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#' AVS -> SHE
#'
#' Converts from absolute vacuum scale (AVS) to SHE scale
#'
#' @param avs Potential in AVS scale
#'
#' @return potential in SHE scale (numeric)
#' @export
AVS2SHE <- function(avs) {
.Deprecated("as.SHE")
she <- -(4.5 + avs)
return(she)
}
#' SHE -> AVS
#'
#' Converts from SHE scale to absolute vacuum (AVS) scale
#'
#' @param she Potential in SHE scale
#'
#' @return potential in AVS scale (numeric)
#' @export
SHE2AVS <- function(she) {
.Deprecated("as.SHE")
avs <- -(4.5 + she)
return(avs)
}
#' Get standardised name of reference electrode
#'
#' Given a reference electrode label, this function returns its canonical name
#' (as defined by this package).
#' This function tries to match against as many variations as possible for each
#' reference electrode.
#'
#' @param refname string
#'
#' @return the canonical name or empty string
#' @export
RefCanonicalName <- function(refname) {
# scale names
electrode.system <- list()
electrode.system[["SHE"]] <-
c("SHE",
"Standard hydrogen",
"Standard hydrogen electrode")
electrode.system[["AgCl/Ag"]] <-
c("AgCl/Ag",
"Ag/AgCl",
"AgCl",
"Silver-Silver chloride",
"Silver chloride",
"SSC") # saturated silver-silver chloride is sometimes abbreviated SSC
electrode.system[["Hg2Cl2/Hg"]] <-
c("Hg2Cl2/Hg",
"Hg/Hg2Cl2",
"Hg2Cl2",
"Calomel-Mercury",
"Mercury-Calomel",
"SCE")
electrode.system[["AVS"]] <-
c("AVS",
"Vacuum",
"Vacuum scale",
"Absolute",
"Absolute scale",
"Absolute vacuum scale")
electrode.system[["Li"]] <-
c("Li",
"Li/Li+",
"Lithium")
# to match the lowercase version, use tolower()
# perhaps also replace hyphens and slashes with space?
matches <-
data.frame(electrode = names(electrode.system),
m = rep(0, length(electrode.system)),
stringsAsFactors = FALSE)
# loop over electrode systems
for (i in 1:length(electrode.system)) {
# check for a match in any cell of this row,
# also trying all lower-case and substituting symbols with spaces
if (any(electrode.system[[i]] == refname) ||
any(tolower(electrode.system[[i]]) == refname) ||
any(gsub("[-/]", " ", electrode.system[[i]]) == refname)) {
matches$m[i] <- 1
}
}
# if everything went as expected we should have just one match
if (sum(matches$m) != 1) {
# something wrong (should probably add warn/error here)
# for now, just return empty string
return("")
} else {
return(matches$electrode[which(matches$m == 1)])
}
}
#' Potentials as SHE
#'
#' This function just outputs a tidy dataframe with potential vs SHE for
#' different scales, electrolytes, concentrations, and temperatures.
#' Using data from literature.
