Major update to cv2df(). Removed df attributes, built-into df instead.

Be advised: This change will break all old reports that used the cv2df() function.
Experimental information (potential limits, scanspeeds, etc.) are now added to the
return dataframe as columns instead of attributes.
With this information built-in to the dataframe, analysis is simplified using melt
and cast and other grouping functions.

CHI.R

@@ -369,44 +369,53 @@ cv2df <- function(datafilename, wearea = 1) {
    for (s in 1:length(starts)) {
       zz <- textConnection(chifile[starts[s]:ends[s]], "r")
       ff <- rbind(ff,
-               data.frame(sampleid, segment = factor(s), cycle = factor(ceiling(s/2)),
+               data.frame(sampleid, segment = s, cycle = as.integer(ceiling(s/2)),
                matrix(scan(zz, what = numeric(), sep = ","),
                   ncol = 3, byrow = T)))
       close(zz)
    }
+   # Column names after initial assignment
    names(ff) <- c("sampleid", "segment", "cycle", "potential", "current", "charge")
    # Calculate current density
    currentdensity <- ff$current / wearea
    ff <- cbind(ff[, 1:5], currentdensity = currentdensity, charge = ff[, 6])
-   #
-   ### Collect attributes of this experiment
-   # These attributes are specific for each kind of experiment,
-   # be careful when adapting to other electrochemical data
-   rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
-                  "^High\\sE\\s\\(V\\)",
-                  "^Low\\sE\\s\\(V\\)",
-                  "^Init\\sP/N",
-                  "^Scan\\sRate\\s\\(V/s\\)",
-                  "^Segment\\s=",
-                  "^Sample\\sInterval\\s\\(V\\)",
-                  "^Quiet\\sTime\\s\\(sec\\)",
-                  "^Sensitivity\\s\\(A/V\\)")
-   names.attr <- c("InitE",
-                   "HighE",
-                   "LowE",
-                   "InitPN",
-                   "ScanRate",
-                   "Segments",
-                   "SamplingInterval",
-                   "QuietTime",
-                   "Sensitivity")
-   for (n in 1:length(rgxp.attr)) {
-      attrow.idx <- regexpr(rgxp.attr[n], chifile)
-      attrow.len <- attr(attrow.idx, "match.length")
-      attr(attrow.idx, "match.length") <- NULL
-      attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
-         "\\s=\\s")[[1]][2]
-   }
+   ## Collect attributes of this experiment
+   # InitE (volt)
+   position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
+   InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
+   ff$InitE <- InitE
+   # HighE (volt)
+   position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
+   HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
+   ff$HighE <- HighE
+   # LowE (volt)
+   position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
+   LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
+   ff$LowE <- LowE
+   # InitPN (positive or negative)
+   position.InitPN <- regexpr("^Init\\sP/N", chifile)
+   InitPN <- strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2]
+   ff$InitPN <- InitPN
+   # ScanRate (volt per second)
+   position.ScanRate <- regexpr("^Scan\\sRate\\s\\(V/s\\)", chifile)
+   ScanRate <- as.numeric(strsplit(chifile[which(position.ScanRate == 1)], "\\s=\\s")[[1]][2])
+   ff$ScanRate <- ScanRate
+   # Segments, number of
+   position.Segment <- regexpr("^Segment\\s=", chifile)
+   Segment <- as.numeric(strsplit(chifile[which(position.Segment == 1)], "\\s=\\s")[[1]][2])
+   ff$Segment <- Segment
+   # SampleInterval (volt)
+   position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(V\\)", chifile)
+   SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
+   ff$SampleInterval <- SampleInterval
+   # Quiet time (seconds)
+   position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
+   QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
+   ff$QuietTime <- QuietTime
+   # Sensitivity (ampere per volt)
+   position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
+   Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
+   ff$Sensitivity <- Sensitivity
    #
    return(ff)
 }