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@ -183,10 +183,37 @@ chronocm2df <- function(datafilename) {
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################# chronoamp2df ###################
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##################################################
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chronoamp2df <- function(datafilename, wearea = 1) {
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# Function description: chronoamperometry data
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# CH Instruments potentiostat records all data using standard SI units,
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# so all potential values are in volts, currents are in amperes,
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# charges in Coulombs, time in seconds, etc.
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## Description:
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## Reads current-time data (from CHI 760 potentiostat)
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## and returns a dataframe with the data and the
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## data attributes (experimental conditions).
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## Usage:
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## chronoamp2df(datafilename, wearea)
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## Arguments:
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## datafilename: text string with full path to experimental file
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## wearea: (optional) area of working electrode (in square centimeters)
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## Value:
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## Dataframe with the following columns (and no extra attributes):
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## $ sampleid : chr
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## $ step : num
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## $ time : num
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## $ current : num
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## $ currentdensity : num
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## $ InitE : num
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## $ HighE : num
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## $ LowE : num
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## $ InitPN : num
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## $ Step : num
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## $ Pulse width : num
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## $ Sample interval : num
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## $ Quiet Time : num
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## $ Sensitivity : num
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## Note:
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## The CH Instruments 760 potentiostat records all data
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## using standard SI units, therefore this function
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## assumes all potential values to be in volts,
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## currents to be in amperes, charges in Coulombs,
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## time in seconds, and so on.
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#
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datafile <- file(datafilename, "r")
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chifile <- readLines(datafile, n = -1) #read all lines of input file
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@ -231,34 +258,44 @@ chronoamp2df <- function(datafilename, wearea = 1) {
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currentdensity <- ff$current / wearea
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ff <- cbind(ff, currentdensity = currentdensity)
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#
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### Collect attributes of this experiment
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# These attributes are specific for each kind of experiment,
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# be careful when adapting to other electrochemical data
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rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
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"^High\\sE\\s\\(V\\)",
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"^Low\\sE\\s\\(V\\)",
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"^Init\\sP/N",
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"^Step\\s",
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"^Pulse\\sWidth\\s\\(sec\\)",
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"^Sample\\sInterval\\s\\(s\\)",
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"^Quiet\\sTime\\s\\(sec\\)",
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"^Sensitivity\\s\\(A/V\\)")
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names.attr <- c("InitE",
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"HighE",
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"LowE",
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"InitPN",
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"Steps",
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"PulseWidth",
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"SamplingInterval",
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"QuietTime",
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"Sensitivity")
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for (n in 1:length(rgxp.attr)) {
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attrow.idx <- regexpr(rgxp.attr[n], chifile)
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attrow.len <- attr(attrow.idx, "match.length")
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attr(attrow.idx, "match.length") <- NULL
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attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
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"\\s=\\s")[[1]][2]
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}
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# InitE (volt)
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position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
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InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
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ff$InitE <- InitE
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# HighE (volt)
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position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
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HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
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ff$HighE <- HighE
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# LowE (volt)
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position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
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LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
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ff$LowE <- LowE
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# InitPN
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position.InitPN <- regexpr("^Init\\sP/N", chifile)
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InitPN <- as.numeric(strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2])
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ff$InitPN <- InitPN
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# Step
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position.Step <- regexpr("^Step\\s", chifile)
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Step <- as.numeric(strsplit(chifile[which(position.Step == 1)], "\\s=\\s")[[1]][2])
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ff$Step <- Step
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# Pulse width (s)
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position.PulseWidth <- regexpr("^Pulse\\sWidth\\s\\(sec\\)", chifile)
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PulseWidth <- as.numeric(strsplit(chifile[which(position.PulseWidth == 1)], "\\s=\\s")[[1]][2])
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ff$PulseWidth <- PulseWidth
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# Sample interval (s)
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position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
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SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
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ff$SampleInterval <- SampleInterval
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# Quiet Time (s)
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position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
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QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
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ff$QuietTime <- QuietTime
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# Sensitivity (A/V)
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position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
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Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
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ff$Sensitivity <- Sensitivity
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#
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return(ff)
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}
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