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Added more data and squashed a few bugs.

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Taha Ahmed 8 years ago
parent b1bed60d40
commit 3f4462aae8
3 changed files with 133 additions and 61 deletions
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2
DESCRIPTION
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@ -1,7 +1,7 @@
Package: common
Type: Package
Title: chepec common
Version: 0.0.0.9003
Version: 0.0.0.9004
Description: Commonly used functions and scripts.
Authors@R: person("Taha", "Ahmed", email = "taha@chepec.se", role = c("aut", "cre"))
License: GPL-3

100
R/unit-converters-electrochemical.R
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@ -57,7 +57,7 @@ RefCanonicalName <- function(refname) {
"AgCl",
"Silver-Silver chloride",
"Silver chloride",
"SSC") # saturated silver-silver chloride is sometimes abbreviated SSC
"SSC") # Sometimes used abbr. for Saturated Silver Chloride
electrode.system[["Hg2Cl2/Hg"]] <-
c("Hg2Cl2/Hg",
"Hg/Hg2Cl2",
@ -76,6 +76,16 @@ RefCanonicalName <- function(refname) {
c("Li",
"Li/Li+",
"Lithium")
electrode.system[["Na"]] <-
c("Na",
"Na+/Na",
"Na/Na+",
"Sodium")
electrode.system[["Mg"]] <-
c("Mg",
"Mg2+/Mg",
"Mg/Mg2+",
"Magnesium")
# defining refname in this manner makes sure to get all possible combinations
# but there might be a number of duplicates, but those we can
@ -83,12 +93,15 @@ RefCanonicalName <- function(refname) {
electrode <-
data.frame(refname =
# here we create lower-case version of electrode.system,
# and version with symbols (-/) subbed with spaces
# a version with symbols (-/) subbed with spaces,
# and a lower-case with symbols subbed with spaces
c(unname(unlist(electrode.system)),
tolower(unname(unlist(electrode.system))),
gsub("[-/]", " ", unname(unlist(electrode.system)))),
gsub("[-/]", " ", unname(unlist(electrode.system))),
gsub("[-/]", " ", tolower(unname(unlist(electrode.system))))),
refcanon =
rep(sub("[0-9]$", "", names(unlist(electrode.system))), 3),
rep(sub("[0-9]$", "", names(unlist(electrode.system))),
4), # this number needs to equal number of elements in c() above!
stringsAsFactors = FALSE)
# detect and remove duplicates
electrode <-
@ -139,7 +152,8 @@ potentials.as.SHE <- function() {
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",
c("AgCl/Ag", "NaCl(aq)", "5.9", "saturated", "25", "0.2630", "9", "CRC 97th ed., 97-05-22",
"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",
@ -183,7 +197,11 @@ potentials.as.SHE <- function() {
"SHE", "", "", "", "-273.15", "0.00", "8", "Inzelt2013",
"SHE", "", "", "", "0", "0.00", "8", "Inzelt2013",
"SHE", "", "", "", "25", "0.00", "8", "Inzelt2013",
"SHE", "", "", "", "580", "0.00", "8", "Inzelt2013"),
# arbitrary max T=580C (temp at which sodalime glass loses rigidity)
"SHE", "", "", "", "580", "0.00", "8", "Inzelt2013",
"Li", "", "1.0", "1.0M at 25C", "25", "-3.0401", "10", "CRC 97th ed., 97-05-22",
"Na", "", "1.0", "1.0M at 25C", "25", "-2.71", "11", "CRC 97th ed., 97-05-22",
"Mg", "", "1.0", "1.0M at 25C", "25", "-2.372", "12", "CRC 97th ed., 97-05-22"),
ncol = 8,
byrow = TRUE), stringsAsFactors = FALSE)
@ -204,7 +222,7 @@ potentials.as.SHE <- function() {
# make room for a dE/dT column
potentials$dEdT <- as.numeric(NA)
# calculate temperature coefficient (dE/dT) for each scale and concentration (ie. set id)
# calculate temperature coefficient (dE/dT) for each scale, concentration, and electrolyte (ie. set id)
for (s in 1:length(unique(potentials$sid))) {
# sid column eas added to data just to make this calculation here easier
subspot <- potentials[which(potentials$sid == unique(potentials$sid)[s]), ]
@ -227,6 +245,7 @@ potentials.as.SHE <- function() {
#'
#' @param potential potential in volt
#' @param scale name of the original scale
#' @param electrolyte optional, specify electrolyte solution, e.g., "KCl(aq)". Must match value in \code{as.SHE.data$electrolyte}.
#' @param concentration of electrolyte in mol/L, or as the string "saturated"
#' @param temperature of system in degrees Celsius
#' @param as.SHE.data dataframe with dataset
@ -235,6 +254,7 @@ potentials.as.SHE <- function() {
#' @export
as.SHE <- function(potential,
scale,
electrolyte = "",
concentration = "saturated",
temperature = 25,
as.SHE.data = potentials.as.SHE()) {
@ -251,25 +271,27 @@ as.SHE <- function(potential,
}
arglength <- length(potential)
# make the concentration and temperature args to this same length,
# make the args concentration, temperature and electrolyte this same length,
# unless the user supplied them (only necessary for > 1)
if (arglength > 1) {
# handle two cases:
# 1. user did not touch concentration or temperature args.
# 1. user did not touch concentration, temperature and electrolyte args.
# Assume they forgot and reset their length and print a message
# 2. user did change concentration or temperature, but still failed to
# 2. user did change concentration or temperature or electrolyte, but still failed to
# ensure length equal to arglength. In this case, abort.
# note: we can get the default value set in the function call using formals()
if (identical(concentration, formals(as.SHE)$concentration) &
identical(temperature, formals(as.SHE)$temperature)) {
identical(temperature, formals(as.SHE)$temperature) &
identical(electrolyte, formals(as.SHE)$electrolyte)) {
