mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-16 00:28:23 +01:00
working on CO2 example
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8570 1feff8c3-07ed-0310-ac33-dd36852eb9cd
This commit is contained in:
Scott R Charlton
parent
b685f71d36
commit
7ed15c09e3
40
R/R.cpp
40
R/R.cpp
@ -1,3 +1,4 @@
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#include <R.h>
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#include <Rdefines.h>
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#include <sstream>
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@ -25,7 +26,7 @@ accumLine(SEXP line)
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const char* str_in;
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// check args
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if (!isString(line) || length(line) != 1) {
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if (!isString(line) || length(line) != 1 || STRING_ELT(line, 0) == NA_STRING) {
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error("AccumulateLine:line is not a single string\n");
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}
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@ -95,8 +96,9 @@ setDumpFileOn(SEXP value)
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{
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SEXP ans = R_NilValue;
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// check args
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if (!isLogical(value) || length(value) != 1) {
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error("SetDumpFileOn:value must either be \"TRUE\" or \"FALSE\"\n");
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if (!isLogical(value) || length(value) != 1 || LOGICAL(value)[0] == NA_LOGICAL) {
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R::singleton().AddError("SetDumpFileOn: value must either be \"TRUE\" or \"FALSE\"");
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error("value must either be \"TRUE\" or \"FALSE\"\n");
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}
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R::singleton().SetDumpFileOn(LOGICAL(value)[0]);
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return(ans);
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@ -107,8 +109,9 @@ setErrorFileOn(SEXP value)
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{
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SEXP ans = R_NilValue;
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// check args
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if (!isLogical(value) || length(value) != 1) {
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error("SetErrorFileOn:value must either be \"TRUE\" or \"FALSE\"\n");
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if (!isLogical(value) || length(value) != 1 || LOGICAL(value)[0] == NA_LOGICAL) {
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R::singleton().AddError("SetErrorFileOn: value must either be \"TRUE\" or \"FALSE\"");
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error("value must either be \"TRUE\" or \"FALSE\"\n");
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}
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R::singleton().SetErrorFileOn(LOGICAL(value)[0]);
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return(ans);
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@ -120,7 +123,8 @@ setLogFileOn(SEXP value)
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SEXP ans = R_NilValue;
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// check args
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if (!isLogical(value) || length(value) != 1) {
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error("SetLogFileOn:value must either be \"TRUE\" or \"FALSE\"\n");
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R::singleton().AddError("SetLogFileOn: value must either be \"TRUE\" or \"FALSE\"");
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error("value must either be \"TRUE\" or \"FALSE\"");
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}
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R::singleton().SetLogFileOn(LOGICAL(value)[0]);
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return(ans);
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@ -132,7 +136,7 @@ setOutputFileOn(SEXP value)
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SEXP ans = R_NilValue;
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// check args
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if (!isLogical(value) || length(value) != 1) {
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error("SetOutputFileOn:value must either be \"TRUE\" or \"FALSE\"\n");
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error("value must either be \"TRUE\" or \"FALSE\"\n");
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}
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R::singleton().SetOutputFileOn(LOGICAL(value)[0]);
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return(ans);
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@ -144,7 +148,7 @@ setSelectedOutputFileOn(SEXP value)
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SEXP ans = R_NilValue;
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// check args
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if (!isLogical(value) || length(value) != 1) {
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error("SetSelectedOutputFileOn:value must either be \"TRUE\" or \"FALSE\"\n");
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error("value must either be \"TRUE\" or \"FALSE\"\n");
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}
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R::singleton().SetSelectedOutputFileOn(LOGICAL(value)[0]);
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return(ans);
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@ -329,9 +333,23 @@ SEXP
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getWarningString(void)
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{
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SEXP ans = R_NilValue;
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PROTECT(ans = allocVector(STRSXP, 1));
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SET_STRING_ELT(ans, 0, mkChar(R::singleton().GetWarningString()));
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UNPROTECT(1);
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const char* warning = R::singleton().GetWarningString();
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if (::strlen(warning)) {
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std::string warn(warning);
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std::istringstream iss(warn);
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std::string line;
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std::vector< std::string > lines;
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while (std::getline(iss, line))
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{
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lines.push_back(line);
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}
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PROTECT(ans = allocVector(STRSXP, lines.size()));
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for (int i = 0; i < lines.size(); ++i)
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{
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SET_STRING_ELT(ans, i, mkChar(lines[i].c_str()));
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}
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UNPROTECT(1);
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}
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return ans;
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}
