MDL: some fixes for CRAN submission

DESCRIPTION

 Package: RedModRphree
-Title: Programmable interface to the phreeqc geochemical solver adding features such as surrogate models, reactive transport and Pourbaix diagrams 
-Version: 0.2
-Authors@R: c(person("Marco", "De Lucia", email = "delucia@gfz-potsdam.de", role = c("aut", "cre"), comment=, comment = c(ORCID = "0000-0003-0918-3766")),
-             person("Janis", "Jatnieks", email = "deltaxzz@gmail.com", role = c("ctb")))
-Author: Marco De Lucia [aut, cre],
-  Janis Jatnieks [ctb]
-Maintainer: Marco De Lucia <delucia@gfz-potsdam.de>
-Description: Programmable interface to the phreeqc geochemical solver adding features such as surrogate models, reactive transport and Pourbaix diagrams.
+Title: Programmable Interface to the PHREEQC Geochemical Solver 
+Version: 0.3.1
+Authors@R: c(person(given = "Marco",
+                    family = "De Lucia",
+                    email = "delucia@gfz-potsdam.de",
+		    role = c("aut", "cre"),
+		    comment = c(ORCID = "0000-0003-0918-3766")),
+             person(given = "Janis",
+	            family = "Jatnieks",
+		    email = "deltaxzz@gmail.com",
+		    role = c("ctb")))
+Description: Programmable interface to the phreeqc geochemical solver
+    adding features such as surrogate models, reactive transport and
+    Pourbaix diagrams.
 Depends: R (>= 3.2.0), doParallel, phreeqc, mgcv, graphics, methods, stats, utils, plyr, foreach
 License: LGPL-2.1
 Encoding: UTF-8
-LLazyData: true
 RoxygenNote: 7.1.1
+LazyData: true

NAMESPACE

@@ -11,7 +11,6 @@ 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 2021-04-12 12:46:35 delucia"
+### Time-stamp: "Last modified 2021-04-28 15:19:27 delucia"
 
 ##' This function runs the generated input buffer (or a list thereof)
 ##' through \code{phreeqc}, which has been already loaded as
 ##' dependency. Also the database must be previously and explicitely
-##' loaded by the user using, e.g.,
-##' \code{db <- RPhreeFile('/path/to/database.dat', is.db=TRUE)}
-##' followed by
-##' \code{phreeqc::phrLoadDatabaseString(db)}
-##' or using one of the databases included in \code{phreeqc}, e.g.,
+##' loaded by the user using, e.g., \code{db <-
+##' RPhreeFile('/path/to/database.dat', is.db=TRUE)} followed by
+##' \code{phreeqc::phrLoadDatabaseString(db)} or using one of the
+##' databases included in \code{phreeqc}, e.g.,
 ##' \code{phreeqc::phrLoadDatabaseString(phreeqc.dat)}.
 ##'
 ##' Parallelization is achieved using \code{%dopar%} from package
@@ -55,7 +54,6 @@ RunPQC <- function(input, procs=1, second=TRUE) {
 
         ## old one
         ## res <- parallel::mclapply(input, .runPQC, mc.silent=TRUE, mc.cores=procs)
-        ## res <- parallel::parLapply(ThisRunCluster, input, .runPQC)
         res <- foreach::foreach(i=seq_along(input), .combine=rbind) %dopar% .runPQC(input[[i]], onlysecond=second)
 
         ## ## a is the string containing the rbind of each element of the list
@@ -79,7 +77,8 @@ RunPQC <- function(input, procs=1, second=TRUE) {
 ##' @param prop The property whose values need to be distributed.
 ##' @param values The numerical value(s) to distribute across the
 ##'     SOLUTIONS/KINETICS blocks.
-##' @param ident The identifier for the line where the actual values will be pasted, defaults to "-m"
+##' @param ident The identifier for the line where the actual values
+##'     will be pasted, defaults to "-m"
 ##' @return A new input buffer
 ##' @author MDL
 ##' @export

R/Rphree_ReactTrans.R

 ##  Functions for dealing with surrogate simulations
 
-### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2018
-### Time-stamp: "Last modified 2021-04-12 13:05:02 delucia"
+### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
+### Time-stamp: "Last modified 2021-04-28 15:30:47 delucia"
 
