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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)
}
#' 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)
}
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