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@ -17,6 +17,10 @@
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##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
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##' @keywords package
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##' @examples
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##'
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##' #########################################################################
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##' # Run ex2 and plot results
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##' #########################################################################
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##'
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##' # load the phreeqc.dat database
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##' phrLoadDatabaseString(phreeqc.dat)
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@ -35,12 +39,51 @@
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##' plot(temp.C., si_gypsum, main=title, xlab=xlabel, ylab=ylabel, col="darkred", xlim=c(25, 75), ylim=c(-0.4, 0.0))
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##' points(temp.C., si_anhydrite, col="darkgreen")
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##' legend("bottomright", c("Gypsum", "Anhydrite"), col = c("darkred", "darkgreen"), pch = c(1, 1))
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##'
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##'
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##'
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##' #########################################################################
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##' # Load data from CSV and calculate pCO2
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##' #########################################################################
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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##'
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NULL
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# Package Functions
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##' Accumlulate line(s) for input to phreeqc.
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##'
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##' Appends a line of text to the input buffer in order to be run using
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@ -56,11 +99,13 @@ NULL
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##' \code{\link{phrGetAccumulatedLines}}, \code{\link{phrRunAccumulated}}
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##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
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##' @keywords ~kwd1 ~kwd2
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' # this example loads the phreeqc.dat database, accumulates input, and
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##' # runs it
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##' phrLoadDatabase("phreeqc/phreeqc.dat")
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##' phrLoadDatabaseString(phreeqc.dat.list)
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##' phrAccumulateLine("TITLE Example 2.--Temperature dependence of solubility")
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##' phrAccumulateLine(" of gypsum and anhydrite")
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##' phrAccumulateLine("SOLUTION 1 Pure water")
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@ -99,12 +144,12 @@ function(line)
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##' @usage phrClearAccumulatedLines()
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##' @return This function returns NULL.
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##' @note %% ~~further notes~~
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##' @author David Parkhurst \email{dlpark@@usgs.gov}\cr Maintainer: Scott
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##' Charlton \email{charlton@@usgs.gov}
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##' @seealso \code{\link{phrAccumulateLine}},
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##' \code{\link{phrGetAccumulatedLines}}, \code{\link{phrRunAccumulated}}
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##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
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##' @keywords ~kwd1 ~kwd2
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' # This example loads some keyword input, clears the input, and displays the results.
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@ -131,16 +176,16 @@ function()
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##' @return A list containing the names of the components defined in the
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##' current system.
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##' @note %% ~~further notes~~
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##' @author David Parkhurst \email{dlpark@@usgs.gov}\cr Maintainer: Scott
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##' Charlton \email{charlton@@usgs.gov}
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##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
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##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
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##' @keywords ~kwd1 ~kwd2
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' # This example runs the ex2 input file and echos the list of components.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrRunString(ex2)
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##' phrLoadDatabaseString(phreeqc.dat.list)
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##' phrRunString(ex2.list)
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##' cat("components:\n")
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##' for (c in phrGetComponentList()) {
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##' cat(c, "\n")
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@ -153,39 +198,33 @@ function()
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}
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##' Returns the contents of the selected output as a data frame.
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##' Returns the contents of the selected output as a list of data frames.
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##'
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##' phrGetSelectedOutput return the results of a phreeqc run specified in the
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##' selected output block of a phreeqc input file.
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##'
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##' Accessing selected outputs having a user number other than 1 requires
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##' setting the current selected output user number with
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##' \code{\link{phrSetCurrentSelectedOutputUserNumber}}.
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##'
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##' *** Should we return a list of data.frames??? ***
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##' phrGetSelectedOutput returns a named list containing the resultant
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##' selected output blocks. The names of each data frame are creating by
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##' concatenating the letter 'n' and the user number of the selected output
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##' block.