#'
#' @return tidy dataframe with the following columns
#' \tabular{ll}{
#' \code{electrode} \tab reference electrode \cr
#' \code{electrolyte} \tab electrolyte \cr
#' \code{conc.num} \tab concentration of electrolyte, mol/L \cr
#' \code{conc.string} \tab concentration of electrolyte, as string, may also note temperature at which conc \cr
#' \code{temp} \tab temperature / degrees Celsius \cr
#' \code{SHE} \tab potential vs SHE / volt \cr
#' \code{sid} \tab set id, just for housekeeping inside this function \cr
#' \code{reference} \tab BibTeX reference \cr
#' \code{dEdT} \tab temperature coefficient / volt/kelvin \cr
#' }
#' @export
potentials.as.SHE <- function() {
# scale name should be one of canonical (see RefCanonicalName)
# follow the convention of "each row one observation" (at different temperatures)
# all potentials vs SHE
potentials <-
as.data.frame(matrix(data =
# electrode # electrolyte # conc/M # conc label # temp # pot vs SHE # set id # ref
c("AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "10", "0.215", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "15", "0.212", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "20", "0.208", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "25", "0.205", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "30", "0.201", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "35", "0.197", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "40", "0.193", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "10", "0.214", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "15", "0.209", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "20", "0.204", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "25", "0.199", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "30", "0.194", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "35", "0.189", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "40", "0.184", "2", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "10", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "15", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "20", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "25", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "30", "0.335", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "35", "0.334", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "40", "0.334", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "10", "0.287", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "20", "0.284", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "25", "0.283", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "30", "0.282", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "40", "0.278", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "10", "0.256", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "15", "0.254", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "20", "0.252", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "25", "0.250", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "30", "0.248", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "35", "0.246", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "40", "0.244", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "10", "0.254", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "15", "0.251", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "20", "0.248", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "25", "0.244", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "30", "0.241", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "35", "0.238", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "40", "0.234", "6", "Sawyer1995",
"AVS", "", "", "", "25", "-4.44", "7", "Trasatti1986"),
ncol = 8,
byrow = TRUE), stringsAsFactors = FALSE)
colnames(potentials) <-
c("electrode",
"electrolyte",
"conc.num",
"conc.string",
"temp",
"SHE",
"sid",
"reference")
# convert these columns to type numeric
potentials[, c("conc.num", "temp", "SHE")] <-
as.numeric(as.character(unlist(potentials[, c("conc.num", "temp", "SHE")])))
# make room for a dE/dT column
potentials$dEdT <- as.numeric(NA)
# calculate temperature coefficient (dE/dT) for each scale and concentration (ie. set id)
for (s in 1:length(unique(potentials$sid))) {
# sid column eas added to data just to make this calculation here easier
subspot <- potentials[which(potentials$sid == unique(potentials$sid)[s]), ]
# a linear fit will give us temperature coefficient as slope
lm.subspot <- stats::lm(SHE ~ temp, data = subspot)
potentials[which(potentials$sid == unique(potentials$sid)[s]), "dEdT"] <-
lm.subspot$coefficients[2]
}
return(potentials)
}
#' Convert from electrochemical or electronic scale to SHE
#'
#' @param potential in the original scale, V or eV
#' @param scale name of the original scale
#' @param concentration of electrolyte in mol/L, or as the string "saturated"
#' @param temperature of system in degrees Celsius
#' @param as.SHE.data dataframe with dataset
#'
#' @return potential in SHE scale
#' @export
as.SHE <- function(potential,
scale,
concentration = "saturated",
temperature = 25,
as.SHE.data = potentials.as.SHE()) {
# if the supplied temperature does not exist in the data, this function will attempt to interpolate
# note that concentration has to match, no interpolation is attempted for conc
if (RefCanonicalName(scale) == "") {
warning("as.SHE(): Sorry, you have supplied an unrecognised electrode scale.")
return(NA)
}
# there is the simple case of
if (RefCanonicalName(scale) == "SHE") {
warning("This function can only convert from scales other than SHE!")
return(NA)
}
# AVS needs special consideration
if (RefCanonicalName(scale) == "AVS") {
# reset arg concentration
concentration <- ""
# second, since AVS scale goes in the opposite direction to the electrochemical scales
# we will define our own function
negifavs <- function(a, b) {
a - b
}
} else {
# we will define the same function differently for
# the case we're not dealing with AVS
negifavs <- function(a, b) {
a + b
}
}
if (is.character(concentration)) {
# supplied concentration is character string
subspot <-
subset(subset(as.SHE.data,
electrode == RefCanonicalName(scale)),
conc.string == concentration)
# if either "scale" or "concentration" are not found in the data, subspot will contain zero rows
if (dim(subspot)[1] == 0) {
warning("as.SHE(): Supplied scale or concentration does not exist in data. Returning NA.")
