Add reference list to output

DESCRIPTION

@@ -1,4 +1,3 @@
-Date: 2020-06-17
 Package: logKcalc
 Version: 0.1.0
 Title: Calculate Equilibrium Constants for GWB Thermodynamic Data Files
@@ -8,7 +7,7 @@ Authors@R: c(
     )
 Maintainer: Jeffrey Dick <[email protected]>
 Depends: CHNOSZ (>= 1.3.0)
-Imports: ggplot2, ggrepel
+Imports: ggplot2, ggrepel, bibtex
 Suggests: knitr, gridExtra, testthat
 Description: Calculate equilibrium constants of reactions for data files
   used in The Geochemist's Workbench®. The main function updates logK values

R/logKcalc.R

@@ -16,6 +16,12 @@
 #source("writedat.R")
 
 logKcalc <- function(infile = "thermo.tdat", outfile = "thermo_OBIGT.tdat", T = NULL, P = "Psat", maxprint = Inf) {
+## for debugging:
+#  infile <- "thermo.tdat"
+#  outfile <- "thermo_OBIGT.tdat"
+#  T <- NULL
+#  P <- "Psat"
+  maxprint <- Inf
   if(!file.exists(infile)) stop("file specified by 'infile' doesn't exist")
   # read the GWB data file
   LINES <- readLines(infile)

R/writedat.R

@@ -184,7 +184,33 @@ writedat <- function(outfile, LINES, HEAD, LOGK) {
 
   }
 
-  # cleanup and write the output to file
+  # cleanup
   out <- stats::na.omit(out)
+  # add reference block 20200618
+  if(utils::packageVersion("CHNOSZ") > "1.3.6") {
+    # get all reference keys used in output GWB file
+    reftypes <- c("redox", "aqueous", "electron", "mineral", "gas")
+    allrefs <- lapply(reftypes, function(x) c(LOGK[[x]]$ref1, LOGK[[x]]$ref2))
+    keys <- sort(unique(stats::na.omit(unlist(allrefs))))
+    # read the bibtex file from CHNOSZ
+    bibfile <- system.file("extdata/OBIGT/obigt.bib", package = "CHNOSZ")
+    bibentry <- bibtex::read.bib(bibfile)
+    # format the printed references
+    op <- options(width = 90)
+    on.exit(options(op))
+    reftext <- utils::capture.output(print(bibentry[keys]))
+    # insert the reference keys before the references
+    keys <- paste0("[", keys, "]")
+    refout <- character()
+    j <- 1
+    for(i in 1:length(reftext)) {
+      if(i==1) { refout <- c(refout, keys[j]); j <- j + 1 }
+      refout <- c(refout, reftext[i])
+      if(reftext[i]=="") { refout <- c(refout, keys[j]); j <- j + 1 }
+    }
+    out <- c(out, refout)
+  }
+
+  # write the output to file
   writeLines(out, outfile)
 }

inst/extdata/tests/ThermoGWB_OBIGT.tdat

@@ -2021,3 +2021,264 @@ S2(g)
    0 oxides
 
 -end-
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