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##'
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##' %% ~~ If necessary, more details than the description above ~~
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##'
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##' @usage phrGetSelectedOutput()
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##' @return Returns a data frame containing the selected_output from the
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##' previous run.
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##' @author David Parkhurst \email{dlpark@@usgs.gov}\cr Maintainer: Scott
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##' Charlton \email{charlton@@usgs.gov}
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##' @seealso \code{\link{phrGetCurrentSelectedOutputUserNumber}},
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##' \code{\link{phrGetSelectedOutputFileOn}},
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##' \code{\link{phrSetCurrentSelectedOutputUserNumber}},
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##' @return Returns a named list of data frames containing the selected_output
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##' from the previous run.
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##' @seealso \code{\link{phrGetSelectedOutputFileOn}}
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##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
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##' @keywords interface
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##'
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##' # Load database and run ex2
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrRunString(ex2)
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##'
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##' # display a summary of the results
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##' df <- phrGetSelectedOutput()
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##' summary(df)
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##' # Load database and run ex2
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##' phrLoadDatabaseString(phreeqc.dat.list)
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##' phrRunString(ex2.list)
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##'
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##' # display a summary of the results
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##' df <- phrGetSelectedOutput()
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##' summary(df$n1)
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##'
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phrGetSelectedOutput =
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function(allow_ = TRUE)
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@ -205,28 +244,30 @@ function(allow_ = TRUE)
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##' Return error string messages.
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##'
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##' Returns a string containing any error messages that were generated
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##' during the last invocation of the following methods:
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##' \code{\link{phrAccumulateLine}}, \code{\link{phrLoadDatabase}},
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##' \code{\link{phrLoadDatabaseString}}, \code{\link{phrRunAccumulatedeadString}},
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##' \code{\link{phrRunFile}}, \code{\link{phrRunString}}
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##'
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##' phrGetErrorString executes a phreeqc run
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##'
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##'
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##' Any details about the operation of this function should go here.
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##' This routine is rarely needed when running interactively since the error
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##' string is displayed when it occurs.
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##'
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##' @usage phrGetErrorString()
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##' @return This function returns the errors that occured during the previous
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##' phrReadDB, phrRun, phrRunFile call.
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##' @author Scott Charlton <charlton@@usgs.gov>
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##'
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##' Lopaka(Rob) Lee <rclee@@usgs.gov>
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##' @seealso \code{\link{phrReadString}}, \code{\link{phrRun}},
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##' \code{\link{phrRunFile}}, \code{\link{phrGetSelectedOutput}}
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##' @references Literature references and web URLs can go here.
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##' @keywords interface
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' # loaddatabase should fail
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##' n <- try(phrLoadDatabase("missing.dat"), silent = TRUE)
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##' # if n is non-NULL display error string
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##' if (!is.null(n)) phrGetErrorString()
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##' # loaddatabase should fail
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##' n <- try(phrLoadDatabase("missing.dat"), silent = TRUE)
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##' # if n is non-NULL display error string
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##' if (!is.null(n)) phrGetErrorString()
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##'
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phrGetErrorString =
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function()
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@ -247,10 +288,11 @@ function()
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
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##' 'comp2'} %% ...
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##' @note %% ~~further notes~~
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##' @author %% ~~who you are~~
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##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
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##' @references %% ~put references to the literature/web site here ~
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##' @keywords ~kwd1 ~kwd2
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' ##---- Should be DIRECTLY executable !! ----
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@ -282,10 +324,11 @@ function()
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
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##' 'comp2'} %% ...
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##' @note %% ~~further notes~~
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##' @author %% ~~who you are~~
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##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
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##' @references %% ~put references to the literature/web site here ~
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##' @keywords ~kwd1 ~kwd2
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' ##---- Should be DIRECTLY executable !! ----
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@ -317,10 +360,11 @@ function(value)
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
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##' 'comp2'} %% ...
