Added option "verbose" to splitMulti* to suppress some messages

DESCRIPTION

@@ -8,4 +8,4 @@ Depends: R (>= 3.2.0), doParallel, plyr, data.table, phreeqc, caret, mgcv, rando
 License: LGPL-2.1
 Encoding: UTF-8
 LLazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1

R/Rphree_Kinetics.R

 ##  Functions for dealing with simulations with kinetics
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2018
-### Time-stamp: "Last modified 2018-08-15 00:16:25 delucia"
+### Time-stamp: "Last modified 2018-12-12 14:25:38 delucia"
 
 ##' This function just runs the generated input buffer - or a list
 ##' thereof - through \code{phreeqc}. Obviously it requires the
@@ -131,10 +131,11 @@ DistributeKin <- function(input, prop=NULL, values, ident="-m0")
 ##' @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
 ##' @author MDL
 ##' @export
-splitMultiKin <- function(data, procs, base, first, prop, minerals, kin, dt, ann, nmax=200)
+splitMultiKin <- function(data, procs, base, first, prop, minerals, kin, dt, ann, nmax=200, verbose=FALSE)
 {
     if (is.matrix(data))
         ntot <- dim(data)[1] ## the total number of pqc simulations
@@ -182,7 +183,8 @@ splitMultiKin <- function(data, procs, base, first, prop, minerals, kin, dt, ann
     }
  
     if (ntot > max(nmax,procs*2) && procs > 1) {
-        msg(" Splitting up ", ntot, "simulations to", procs, "processes...")
+        if (verbose)
+            msg(" Splitting up ", ntot, "simulations to", procs, "processes...")
         ## find best division in n
         nsim <- ntot%/%procs
         nlast <- nsim + ntot%%procs
@@ -209,7 +211,8 @@ splitMultiKin <- function(data, procs, base, first, prop, minerals, kin, dt, ann
         return(inputlist)
 
     } else  {
-        msg("won't parallelize... procs=", procs," ntot=", ntot)
+        if(verbose)
+            msg("won't parallelize... procs=", procs," ntot=", ntot)
         BigInp <- RepSol(base, ntot)
         tmp <- DistributeKinMatrix(input=BigInp, prop=prop, values=data, minerals=minerals, kin=kin, dt=dt, ann=ann)
         input <- c(first, tmp)
@@ -352,10 +355,11 @@ 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
 ##' @return a list with n=procs inputs
 ##' @author MDL
 ##' @export
-splitMultiFix <- function(data, procs, base, first, prop, minerals, nmax=200)
+splitMultiFix <- function(data, procs, base, first, prop, minerals, nmax=200, verbose=FALSE)
 {
     if (is.matrix(data))
         ntot <- dim(data)[1] ## the total number of pqc simulations
@@ -369,7 +373,8 @@ splitMultiFix <- function(data, procs, base, first, prop, minerals, nmax=200)
     if ( ntot  ==1) ## try and call normal Distribute (i.e., ##!is.matrix(data) ||
         ## just 1 simulation!)
     {
-        msg("just 1 simulation, reverting back to normal Distribute")
+        if (verbose)
+            msg("just 1 simulation, reverting back to normal Distribute")
         BigInp <- RepSol(base, 1, first=first)
         namdis <- colnames(data)
         indminer <- minerals
@@ -385,7 +390,8 @@ splitMultiFix <- function(data, procs, base, first, prop, minerals, nmax=200)
     }
  
     if (ntot > nmax && procs > 1)   {
-        msg("Splitting up ", ntot, "simulations to", procs, "processes...")
+        if (verbose)
+            msg("Splitting up ", ntot, "simulations to", procs, "processes...")
         ## find best division in n
         nsim <- ntot%/%procs
         nlong <- nsim + ntot%%procs

man/AnalyticalLogK.Rd

@@ -15,6 +15,9 @@ logK}
 \value{
 The logK at wanted temperature
 }
+\description{
+Calculates the logK of reaction for a given temperature
+}
 \author{
 MDL
 }

man/BalanceEquations.Rd

@@ -16,6 +16,10 @@ defaults to c("C","Ca","Mg","Cl")}
 \value{
 a structure (list) containing the balance equations
 }
+\description{
+Form the balance equations from a full stoichiometric
+    matrix
+}
 \author{
 MDL
 }

man/CheckBalance.Rd

@@ -21,6 +21,10 @@ mass balance check}
 a matrix containing a mass balance error, one column for
     each tested equation (=element)
 }
+\description{
+Check mass balance between design and results for
+    surrogates
+}
 \author{
 MDL
 }

man/DistributeMatrix.Rd

@@ -20,6 +20,9 @@ DistributeMatrix(input, prop, values, minerals, SI = FALSE)
 \value{
 input buffer with the values in correct places
 }
+\description{
+Distribute all values from a matrix into a buffer, EQUILIBRIUM case
+}
 \author{
 MDL
 }

