7 +359,8 @@ DistributeKinMatrix <- function(input, prop, values, minerals, kin, dt, ann)
 ##' @param prop vector containing the names of the properties
 ##' @param minerals indeces of EQUILIBRIUM minerals
 ##' @param nmax max number of simulations in each input
-##' @param verbose logical, defaulting to FALSE. If TRUE, some message are displayed
+##' @param verbose logical, defaulting to FALSE. If TRUE, some message
+##'     are displayed
 ##' @return a list with n=procs inputs
 ##' @author MDL
 ##' @export

man/AdvectionPQC.Rd

@@ -7,7 +7,8 @@
 AdvectionPQC(conc, inflow = rep(0, ncol(conc)), dx, dt, U)
 }
 \arguments{
-\item{conc}{matrix containing the chemical state}
+\item{conc}{either a vector or a matrix containing the chemical
+state to be updated}
 
 \item{inflow}{vector of concentrations entering the inlet}
 
@@ -21,7 +22,12 @@ AdvectionPQC(conc, inflow = rep(0, ncol(conc)), dx, dt, U)
 a matrix containing the state after the advection
 }
 \description{
-Todo
+This function takes the current state of a chemical system in form
+of a matrix, a vector of concentrations representing boundary
+conditions (injection), the required time step (dt/s), grid spcing
+(dx/m) and U (Darcy velocity/m^3/s). Note that it is
+responsibility of user to check that the required dt does not
+trespass the CFL condition.
 }
 \author{
 MDL

man/DistributeKinMatrix.Rd

@@ -27,9 +27,6 @@ input buffer with the values in correct places
 \description{
 This function \link{DistributeKin} a matrix of properties values into a buffer
 }
-\details{
-TODO
-}
 \author{
 MDL
 }

man/ExtractPphases.Rd

@@ -11,9 +11,6 @@ ExtractPphases(flatlist, pphases)
 
 \item{pphases}{character vector containing the names of the Pure
 Phases whose values are to be extracted}
-
-\item{species}{vector containing the names of the species to
-search for}
 }
 \value{
 a matrix containing as many columns as specified pphases

man/ReactTranspBalanceEq.Rd

@@ -73,7 +73,7 @@ a list containing lots of stuff. Each element of the list
     after the chemistry
 }
 \description{
-TODO
+Cfr \code{demo}
 }
 \author{
 MDL

man/RecomposeState.Rd

@@ -15,7 +15,7 @@ RecomposeState(state, reduced)
 a state with the original (full-grid) number of elements
 }
 \description{
-TODO
+Recompose a chemical state after reduction
 }
 \author{
 MDL

man/ReduceState.Rd

@@ -10,14 +10,13 @@ ReduceState(data)
 \item{data}{the matrix}
 }
 \value{
-a matrix plus an attribute containing the indeces of the
-    compressed matrix
+a matrix with attached attribute containing the indeces of
+    the compressed matrix for later restoring and the "immobile"
+    indices
 }
 \description{
-This functions requires the package \code{mgcv}
-}
-\details{
-TODO
+Applies \code{mgcv::uniquecombs} to the matrix representing the
+current chemical state.
 }
 \author{
 MDL

man/splitMultiFix.Rd

@@ -30,7 +30,8 @@ splitMultiFix(
 
 \item{nmax}{max number of simulations in each input}
 
-\item{verbose}{logical, defaulting to FALSE. If TRUE, some message are displayed}
+\item{verbose}{logical, defaulting to FALSE. If TRUE, some message
+are displayed}
 }
 \value{
 a list with n=procs inputs

man/splitMultiKin.Rd

@@ -2,7 +2,8 @@
 % Please edit documentation in R/Rphree_Kinetics.R
 \name{splitMultiKin}
 \alias{splitMultiKin}
-\title{Splits a named matrix of data (a column is a variable) in n simulations to run in parallel}
+\title{Splits a named matrix of data (a column is a variable) in n
+    simulations to run in parallel}
 \usage{
 splitMultiKin(
   data,
@@ -19,17 +20,20 @@ splitMultiKin(
 )
 }
 \arguments{
-\item{data}{The matrix or data.frame containing the values to be splitted}
+\item{data}{The matrix or data.frame containing the values to be
+splitted}
 
 \item{procs}{How many processors?}
 
 \item{base}{The base script SOLUTION block}
 
-\item{first}{The first block to be prepended to each generated input}
+\item{first}{The first block to be prepended to each generated
+input}
 
 \item{prop}{The names of the properties}
 
-\item{minerals}{vector containing the indeces of the EQUILIBRIUM minerals}
+\item{minerals}{vector containing the indeces of the EQUILIBRIUM
+minerals}
 
 \item{kin}{vector containing indeces of KINETICS minerals}
 
@@ -39,16 +43,16 @@ splitMultiKin(
 
 \item{nmax}{minimum number of simulations in one "split"}
 
-\item{verbose}{logical, defaulting to FALSE. If TRUE, some message are displayed}
+\item{verbose}{logical, defaulting to FALSE. If TRUE, some message
+are displayed}
 }
 \value{
-a list of length "procs" with the inputs, ready to be run in parallel
+a list of length "procs" with the inputs, ready to be run
+    in parallel
 }
 \description{
-TODO
-}
-\details{
-TODO
+Splits a named matrix of data (a column is a variable) in n
+    simulations to run in parallel
 }
 \author{
 MDL