 
 ##' Todo
@@ -203,19 +203,24 @@ ReduceState <- function(data)
 ##'     occurences of a geochemical problem?
 ##' @param ebreak logical, defaults to FALSE. If TRUE, an early break
 ##'     is invoked
-##' @param writeout logical, defaults to FALSE.
+##' @param writeout logical, defaults to FALSE. Should we write the
+##'     phreeqc output on disk?
 ##' @param surrogate logical, defaults to FALSE. Should we use
 ##'     surrogates instead of phreeqc?
 ##' @param surrogate.FUN The function which calls the surrogate
-##' @param model The list of surrogate models, one element per
-##'     variable
+##' @param model a list containing all surrogate models, one element
+##'     per variable
 ##' @param baleq data structure containing the balance equations
-##' @param tol absolute tolerance on the mass balance
+##' @param tol absolute tolerance on the mass balance. If this is
+##'     trespassed, phreeqc is called instead
 ##' @param call_pqc logical, defaults to TRUE: if TRUE, calls phreeqc
 ##'     on the surrogate simulations which trespass the tolerance
-##' @return a list containing lots of stuff
+##' @return a list containing lots of stuff. Each element of the list
+##'     represent an iteration and has two elements: $T
+##'     (concentrations after the transport) and $C, concentrations
+##'     after the chemistry
 ##' @author MDL
-##' @export 
+##' @export
 ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix_dt"),
                                  db="phreeqc.dat", procs=1, maxsim=150,
                                  reduce=TRUE, ebreak=FALSE, writeout=FALSE, surrogate=FALSE,
@@ -243,9 +248,9 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
 
     if (procs > 1) {
         if (Sys.info()[["sysname"]]=="Windows") {
-            ThisRunCluster <<- parallel::makePSOCKcluster(procs)
+            ThisRunCluster <- parallel::makePSOCKcluster(procs)
         } else {
-            ThisRunCluster <<- parallel::makeForkCluster(procs)
+            ThisRunCluster <- parallel::makeForkCluster(procs)
         }
 
         doParallel::registerDoParallel(ThisRunCluster)
@@ -480,7 +485,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
     on.exit()
     
     if (procs > 1) {
-        stopCluster(ThisRunCluster)
+        parallel::stopCluster(ThisRunCluster)
         msg("Parallelization cluster stopped")
     }
 
@@ -553,9 +558,9 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
 
     if (procs > 1) {
         if (Sys.info()[["sysname"]]=="Windows") {
-            ThisRunCluster <<- parallel::makePSOCKcluster(procs)
+            ThisRunCluster <- parallel::makePSOCKcluster(procs)
         } else {
-            ThisRunCluster <<- parallel::makeForkCluster(procs)
+            ThisRunCluster <- parallel::makeForkCluster(procs)
         }
 
         doParallel::registerDoParallel(ThisRunCluster)
@@ -791,7 +796,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
     on.exit()
 
     if (procs > 1) {
-        stopCluster(ThisRunCluster)
+        parallel::stopCluster(ThisRunCluster)
         msg("Parallelization cluster stopped")
     }
 

R/Rphree_SurrogateUtils.R

 ##  Functions for dealing with surrogate simulations
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
-### Time-stamp: "Last modified 2021-04-12 11:45:32 delucia"
+### Time-stamp: "Last modified 2021-04-28 15:32:05 delucia"
 
 ##' Computes the average of absolute values of a vector
 ##' @title Average of absolute values
@@ -90,13 +90,14 @@ ExtractSpecies <- function(flatlist, species) {
    return(tmp)
 }
 