return(NA)
}
# so far, we have
# scale: checked!
# concentration: checked!
# only temperature remains to be handled
# temperature value could happen to match a value in the data, or lie somewhere in between
# note: we will not allow extrapolation
if (!any(subspot$temp == temperature)) {
# if sought temperature is not available in dataset, check that it falls inside
if ((temperature < max(subspot$temp)) && (temperature > min(subspot$temp))) {
# within dataset range, do linear interpolation
lm.subspot <- stats::lm(SHE ~ temp, data = subspot)
# interpolated temperature, calculated based on linear regression
# (more accurate than simple linear interpolation with approx())
potinterp <-
lm.subspot$coefficients[2] * temperature + lm.subspot$coefficients[1]
### CALC RETURN POTENTIAL
return(negifavs(potinterp, potential))
} else {
# outside dataset range, warning and return NA (we don't extrapolate)
warning("as.SHE(): the temperature you requested falls outside data range.")
return(NA)
}
} else {
# requested temperature does exist in dataset
### CALC RETURN POTENTIAL
return(negifavs(subset(subspot, temp == temperature)$SHE, potential))
}
# outer-most if-else
} else {
# supplied concentration is numeric
# note: all code inside this else is the same as inside the if,
# just for the case of numeric concentration
subspot <-
subset(subset(as.SHE.data,
electrode == RefCanonicalName(scale)),
conc.num == concentration)
# if either "scale" or "concentration" are not found in the data, subspot will contain zero rows
if (dim(subspot)[1] == 0) {
warning("as.SHE(): Supplied scale or concentration does not exist in data. Returning NA.")
return(NA)
}
if (!any(subspot$temp == temperature)) {
# if sought temperature is not available in dataset, check that it falls inside
if ((temperature < max(subspot$temp)) && (temperature > min(subspot$temp))) {
# within dataset range, do linear interpolation
lm.subspot <- stats::lm(SHE ~ temp, data = subspot)
# interpolated temperature, calculated based on linear regression
# (more accurate than simple linear interpolation with approx())
potinterp <-
lm.subspot$coefficients[2] * temperature + lm.subspot$coefficients[1]
### CALC RETURN POTENTIAL
return(negifavs(potinterp, potential))
} else {
# outside dataset range, warning and return NA (we don't extrapolate)
warning("as.SHE(): the temperature you requested falls outside data range.")
return(NA)
}
} else {
# requested temperature does exist in dataset
### CALC RETURN POTENTIAL
return(negifavs(subset(subspot, temp == temperature)$SHE, potential))
}
}
}
#' ConvertRefPotEC
#'
#' This function does the heavy lifting.
#' Converts from an electrochemical reference scale into another.
#' SHE: standard hydrogen electrode
#' Ag/AgCl: silver silver-chloride electrode (3M KCl)
#' SCE: saturated calomel electrode
#'
#' @param argpotential potential (numeric)
#' @param argrefscale input reference scale (character string)
#' @param valuerefscale output reference scale (character string)
#'
#' @return potential in output reference scale (numeric)
ConvertRefPotEC <- function(argpotential, argrefscale, valuerefscale) {
.Deprecated("as.SHE")
##### Add more reference electrodes here >>
refpotatSHEzero <- c( 0, -0.21, -0.24, 3)
refrownames <- c( "SHE", "Ag/AgCl", "SCE", "Li/Li+")
refcolnames <- c("SHE0", "AgCl0", "SCE0", "Li0")
##### Add more reference electrodes here <<
#
SHE0 <-
data.frame(matrix(refpotatSHEzero,
ncol = length(refpotatSHEzero),
byrow = T))
refpotmtx <- matrix(NA, length(SHE0), length(SHE0))
refpotmtx[,1] <- matrix(as.matrix(SHE0), ncol = 1, byrow = T)
for (c in 2:length(SHE0)) {
# loop over columns (except the first)
for (r in 1:length(SHE0)) {
# loop over rows
refpotmtx[r, c] <- refpotmtx[r, 1] - refpotmtx[c, 1]
}
}
refpotdf <- as.data.frame(refpotmtx)