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##' @note %% ~~further notes~~
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##' @author %% ~~who you are~~
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##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
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##' @references %% ~put references to the literature/web site here ~
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##' @keywords ~kwd1 ~kwd2
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' ##---- Should be DIRECTLY executable !! ----
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@ -352,10 +396,11 @@ function(value)
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
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##' 'comp2'} %% ...
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||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' ##---- Should be DIRECTLY executable !! ----
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@ -387,10 +432,11 @@ function(value)
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
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##' 'comp2'} %% ...
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||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' ##---- Should be DIRECTLY executable !! ----
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@ -422,10 +468,11 @@ function(value)
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
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||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
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##' @useDynLib phreeqc
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##' @export
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##' @examples
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##'
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##' ##---- Should be DIRECTLY executable !! ----
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@ -457,10 +504,11 @@ function(value)
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
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##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
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##' @keywords ~kwd1 ~kwd2
|
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##' @useDynLib phreeqc
|
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##' @export
|
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##' @examples
|
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##'
|
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##' ##---- Should be DIRECTLY executable !! ----
|
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@ -492,10 +540,11 @@ function(value)
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
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##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
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##' @keywords ~kwd1 ~kwd2
|
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##' @useDynLib phreeqc
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##' @export
|
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##' @examples
|
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##'
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##' ##---- Should be DIRECTLY executable !! ----
|
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@ -527,10 +576,11 @@ function(value)
|
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##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -562,10 +612,11 @@ function(value)
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -597,10 +648,11 @@ function(value)
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -633,10 +685,11 @@ function(value)
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -668,10 +721,11 @@ function(filename)
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -703,10 +757,11 @@ function(filename)
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -738,10 +793,11 @@ function(filename)
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -773,10 +829,11 @@ function(filename)
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -806,16 +863,16 @@ function(filename)
|
||||
##' @usage phrGetDumpFileName()
|
||||
##' @return The name of the dump file as a string.
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author David Parkhurst \email{dlpark@@usgs.gov}\cr Maintainer: Scott
|
||||
##' Charlton \email{charlton@@usgs.gov}
|
||||
##' @seealso \code{\link{phrGetDumpFileOn}}, \code{\link{phrGetDumpString}},
|
||||
##' \code{\link{phrGetDumpStringOn}}, \code{\link{phrSetDumpFileName}},
|
||||
##' \code{\link{phrSetDumpFileOn}}, \code{\link{phrSetDumpStringOn}}
|
||||
##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' phrLoadDatabase("phreeqc/phreeqc.dat")
|
||||
##' phrLoadDatabaseString(phreeqc.dat.list)
|
||||
##' phrSetDumpFileOn(TRUE)
|
||||
##'
|
||||
##' input <- "SOLUTION 1 Pure water \n"
|
||||
@ -852,10 +909,11 @@ function()
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -886,10 +944,11 @@ function()
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -920,10 +979,11 @@ function()
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -954,10 +1014,11 @@ function()
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -988,17 +1049,16 @@ function()
|
||||
##' @usage phrGetDumpString()
|
||||
##' @return The dump output as a string.