-##' @title Extract all phases from a flatted Rphree list
+##' @title Extract all equilibrium phases from a flattened output list
 ##' @param flatlist the list as input to search in
-##' @param totals vector containing the names of the phases to search
-##'     for
-##' @return matix with one pphases per column
+##' @param pphases character vector containing the names of the Pure
+##'     Phases whose values are to be extracted
+##' @param species vector containing the names of the species to
+##'     search for
+##' @return a matrix containing as many columns as specified pphases
 ##' @author MDL
-##' @export
 ExtractPphases <- function(flatlist, pphases) {
    tmp <- matrix(NA, len <- length(flatlist), speclen <- length(pphases))
    colnames(tmp) <- pphases
@@ -305,7 +306,7 @@ CheckBalance <- function(baleq, des, res, elements)
 ##' @title Extract the changes in stateC due to transport
 ##' @param sim a result of Reactive Transport (for each time step, a T
 ##'     and a C data.frame)
-##' @return a list 
+##' @return a list
 ##' @author MDL
 ##' @export
 TranspAsPert <- function (sim) {

R/Rphree_Utils.R

 ### Utility functions for RedModRphree
 
-### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2018
-### Time-stamp: "Last modified 2021-04-12 12:58:36 delucia"
+### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
+### Time-stamp: "Last modified 2021-04-28 14:50:36 delucia"
 
 ##' Replicates an input buffer containing only one SOLUTION, taking
 ##' care of SOLUTION/KINETICS/PURE identifiers. Eventually insert a
-##' block (e.g: PUNCH) under the first SOLUTION.
+##' block (e.g: PUNCH) just once under the first SOLUTION.
 ##'
 ##' Analogous to standard \code{rep} function.
 ##' @title Replicate a SOLUTION 
-##' @param sol The initial phreeqc buffer that needs to be replicated.
-##' @param n Number of replicates to generate.
+##' @param sol The initial phreeqc buffer that needs to be replicated
+##' @param n Number of replicates to generate
 ##' @param first A new block which needs to be inserted only in the
-##' first solution (typically, PUNCH and alike).
-##' @return A buffer upon which Rphree can be called.
+##' first solution (typically, PUNCH and alike)
+##' @return A buffer upon which RunPQC can be called
 ##' @author MDL
 ##' @export
 RepSol <- function(sol, n, first=NULL)
@@ -62,8 +62,6 @@ RepSol <- function(sol, n, first=NULL)
 
 ##' Function that adds a new property (species, pure phase, ...) to an
 ##' input buffer.
-##'
-##' .. content for DETAILS ..
 ##' @title Add a new property (species, pure phase, ...) to an input
 ##' buffer
 ##' @param input The input buffer.
@@ -72,14 +70,13 @@ RepSol <- function(sol, n, first=NULL)
 ##' @param values The value(s) of the property.
 ##' @param cat The category of the property. Must be one of
 ##' \code{c("tot","pphases","kin")}
-##' @param kinpar Kinetics parameters for the KINETICS case.
+##' @param kinpar Kinetics parameters for the KINETICS case
 ##' @param first A block to be added in the first SOLUTION, as in
-##' \code{RepSol} and \code{Distribute}.
-##' @return The new input buffer upon which Rphree can be called.
+##' \code{RepSol} and \code{Distribute}
+##' @return The new input buffer upon which RunPQC can be called
 ##' @author MDL
 ##' @export
 AddProp <- function(input, name, values, cat, kinpar=NULL, first=NULL)
-### Add a property (species, pure phase, ...) to an input buffer
 {
     cat <- match.arg(cat,c("tot","pphases","kin"))
     
@@ -150,16 +147,18 @@ AddProp <- function(input, name, values, cat, kinpar=NULL, first=NULL)
 ##' replicated length(values) times by RepSol. For KINETICS use
 ##' \code{DistributeKin}.
 ##' 
-##' @title Distribute properties in an input buffer.
-##' @param input The initial input buffer.
-##' @param prop The property whose values need to be distributed.
-##' @param values The numerical value(s) to distribute across the SOLUTIONS.
+##' @title Distribute properties in an input buffer
+##' @param input The initial input buffer
+##' @param prop The property whose values need to be distributed
+##' @param values The numerical value(s) to distribute across the
+##'     SOLUTIONS
 ##' @param newname Optional name of a property which is not initially
-##' present in the input buffer.
+##'     present in the input buffer
 ##' @param first The \code{first} block which will be passed to
-##' \code{\link{RepSol}} if needed
-##' @param wholeline logical. if TRUE, comments after the properties (i.e. "as HCO3") get also distributed.
-##' @return A new input buffer upon which Rphree can be run.
+##'     \code{\link{RepSol}} if needed
+##' @param wholeline logical. if TRUE, comments after the properties
+##'     (i.e. "as HCO3") get also distributed.
+##' @return A new input buffer upon which RunPQC can be run
 ##' @author MDL
 ##' @export
 Distribute <- function(input, prop, values, newname=NULL, first=NULL, wholeline=TRUE)
@@ -203,7 +202,6 @@ Distribute <- function(input, prop, values, newname=NULL, first=NULL, wholeline=
 