names(refpotdf) <- refcolnames
row.names(refpotdf) <- refrownames
## So far we have made a matrix of all the possible combinations,
## given the vector refpotatSHEzero. The matrix is not strictly necessary,
## but it may prove useful later. It does.
#
# Match argrefscale to the refrownames
argmatch <- match(argrefscale, refrownames, nomatch = 0)
# Match valuerefscale to the refrownames
valuematch <- match(valuerefscale, refrownames, nomatch = 0)
# We simply assume that the match was well-behaved
valuepotential <- argpotential + refpotdf[valuematch, argmatch]
# Check that arg and value electrodes are within bounds for a match
if (argmatch == 0 || valuematch == 0) {
# No match
# Perform suitable action
message("Arg out of bounds in call to ConvertRefPot")
valuepotential <- NA
}
return(valuepotential)
}
#' Convert from one electrochemical scale to another
#'
#' @param argpotential potential (numeric)
#' @param argrefscale input reference scale (char string)
#' @param valuerefscale output reference scale (char string)
#'
#' @return potential in output reference scale (numeric)
#' @export
ConvertRefPot <- function(argpotential, argrefscale, valuerefscale) {
.Deprecated("as.SHE")
# You should check that argpotential is valid numeric
# IDEA: make a matrix out of these (scale names and flags)
# Valid scales
scale.names <- list()
scale.names[["SHE"]] <- c("SHE", "NHE", "she", "nhe")
scale.names[["AgCl"]] <- c("Ag/AgCl", "AgCl", "ag/agcl", "agcl")
scale.names[["SCE"]] <- c("SCE", "sce")
scale.names[["Li"]] <- c("Li/Li+", "Li", "Li+", "li", "li+", "li/li+")
scale.names[["AVS"]] <- c("AVS", "avs")
# Set flags
bool.flags <-
as.data.frame(matrix(0,
nrow = length(scale.names),
ncol = 2))
names(bool.flags) <- c("argref", "valueref")
row.names(bool.flags) <- names(scale.names)
# argrefscale
# Check that argrefscale is valid character mode
# ...
# steps through all scale names, "row-by-row",
# looking for any cell matching "argrefscale" string
# if found, save the position of that refelectrode (in scale.names) to
# that row and "argref" column of bool.flags
for (j in 1:length(row.names(bool.flags))) {
if (any(scale.names[[row.names(bool.flags)[j]]] == argrefscale)) {
bool.flags[row.names(bool.flags)[j], "argref"] <- j
}
}
# valuerefscale
# Check that valuerefscale is valid character mode
# ...
for (k in 1:length(row.names(bool.flags))) {
if (any(scale.names[[row.names(bool.flags)[k]]] == valuerefscale)) {
bool.flags[row.names(bool.flags)[k], "valueref"] <- k
}
}
# Depending on which flags are set, call the corresponding function
decision.vector <- colSums(bool.flags)
# Check if both scales are the same (no conversion needed). If so, abort gracefully.
# ...
if (decision.vector["argref"] == 5 || decision.vector["valueref"] == 5) {
# AVS is requested, deal with it it
if (decision.vector["argref"] == 5) {
# Conversion _from_ AVS
rnpotential <- ConvertRefPotEC(AVS2SHE(argpotential),
"SHE",
scale.names[[decision.vector["valueref"]]][1])
}
if (decision.vector["valueref"] == 5) {
# Conversion _to_ AVS
rnpotential <- SHE2AVS(ConvertRefPotEC(argpotential,
scale.names[[decision.vector["argref"]]][1],
"SHE"))
}
} else {
rnpotential <- ConvertRefPotEC(argpotential,
scale.names[[decision.vector["argref"]]][1],
scale.names[[decision.vector["valueref"]]][1])
}
return(rnpotential)
}