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author David Parkhurst \email{dlpark@@usgs.gov}\cr Maintainer: Scott
|
||||
##' Charlton \email{charlton@@usgs.gov}
|
||||
##' @seealso \code{\link{phrGetDumpFileName}}, \code{\link{phrGetDumpFileOn}},
|
||||
##' \code{\link{phrGetDumpStringOn}}, \code{\link{phrSetDumpFileName}},
|
||||
##' \code{\link{phrSetDumpFileOn}}, \code{\link{phrSetDumpStringOn}}
|
||||
##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##'
|
||||
##' phrLoadDatabase("phreeqc/phreeqc.dat")
|
||||
##' phrLoadDatabaseString(phreeqc.dat.list)
|
||||
##' phrSetDumpStringOn(TRUE)
|
||||
##'
|
||||
##' input <- "SOLUTION 1 Pure water \n"
|
||||
@ -1016,6 +1076,24 @@ function()
|
||||
##' cat(phrGetDumpString())
|
||||
##'
|
||||
##'
|
||||
##' phrLoadDatabaseString(phreeqc.dat.list)
|
||||
##' phrSetDumpStringOn(TRUE)
|
||||
##'
|
||||
##' input <- "SOLUTION 1 Pure water \n"
|
||||
##' input <- paste(input, "EQUILIBRIUM_PHASES 1 \n")
|
||||
##' input <- paste(input, " Calcite 0 10 \n")
|
||||
##' input <- paste(input, "SAVE solution 1 \n")
|
||||
##' input <- paste(input, "SAVE equilibrium_phases 1 \n")
|
||||
##' input <- paste(input, "DUMP \n")
|
||||
##' input <- paste(input, " -solution 1 \n")
|
||||
##' input <- paste(input, " -equilibrium_phases 1\n")
|
||||
##'
|
||||
##' if (!is.null(phrRunString(input))) {
|
||||
##' cat(phrGetErrorString())
|
||||
##' }
|
||||
##' cat(phrGetDumpString())
|
||||
##'
|
||||
##'
|
||||
phrGetDumpString =
|
||||
function()
|
||||
{
|
||||
@ -1035,10 +1113,11 @@ function()
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -1069,10 +1148,11 @@ function()
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -1103,10 +1183,11 @@ function()
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -1126,31 +1207,37 @@ function()
|
||||
|
||||
|
||||
|
||||
##' TODO
|
||||
##' Retrieve warning messages.
|
||||
##'
|
||||
##' %% ~~ A concise (1-5 lines) description of what the function does. ~~
|
||||
##' Returns a character vector containing any warning messages that were
|
||||
##' generated during the last invocation of the following methods:
|
||||
##' \code{\link{phrAccumulateLine}}, \code{\link{phrLoadDatabase}},
|
||||
##' \code{\link{phrLoadDatabaseString}}, \code{\link{phrRunAccumulatedeadString}},
|
||||
##' \code{\link{phrRunFile}}, \code{\link{phrRunString}}
|
||||
##'
|
||||
##' %% ~~ If necessary, more details than the description above ~~
|
||||
##'
|
||||
##' @usage phrGetWarningString()
|
||||
##' @return %% ~Describe the value returned %% If it is a LIST, use %%
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @return A character vector containing warning messages.
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
##' ##-- ==> Define data, use random,
|
||||
##' ##-- or do help(data=index) for the standard data sets.
|
||||
##'
|
||||
##' ## The function is currently defined as
|
||||
##' function ()
|
||||
##' {
|
||||
##' }
|
||||
##' # This example loads the phreeqc.dat database and attempts to use the
|
||||
##' # \code{DATABASE} keyword to set the database to wateq4f.dat. A
|
||||
##' # warning is displayed stating that the DATABASE keyword is ignored
|
||||
##' # in the 'R' implementation.
|
||||
##' phrLoadDatabaseString(phreeqc.dat.list)
|
||||
##' phrAccumulateLine("DATABASE wateq4f.dat")
|
||||
##' phrAccumulateLine("SOLUTION 1")
|
||||
##' phrRunAccumulated()
|
||||
##' if (is.null(phrGetWarningString())) {
|
||||
##' cat(phrGetWarningString())
|
||||
##' }
|
||||
##'
|
||||
phrGetWarningString =
|
||||
function()
|
||||
@ -1159,9 +1246,6 @@ function()
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
##' Load a phreeqc database file
|
||||
##'
|
||||
##' Loads the given phreeqc database into phreeqc. Returns NULL if successful.
|
||||
@ -1170,10 +1254,11 @@ function()
|
||||
##' @usage phrLoadDatabase(filename)
|
||||
##' @param filename The file name of the database.
|
||||
##' @return This function returns NULL.
|
||||
##' @author Scott Charlton \email{charlton@@usgs.gov}
|
||||
##' @seealso \code{\link{phrLoadDatabaseString}}
|
||||
##' @references Literature references and web URLs can go here.
|
||||
##' @keywords interface
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##'
|
||||
@ -1192,10 +1277,9 @@ function(filename)
|
||||
}
|
||||
|
||||
|
||||
|
||||
##' Load a phreeqc database as a string.
|
||||
##' Load a phreeqc database as a string or a list of strings.
