Fixed a bug: electrode scales Li, Mg, or Na did not work

The matching algorithm would fail for any electrode scale that had string in potentials.as.SHE()$conc.string that was not "saturated" (which happened to be the alkali metals). Fixed this issue by making the matching step-wise, and adding a few more checks for zero rows returned.
master
Taha Ahmed 7 years ago
parent 969244320c
commit 3da30f2920

@ -1,7 +1,7 @@
Package: common
Type: Package
Title: chepec common
Version: 0.0.0.9008
Version: 0.0.0.9009
Description: Commonly used functions and scripts.
Authors@R: person("Taha", "Ahmed", email = "taha@chepec.se", role = c("aut", "cre"))
License: GPL-3

@ -75,6 +75,7 @@ RefCanonicalName <- function(refname) {
electrode.system[["Li"]] <-
c("Li",
"Li/Li+",
"Li+/Li",
"Lithium")
electrode.system[["Na"]] <-
c("Na",
@ -331,14 +332,34 @@ as.SHE <- function(potential,
# now just work our way through df, line-by-line to determine potential as SHE
# all necessary conditions should be recorded right here in df
for (p in 1:dim(df)[1]) {
# Fixed a bug 2018-03-04
# Issue: if scale was {Li,Na,Mg} the default electrolyte string "saturated" caused
# zero rows to be returned in the subset.SHE.data match, with error returned to user.
# Fixed by making the matching more step-wise:
# + first, subset against electrode scale. If only one row, done. If more,
# + subset against either conc.string or conc.num. Stop if zero rows (error), otherwise proceed.
subset.scale <- subset(as.SHE.data, electrode == df$scale[p])
if (dim(subset.scale)[1] > 1) {
# continue matching, now against conc.string or conc.num
if (is.character(df$concentration[p])) {
subset.SHE.data <-
subset(subset(as.SHE.data, conc.string == df$concentration[p]),
electrode == df$scale[p])
subset.concentration <-
subset(subset.scale, conc.string == df$concentration[p])
} else {
subset.SHE.data <-
subset(subset(as.SHE.data, conc.num == df$concentration[p]),
electrode == df$scale[p])
subset.concentration <-
subset(subset.scale, conc.num == df$concentration[p])
}
# stop if the resulting dataframe after matching contains no rows
if (dim(subset.concentration)[1] == 0) {
stop("Sorry, it seems we failed to find any matching entries in potentials.as.SHE().")
}
# Note: it's ok at this point if the resulting df contains more than one row as
# more matching will be done below
# If we haven't had reason to stop(), we should be good
# just housekeeping: rename the variable so we don't have to edit code below
subset.SHE.data <- subset.concentration
} else {
# just housekeeping: rename the variable so we don't have to change the code that follows
subset.SHE.data <- subset.scale
}
# use KCl(aq) as default to avoid aborting
@ -354,13 +375,14 @@ as.SHE <- function(potential,
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$scale[p], ".\n",
"Using electrolyte", default.electrolyte))
"Using electrolyte: ", default.electrolyte))
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == default.electrolyte)
} else {
# else the user did change the electrolyte arg, use the user's value
subset.SHE.data <-
subset.SHE.data[which(subset.SHE.data$electrolyte == electrolyte), ]
# print only for debugging - disable before production!
print(subset.SHE.data)
# stop if the resulting dataframe contains no rows
if (dim(subset.SHE.data)[1] == 0) {

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