# case 1
# message("NOTE: default concentration and temperature values used for all potentials and scales.")
message(paste0("Default concentration (", formals(as.SHE)$concentration, ") and default temperature (", formals(as.SHE)$temperature, "C) used for all supplied potential and scale values."))
message(paste0("Default concentration (", formals(as.SHE)$concentration, "), temperature (", formals(as.SHE)$temperature, "C) used for all supplied potential and scale values."))
concentration <- rep(concentration, arglength)
temperature <- rep(temperature, arglength)
electrolyte <- rep(electrolyte, arglength)
} else {
# case 2
stop("Arguments concentration and temperature must have same number of elements as potential and scale!")
stop("Concentration, temperature and electrolyte arguments must have the same number of elements as potential and scale!")
}
}
@ -279,6 +301,7 @@ as.SHE <- function(potential,
df <-
data.frame(potential = potential,
scale = RefCanonicalName(scale),
electrolyte = electrolyte,
concentration = concentration,
temperature = temperature,
stringsAsFactors = FALSE)
@ -291,6 +314,7 @@ as.SHE <- function(potential,
# 1. concentration is constant
if (any(df$scale == RefCanonicalName("SHE"))) {
df$concentration[which(df$scale == RefCanonicalName("SHE"))] <- ""
df$electrolyte[which(df$scale == RefCanonicalName("SHE"))] <- ""
}
# AVS scale special considerations
@ -300,6 +324,7 @@ as.SHE <- function(potential,
# concentration is meaningless for AVS (no electrolyte)
# so for those rows, we'll reset it
df$concentration[which(df$scale == RefCanonicalName("AVS"))] <- ""
df$electrolyte[which(df$scale == RefCanonicalName("AVS"))] <- ""
df$vacuum[which(df$scale == RefCanonicalName("AVS"))] <- TRUE
}
@ -316,13 +341,58 @@ as.SHE <- function(potential,
electrode == df$scale[p])
}
# use KCl(aq) as default to avoid aborting
# (good assumption at this point, as we always have KCl for the cases
# where an electrode system has more than one electrolyte)
default.electrolyte <- "KCl(aq)"
# If this subset contains more than one unique electrolyte (e.g., NaCl and KCl)
# the user MUST have made a choice (in the "electrolyte" argument) that results
# in a single electrolyte remaining, or else we will warn and abort
if (length(unique(subset.SHE.data$electrolyte)) > 1) {
# data (in subset.SHE.data) contains more than one electrolyte
# if user did not change electrolyte arg value, use default and issue warning
if (identical(electrolyte, formals(as.SHE)$electrolyte)) {
warning(paste0("You did not specify an electrolyte, but more than one ",
"is available for E = ", df$potential[p], " V vs ", df$scale[p], ".\n",
"Using electrolyte", default.electrolyte))
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == default.electrolyte)
} else {
# else the user did change the electrolyte arg, use the user's value
subset.SHE.data <-
subset.SHE.data[which(subset.SHE.data$electrolyte == electrolyte), ]
print(subset.SHE.data)
# stop if the resulting dataframe contains no rows
if (dim(subset.SHE.data)[1] == 0) {
stop("Your choice of electrolyte does not match any data!")
}
}
} else {
# data only contains one electrolyte
# just check that it matches whatever the user supplied, if not,
# issue a warning (but don't abort, typically the user did not set it
# because they don't care and want whatever is in the data)
if (unique(subset.SHE.data$electrolyte) != electrolyte) {
warning(paste0("The requested electrolyte: ",
ifelse(electrolyte == "", "<none specified>", electrolyte),
" was not found for E = ", df$potential[p], " V vs ", df$scale[p], ".\n",
"My data only lists one electrolyte for that scale - return value calculated on that basis."))
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == unique(subset.SHE.data$electrolyte))
} else {
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == electrolyte)
}
}
# temperature
# either happens to match a temperature in the dataset, or we interpolate
# (under the assumption that potential varies linearly with temperature)
if (!any(subset.SHE.data$temp == df$temperature[p])) {
# sought temperature was not available in dataset, check that it falls inside
if ((df$temperature[p] < max(subset.SHE.data$temp)) &&
(df$temperature[p] > min(subset.SHE.data$temp))) {
# note: important to use less/more-than-or-equal in case data only contains one value
if ((df$temperature[p] <= max(subset.SHE.data$temp)) &&
(df$temperature[p] >= min(subset.SHE.data$temp))) {
# within dataset range, do linear interpolation
lm.subset <- stats::lm(SHE ~ temp, data = subset.SHE.data)
# interpolated temperature, calculated based on linear regression

6
man/as.SHE.Rd
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@ -4,14 +4,16 @@
\alias{as.SHE}
\title{Convert from electrochemical or electronic scale to SHE}
\usage{
as.SHE(potential, scale, concentration = "saturated", temperature = 25,
as.SHE.data = potentials.as.SHE())
as.SHE(potential, scale, electrolyte = "", concentration = "saturated",
temperature = 25, as.SHE.data = potentials.as.SHE())
}
\arguments{
\item{potential}{potential in volt}
\item{scale}{name of the original scale}
\item{electrolyte}{optional, specify electrolyte solution, e.g., "KCl(aq)". Must match value in \code{as.SHE.data$electrolyte}.}
\item{concentration}{of electrolyte in mol/L, or as the string "saturated"}
\item{temperature}{of system in degrees Celsius}

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