 ##' Erases the SOLUTION number n (label, not position) from an input
 ##' buffer containing many.
-##'
 ##' @title Suppress a simulation from an input buffer
 ##' @param biginp The input buffer
 ##' @param n The number of the simulation to erase
@@ -218,22 +216,22 @@ SuppressSim <- function(biginp, n=1L)
 }
 
 
-##' This functions extracts informations from calculated Rphree
-##' formatted solutions.
-##'
-##' @title Extract specific values from an Rphree output
-##' @param lin The list containg the Rphree solution(s)
+##' This functions extracts informations extracted from standard
+##' PHREEQC output files
+##' @title Extract specific values from a phreeqc output
+##' @param lin The list containg the parsed phreeqc solution(s)
 ##' @param cat A string indicating the category (or output block) to
-##' search in, must be one of: "tot, desc, pphases, master, species,
-##' kin, SI"
+##'     search in, must be one of:
+##'     "tot, desc, pphases, master, species, kin, SI"
 ##' @param prop The name of the inquired property (element, species,
-##' mineral phase,\dots) whose value(s)
-##' @param force Logical. If TRUE (default if left unspecified), a valid numeric value (0) is returned even if the property is not found
-##' value is returned if the inquired property is not found in the
-##' solution
+##'     mineral phase,\dots) whose value(s)
+##' @param force Logical. If TRUE (default if left unspecified), a
+##'     valid numeric value (0) is returned even if the property is
+##'     not found value is returned if the inquired property is not
+##'     found in the solution
 ##' @param flex Logical. If TRUE, expects no "ListInfo" in the
-##' formatted solution list and performs heuristics to circumvent this
-##' absence
+##'     formatted solution list and performs heuristics to circumvent
+##'     this absence
 ##' @return A numeric vector containing the inquired properties
 ##' @author MDL
 ##' @examples
@@ -290,12 +288,11 @@ RPinfo <- function(lin, cat=c("tot","desc","pphases","master","species","kin","S
 ##' Workhorse function for extraction of results from a solution,
 ##' primarily intended to be used by \code{\link{RPinfo}}, where it is
 ##' called inside a \code{sapply} statement.
-##'
 ##' @title Workhorse function for extraction of informations from a
-##' solution
+##'     solution
 ##' @param sol The solution outputted by Rphree
 ##' @param cat String: the category or output block where to look for
-##' the property \code{prop}
+##'     the property \code{prop}
 ##' @param prop The name of the property to look for
 ##' @return Numeric of length 1, the inquired value for the property
 ##' @author MDL
@@ -309,14 +306,15 @@ RPhreeExt <- function(sol, cat, prop)
 }
 
 ##' Workhorse function for extraction of results from a solution,
-##' specifically equilibrium phases. 
+##' specifically equilibrium phases.
 ##'
-##' @title Workhorse function for extraction of 
+##' @title Workhorse function for extraction of equilibrium phases
+##'     from a solution list
 ##' @param lin The solution outputted by Rphree
 ##' @param which String containing the name of the specific pphase to
-##' look for. If omitted, all pphases are returned.
+##'     look for. If omitted, all pphases are returned.
 ##' @param delta Logical. If TRUE, delta min are returned, if FALSE,
-##' total amount
+##'     total amount
 ##' @return A data.frame containing the results of equilibrium phases
 ##' @author MDL
 ##' @export
@@ -336,10 +334,10 @@ RGetPhases <- function(lin, which=NULL, delta=TRUE)
 
 
 ##' Workhorse function for extraction of results from a solution,
-##' specifically equilibrium phases. Variant.
+##' specifically equilibrium phases. 
 ##'
-##' @title extract the phases from a Rphree solution
-##' @param lin The solution outputted by Rphree
+##' @title extract the phases from a PHREEQC output
+##' @param lin The solution outputted by phree
 ##' @return A data.frame containing the results of equilibrium phases
 ##' @author MDL
 ##' @export