|
||||
##'
|
||||
##' Load the specified string as a database into phreeqc. Returns NULL if
|
||||
##' Load the specified string(s) as a database into phreeqc. Returns NULL if
|
||||
##' successful.
|
||||
##'
|
||||
##' %% ~~ If necessary, more details than the description above ~~
|
||||
@ -1204,29 +1288,23 @@ function(filename)
|
||||
##' @param input String containing data to be used as the phreeqc database.
|
||||
##' @return This function returns NULL.
|
||||
##' @note All previous definitions are cleared.
|
||||
##' @author David Parkhurst \email{dlpark@@usgs.gov}\cr Maintainer: Scott
|
||||
##' Charlton \email{charlton@@usgs.gov}
|
||||
##' @seealso \code{\link{phrLoadDatabase}}
|
||||
##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' # this example loads the phreeqc.dat database, turns on the
|
||||
##' # output file and runs ex2 as a string
|
||||
##' phrLoadDatabaseString(phreeqc.dat.string)
|
||||
##' phrLoadDatabaseString(phreeqc.dat.list)
|
||||
##' phrSetOutputFileOn(TRUE)
|
||||
##' if (is.null(phrRunString(ex2))) {
|
||||
##' if (is.null(phrRunString(ex2.list))) {
|
||||
##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep=""))
|
||||
##' }
|
||||
##'
|
||||
phrLoadDatabaseString =
|
||||
function(input)
|
||||
{
|
||||
invisible(.Call("loadDBStr", as.character(input), PACKAGE=.packageName))
|
||||
}
|
||||
|
||||
phrLoadDatabaseList =
|
||||
function(input)
|
||||
{
|
||||
invisible(.Call("loadDBLst", as.character(input), PACKAGE=.packageName))
|
||||
}
|
||||
@ -1242,11 +1320,11 @@ function(input)
|
||||
##' @usage phrGetAccumulatedLines()
|
||||
##' @return The input as a single string.
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author David Parkhurst \email{dlpark@@usgs.gov}\cr Maintainer: Scott
|
||||
##' Charlton \email{charlton@@usgs.gov}
|
||||
##' @seealso \code{\link{phrAccumulateLine}}, \code{\link{phrRunAccumulated}}
|
||||
##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' # This example loads some keyword input and displays the contents.
|
||||
@ -1260,12 +1338,6 @@ function()
|
||||
return(.Call("getAccumLines", PACKAGE=.packageName))
|
||||
}
|
||||
|
||||
phrGetAccumulatedLines =
|
||||
function()
|
||||
{
|
||||
return(.Call("getAccumLines", PACKAGE=.packageName))
|
||||
}
|
||||
|
||||
|
||||
|
||||
##' TODO
|
||||
@ -1279,10 +1351,11 @@ function()
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
@ -1313,13 +1386,12 @@ function()
|
||||
##' @usage phrRunFile(filename)
|
||||
##' @param filename The file name of the phreeqc input file.
|
||||
##' @return This function returns NULL.
|
||||
##' @author Scott Charlton <charlton@@usgs.gov>
|
||||
##'
|
||||
##' Lopaka(Rob) Lee <rclee@@usgs.gov>
|
||||
##' @seealso \code{\link{phrReadString}}, \code{\link{phrRun}},
|
||||
##' \code{\link{phrGetSelectedOutput}}
|
||||
##' @references Literature references and web URLs can go here.
|
||||
##' @keywords interface
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##'
|
||||
@ -1346,10 +1418,11 @@ function(filename)
|
||||
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
|
||||
##' 'comp2'} %% ...
|
||||
##' @note %% ~~further notes~~
|
||||
##' @author %% ~~who you are~~
|
||||
##' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
|
||||
##' @references %% ~put references to the literature/web site here ~
|
||||
##' @keywords ~kwd1 ~kwd2
|
||||
##' @useDynLib phreeqc
|
||||
##' @export
|
||||
##' @examples
|
||||
##'
|
||||
##' ##---- Should be DIRECTLY executable !! ----
|
||||
|
||||
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Reference in New Issue
Block a user