fixed RunPQC adding optional "second"

R/Rphree_Kinetics.R

 ##  Functions for dealing with simulations with kinetics
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2018
-### Time-stamp: "Last modified 2018-05-17 15:52:34 delucia"
+### Time-stamp: "Last modified 2018-05-24 18:01:01 delucia"
 
 ##' This function just runs the generated input buffer - or a list
 ##' thereof - through \code{phreeqc}. Obviously it requires the
@@ -17,14 +17,15 @@
 ##' @title Run the generated input buffer using phreeqc
 ##' @param input The input buffer, or list of inputs
 ##' @param procs the number of processes to employ
+##' @param second logical, if TRUE skips each odd row
 ##' @return a data.frame containing the SELECTED_OUTPUT, ordered if
 ##'     multiple parallel simulations were called. Some manipulations
 ##'     of the colnames are also made.
 ##' @author MDL
 ##' @export
-RunPQC <- function(input, procs=1) {
+RunPQC <- function(input, procs=1, second=TRUE) {
 
-    .runPQC <- function(input) {
+    .runPQC <- function(input, second=TRUE) {
         require(phreeqc)
         phreeqc::phrRunString(input)
         out <- phreeqc::phrGetSelectedOutput()[[1]]
@@ -33,7 +34,8 @@ RunPQC <- function(input, procs=1) {
         nso <- sub('.mol.kgw.','',nso, fixed=TRUE)
         nso <- sub('^k_','',nso)
         nso <- sub('.g.','(g)',nso, fixed=TRUE)
-        out <- out[seq(2, nrow(out), by=2),]
+        if (second)
+            out <- out[seq(2, nrow(out), by=2),]
         colnames(out) <- nso
         return(data.matrix(out))
     }
@@ -41,7 +43,7 @@ RunPQC <- function(input, procs=1) {
     ## is lin a list of inputs?
     if (!is.list(input)) {
         if(is.character(input)) { ## normal sequential run
-            res <- .runPQC(input)
+            res <- .runPQC(input, second=second)
         } else {
             stopmsg("something wrong with the input, dying!")
         }
@@ -51,7 +53,7 @@ RunPQC <- function(input, procs=1) {
         ## old one
         ## res <- parallel::mclapply(input, .runPQC, mc.silent=TRUE, mc.cores=procs)
         ## res <- parallel::parLapply(ThisRunCluster, input, .runPQC)
-        res <- foreach(i=seq_along(input), .combine=rbind) %dopar% .runPQC(input[[i]])
+        res <- foreach(i=seq_along(input), .combine=rbind) %dopar% .runPQC(input[[i]], second=second)
 
         ## ## a is the string containing the rbind of each element of the list
         ## a <- paste("rbind(",paste("res[[",1:procs,"]]",sep="", collapse = ", "),")")

man/RunPQC.Rd

@@ -4,12 +4,14 @@
 \alias{RunPQC}
 \title{Run the generated input buffer using phreeqc}
 \usage{
-RunPQC(input, procs = 1)
+RunPQC(input, procs = 1, second = TRUE)
 }
 \arguments{
 \item{input}{The input buffer, or list of inputs}
 
 \item{procs}{the number of processes to employ}
+
+\item{second}{logical, if TRUE skips each odd row}
 }
 \value{
 a data.frame containing the SELECTED_OUTPUT, ordered if
@@ -26,7 +28,7 @@ RPhreeFile("phreeqc.dat", is.db=TRUE ))}
 }
 \details{
 Currently parallelization is achieved using
-\code{parallel::mclapply}, this can change in the future. At the
+\code{parallel::parLapply}, this can change in the future. At the
 moment the function doesn't check that the SELCTED_OUTPUT block is
 well-formed, so this is responsibility of the user.
 }