man/ElementalBalanceMin.Rd

@@ -5,7 +5,8 @@
 \title{Returns the composition of a mineral in terms of chemical
     elements (not of species)}
 \usage{
-ElementalBalanceMin(pphase, stoichmat, elements = c("C", "Ca", "Mg", "Cl"))
+ElementalBalanceMin(pphase, stoichmat, elements = c("C", "Ca", "Mg",
+  "Cl"))
 }
 \arguments{
 \item{pphase}{name of the mineral to parse}
@@ -19,6 +20,10 @@ defaults to c("C","Ca","Mg","Cl")}
 named vector with stoichiometric coefficients of chemical
     elements for the pphase mineral
 }
+\description{
+Returns the composition of a mineral in terms of chemical
+    elements (not of species)
+}
 \author{
 MDL
 }

man/ExtractPphases.Rd

@@ -15,6 +15,9 @@ for}
 \value{
 matix with one pphases per column
 }
+\description{
+Extract all phases from a flatted Rphree list
+}
 \author{
 MDL
 }

man/ExtractSamples.Rd

@@ -21,6 +21,10 @@ variables are selected}
 \value{
 a list with 2 elements: design and result
 }
+\description{
+Extracts input/output tables from a list of Reactive
+    Transport Simulations
+}
 \author{
 MDL
 }

man/ExtractSpecies.Rd

@@ -15,6 +15,9 @@ search for}
 \value{
 matix with one species per column
 }
+\description{
+Extract species from a flatted Rphree list
+}
 \author{
 MDL
 }

man/ExtractTotals.Rd

@@ -16,6 +16,10 @@ search for}
 \value{
 Matrix with one element per column
 }
+\description{
+Extract total element concentrations from a flatted Rphree
+    list
+}
 \author{
 MDL
 }

man/FindAllMinNames.Rd

@@ -12,6 +12,9 @@ FindAllMinNames(flatlist)
 \value{
 vector with unique occurrences of pphases names
 }
+\description{
+Find all pphases occurring in the ensemble
+}
 \author{
 MDL
 }

man/FindAllSpeciesNames.Rd

@@ -12,6 +12,9 @@ FindAllSpeciesNames(flatlist)
 \value{
 vector with unique occurrences of species names
 }
+\description{
+Find all species occurring in the ensemble
+}
 \author{
 MDL
 }

man/FindAllTotNames.Rd

@@ -12,6 +12,9 @@ FindAllTotNames(flatlist)
 \value{
 vector with unique occurrences of element names
 }
+\description{
+Find all totals occurring in the ensemble
+}
 \author{
 MDL
 }

man/FindLogK.Rd

@@ -17,6 +17,10 @@ FindLogK(species, db, type = c("analytical"))
 \value{
 the requested logK
 }
+\description{
+Finds the expression of a logK of a given compound/mineral
+    in a PHREEQC database
+}
 \author{
 MDL
 }

man/FindPhase.Rd

@@ -16,6 +16,9 @@ a list with the components of the formula and the
     stoichiometric coefficients, plus the corresponding line in
     the db as attr(,"line")
 }
+\description{
+Find a PURE_PHASE in a database and parses its formula
+}
 \author{
 MDL
 }

man/FormulaFromBal.Rd

@@ -14,6 +14,9 @@ minerals}
 a named vector with the stoichiometric formula of the
     minerals
 }
+\description{
+Figures out the formula from a baleq structure
+}
 \author{
 MDL
 }

man/Matplot.Rd

@@ -5,8 +5,8 @@
 \title{Display the profiles of some variables for 2 reactive
     transport simulation (one using surrogates)}
 \usage{
-Matplot(sur, sim, sample = 1L, vars = c("Ca", "Mg", "Calcite", "Dolomite"),
-  ...)
+Matplot(sur, sim, sample = 1L, vars = c("Ca", "Mg", "Calcite",
+  "Dolomite"), ...)
 }
 \arguments{
 \item{sur}{The simulation with surrogate}
@@ -22,6 +22,10 @@ variables to display (up to 7)}
 \item{...}{further parameters passed to \code{matplot}, such as
 main, xlab, ylab...}
 }
+\description{
+Display the profiles of some variables for 2 reactive
+    transport simulation (one using surrogates)
+}
 \author{
 MDL
 }

man/MatplotSingle.Rd

@@ -5,8 +5,8 @@
 \title{Display the profiles of some variables along a 1D reactive
     transport simulation}
 \usage{
-MatplotSingle(sim, sample = 1L, vars = c("Ca", "Mg", "Calcite", "Dolomite"),
-  ...)
+MatplotSingle(sim, sample = 1L, vars = c("Ca", "Mg", "Calcite",
+  "Dolomite"), ...)
 }
 \arguments{
 \item{sim}{The simulation to display}
@@ -20,6 +20,10 @@ variables to display (up to 7)}
 \item{...}{further parameters passed to \code{matplot}, such as
 main, xlab, ylab...}
 }
+\description{
+Display the profiles of some variables along a 1D reactive
+    transport simulation
+}
 \author{
 MDL
 }

man/ParseFormula.Rd

@@ -15,6 +15,9 @@ ParseFormula(line, type = "all")
 a list containing components and coefficients.
     Coefficients of left hand side are negated.
 }
+\description{
+Parses a formula as it is written in a PHREEQC database
+}
 \author{
 MDL
 }