R/Rphree_Viz.R

 ### RedModRphree, functions to perform basic visualization
 ### Licence: LGPL version 2.1
-### Time-stamp: "Last modified 2018-05-06 19:30:10 delucia"
+### Time-stamp: "Last modified 2021-04-28 15:16:50 delucia"
 
 ##' @title Display the profiles of some variables along a 1D reactive
 ##'     transport simulation
@@ -79,7 +79,7 @@ PlotModsInSample <- function(mod, res, des, sample=seq(1,nrow(res)), column=TRUE
     else
         par(mfrow=c(2,nr))
     for (i in seq_along(mod)) {
-        plot(result[,i], predict(mod[[i]], design),"p",pch=3, main=names(mod)[i],
+        plot(result[,i], stats::predict(mod[[i]], design),"p",pch=3, main=names(mod)[i],
              xlab="Full physics", ylab="Surrogate", ...)
         abline(0,1,lty="dashed",col="grey")
     }

R/Surr_Prepare.R

-## Time-stamp: "Last modified 2021-04-12 11:40:11 delucia"
+## Time-stamp: "Last modified 2021-04-28 15:14:00 delucia"
+
 ##' @title Extracts input/output tables from a list of Reactive
 ##'     Transport Simulations
 ##' @param simlist a list containing the simulations

man/AddProp.Rd

@@ -18,21 +18,18 @@ mineral,...)}
 \item{cat}{The category of the property. Must be one of
 \code{c("tot","pphases","kin")}}
 
-\item{kinpar}{Kinetics parameters for the KINETICS case.}
+\item{kinpar}{Kinetics parameters for the KINETICS case}
 
 \item{first}{A block to be added in the first SOLUTION, as in
-\code{RepSol} and \code{Distribute}.}
+\code{RepSol} and \code{Distribute}}
 }
 \value{
-The new input buffer upon which Rphree can be called.
+The new input buffer upon which RunPQC can be called
 }
 \description{
 Function that adds a new property (species, pure phase, ...) to an
 input buffer.
 }
-\details{
-.. content for DETAILS ..
-}
 \author{
 MDL
 }

man/Distribute.Rd

@@ -2,27 +2,29 @@
 % Please edit documentation in R/Rphree_Utils.R
 \name{Distribute}
 \alias{Distribute}
-\title{Distribute properties in an input buffer.}
+\title{Distribute properties in an input buffer}
 \usage{
 Distribute(input, prop, values, newname = NULL, first = NULL, wholeline = TRUE)
 }
 \arguments{
-\item{input}{The initial input buffer.}
+\item{input}{The initial input buffer}
 
-\item{prop}{The property whose values need to be distributed.}
+\item{prop}{The property whose values need to be distributed}
 
-\item{values}{The numerical value(s) to distribute across the SOLUTIONS.}
+\item{values}{The numerical value(s) to distribute across the
+SOLUTIONS}
 
 \item{newname}{Optional name of a property which is not initially
-present in the input buffer.}
+present in the input buffer}
 
 \item{first}{The \code{first} block which will be passed to
 \code{\link{RepSol}} if needed}
 
-\item{wholeline}{logical. if TRUE, comments after the properties (i.e. "as HCO3") get also distributed.}
+\item{wholeline}{logical. if TRUE, comments after the properties
+(i.e. "as HCO3") get also distributed.}
 }
 \value{
-A new input buffer upon which Rphree can be run.
+A new input buffer upon which RunPQC can be run
 }
 \description{
 Function to distribute different values of one property

man/DistributeKin.Rd

@@ -14,7 +14,8 @@ DistributeKin(input, prop = NULL, values, ident = "-m0")
 \item{values}{The numerical value(s) to distribute across the
 SOLUTIONS/KINETICS blocks.}
 
-\item{ident}{The identifier for the line where the actual values will be pasted, defaults to "-m"}
+\item{ident}{The identifier for the line where the actual values
+will be pasted, defaults to "-m"}
 }
 \value{