refactor: change colnames of chromatogram() data.frame

- Change the column names of the `data.frame` returned by `chromatogram()` to
  `"rtime"` and `"intensity"` (issue sneumann#304).

DESCRIPTION

@@ -2,7 +2,7 @@ Package: mzR
 Type: Package
 Title: parser for netCDF, mzXML and mzML and mzIdentML files
        (mass spectrometry data)
-Version: 2.41.1
+Version: 2.41.2
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
 Authors@R: c(
     person("Steffen", "Neumann", email="[email protected]", role=c("aut","cre")),

NEWS

@@ -1,3 +1,8 @@
+CHANGES IN VERSION 2.41.2
+-------------------------
+o Use "rtime" and "intensity" as column names for the data.frame returned by
+  chromatogram() (# 304).
+
 CHANGES IN VERSION 2.41.1
 -------------------------
 o Fix compilation error with stricter compiler checks

inst/unitTests/test_chromatograms.R

@@ -11,6 +11,8 @@ test_chromatograms1 <- function() {
     checkIdentical(nrow(chromatogram(x, 136L)), 527L)
     checkIdentical(nrow(chromatogram(x, 137L)), 567L)
     checkIdentical(nrow(chromatogram(x, 138L)), 567L)
+    chr <- chromatogram(x, 138L)
+    checkIdentical(colnames(chr), c("rtime", "intensity"))
 }
 
 test_chromatograms2 <- function() {

man/peaks.Rd

@@ -125,9 +125,8 @@
 
   The \code{chromatogram} (\code{chromatograms}) accessors return
   chromatograms for the MS file handle. If a single index is provided,
-  as \code{data.frame} containing the retention time (1st columns) and
-  intensities (2nd column) is returned. The name of the former is always
-  \code{time}, while the latter will depend on the run parameters.
+  as \code{data.frame} containing the retention time (\code{"rtime"},
+  1st column) and intensities (\code{"intensity"}, 2nd column) is returned.
 
   If more than 1 or no chromatogram indices are provided, then a list of
   chromatograms is returned; either those passed as argument or all of

src/RcppPwiz.cpp

@@ -866,8 +866,8 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )
 	intensity.push_back(p.intensity);
       }
 
-      chromatogramsInfo = Rcpp::DataFrame::create(Rcpp::_["time"] = time,
-						  Rcpp::_[c->id]  = intensity);
+      chromatogramsInfo = Rcpp::DataFrame::create(Rcpp::_["rtime"] = time,
+						  Rcpp::_["intensity"] = intensity);
 
     }
     return(chromatogramsInfo);