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Tweaked behaviour of scale argument if length==1

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scale arg is recycled if it has unit length and length(potential) > 1. This saves the user some typing and makes the functions as.SHE() and from.SHE() easier to use.
master
Taha Ahmed 7 years ago
parent cae4c711b3
commit da7fa41179
3 changed files with 35 additions and 11 deletions
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2
DESCRIPTION
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@ -1,7 +1,7 @@
Package: common Package: common
Type: Package Type: Package
Title: chepec common Title: chepec common
Version: 0.0.0.9010 Version: 0.0.0.9011
Description: Commonly used functions and scripts. Description: Commonly used functions and scripts.
Authors@R: person("Taha", "Ahmed", email = "taha@chepec.se", role = c("aut", "cre")) Authors@R: person("Taha", "Ahmed", email = "taha@chepec.se", role = c("aut", "cre"))
License: GPL-3 License: GPL-3

36
R/unit-converters-electrochemical.R
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@ -302,7 +302,14 @@ as.SHE <- function(potential,
if (length(potential) == 0 | length(scale) == 0) { if (length(potential) == 0 | length(scale) == 0) {
stop("Arguments potential or scale cannot be empty!") stop("Arguments potential or scale cannot be empty!")
} else if (length(potential) != length(scale)) { } else if (length(potential) != length(scale)) {
stop("Arguments potential and scale must have equal number of elements") # stop, unless length(scale) == 1 where we will assume it should be recycled
if (length(scale) == 1) {
message("Argument <scale> has unit length. Recycling it to match length of <potential>. ")
scale <- rep(scale, length(potential))
} else {
stop(paste0("Correspondence between the supplied potentials and scales could not be worked out.\n",
"Please make sure the number of elements in each match, or make <scale> unit length."))
}
} }
arglength <- length(potential) arglength <- length(potential)
@ -428,9 +435,11 @@ as.SHE <- function(potential,
# just check that it matches whatever the user supplied, if not, # 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 # 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) # because they don't care and want whatever is in the data)
if (unique(subset.SHE.data$electrolyte) != electrolyte) { if (any(subset.SHE.data$electrolyte != electrolyte)) {
warning(paste0("The requested electrolyte: ", warning(paste0("The requested electrolyte: ",
ifelse(electrolyte == "", "<none specified>", electrolyte), ifelse(any(electrolyte == ""),
"<none specified>",
electrolyte),
" was not found for E = ", df$potential[p], " V vs ", df$scale[p], ".\n", " 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.")) "My data only lists one electrolyte for that scale - return value calculated on that basis."))
subset.SHE.data <- subset.SHE.data <-
@ -505,7 +514,14 @@ from.SHE <- function(potential,
if (length(potential) == 0 | length(scale) == 0) { if (length(potential) == 0 | length(scale) == 0) {
stop("Arguments potential or scale cannot be empty!") stop("Arguments potential or scale cannot be empty!")
} else if (length(potential) != length(scale)) { } else if (length(potential) != length(scale)) {
stop("Arguments potential and scale must have the same number of elements") # stop, unless length(scale) == 1 where we will assume it should be recycled
if (length(scale) == 1) {
message("Argument <scale> has unit length. Recycling it to match length of <potential>. ")
scale <- rep(scale, length(potential))
} else {
stop(paste0("Correspondence between the supplied potentials and scales could not be worked out.\n",
"Please make sure the number of elements in each match, or make <scale> unit length."))
}
} }
arglength <- length(potential) arglength <- length(potential)
@ -513,7 +529,7 @@ from.SHE <- function(potential,
# unless the user supplied them (only necessary for > 1) # unless the user supplied them (only necessary for > 1)
if (arglength > 1) { if (arglength > 1) {
# handle two cases: # handle two cases:
# 1. user did not touch concentration, temperature and electrolyte args. # 1. user did not touch concentration, temperature or electrolyte args.
# Assume they forgot and reset their length and print a message # Assume they forgot and reset their length and print a message
# 2. user did change concentration or temperature or electrolyte, 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. # ensure length equal to arglength. In this case, abort.
@ -618,9 +634,11 @@ from.SHE <- function(potential,
# just check that it matches whatever the user supplied, if not, # 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 # 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) # because they don't care and want whatever is in the data)
if (unique(subset.SHE.data$electrolyte) != electrolyte) { if (any(subset.SHE.data$electrolyte != electrolyte)) {
warning(paste0("The requested electrolyte: ", warning(paste0("The requested electrolyte: ",
ifelse(electrolyte == "", "<none specified>", electrolyte), ifelse(any(electrolyte == ""),
"<none specified>",
electrolyte),
" was not found for E = ", df$potential[p], " V vs ", df$scale[p], ".\n", " 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.")) "My data only lists one electrolyte for that scale - return value calculated on that basis."))
subset.SHE.data <- subset.SHE.data <-
@ -645,7 +663,7 @@ from.SHE <- function(potential,
# (more accurate than simple linear interpolation with approx()) # (more accurate than simple linear interpolation with approx())
pot.interp <- pot.interp <-
lm.subset$coefficients[2] * df$temperature[p] + lm.subset$coefficients[1] lm.subset$coefficients[2] * df$temperature[p] + lm.subset$coefficients[1]
message("Calc potential using interp temperature") # message("Calc potential using interp temperature")
### CALC POTENTIAL vs requested scale ### CALC POTENTIAL vs requested scale
if (df$scale[p] == common::RefCanonicalName("AVS")) { if (df$scale[p] == common::RefCanonicalName("AVS")) {
# message("Target scale is AVS") # message("Target scale is AVS")
@ -660,7 +678,7 @@ from.SHE <- function(potential,
} else { } else {
# requested temperature does exist in dataset # requested temperature does exist in dataset
### CALC POTENTIAL vs requested scale ### CALC POTENTIAL vs requested scale
message("Calc potential using exact temperature match") # message("Calc potential using exact temperature match")
if (df$scale[p] == common::RefCanonicalName("AVS")) { if (df$scale[p] == common::RefCanonicalName("AVS")) {
# message("Target scale is AVS") # message("Target scale is AVS")
df$potentialvsscale[p] <- df$potentialvsscale[p] <-

8
README
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@ -1,4 +1,10 @@
A collection of general functions and data ## A collection of general functions and data
Includes common numerical functions, unit converters, Includes common numerical functions, unit converters,
some LaTeX-specific functions, as well as reference data. some LaTeX-specific functions, as well as reference data.
## Known bugs
`as.SHE()` and `from.SHE()` will fail to return any results if a vector of potentials is supplied along with a vector containing more than one reference scale (e.g., `as.SHE(potentials = c(0.24, 0.46, -0.15), scale = c("AgCl", "SCE", "AVS"))`).
This bug was first confirmed for vesion `0.0.0.9011`.

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