@ -89,7 +89,7 @@ RefCanonicalName <- function(refname) {
" Mg/Mg2+" ,
" Magnesium" )
# if no argument or empty string supplied as arg, return the the entire list as df
# if no argument or empty string supplied as arg, return the entire list as df
# to give the user a nice overview of all available options
if ( missing ( refname ) || refname == " " ) {
max.row.length <- 0
@ -185,60 +185,61 @@ potentials.as.SHE <- function() {
# 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" , " 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" ,
" 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" ,
" SHE" , " " , " " , " " , " -273.15" , " 0.00" , " 8" , " Inzelt2013" ,
" SHE" , " " , " " , " " , " 0" , " 0.00" , " 8" , " Inzelt2013" ,
" SHE" , " " , " " , " " , " 25" , " 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 )
as.data.frame (
matrix ( data =
# electrode # electrolyte # conc/M # conc label # temp # pot vs SHE # set id # ref
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" ,
" 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" ,
" SHE" , " " , " " , " " , " -273.15" , " 0.00" , " 8" , " Inzelt2013" ,
" SHE" , " " , " " , " " , " 0" , " 0.00" , " 8" , " Inzelt2013" ,
" SHE" , " " , " " , " " , " 25" , " 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 )
colnames ( potentials ) <-
c ( " electrode" ,
@ -297,24 +298,23 @@ as.SHE <- function(potential,
# 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
# make this work for arbitrary-length vectors of potential and scale
# make sure potential and scale args have the same length
# potential and scale vectors supplied by user could have arbitrary length
# just make sure potential and scale args have the same length (or length(scale) == 1)
if ( length ( potential ) == 0 | length ( scale ) == 0 ) {
stop ( " Arguments potential or scale cannot be empty!")
stop ( " Potential or scale arguments cannot be empty!")
} else if ( length ( potential ) != length ( scale ) ) {
# stop, unless length(scale) == 1 where we will assume it should be recycled
if ( length ( scale ) == 1 ) {
message ( " Arg ument <scale> has unit length. Recycling it to match length of <potential>. ")
message ( " Arg <scale> has unit length. We'll recycle 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." ) )
stop ( " Length of <potential> and <scale> must be equal OR <scale> may be unit length." )
}
}
arglength <- length ( potential )
# make the args concentration, temperature and electrolyte this same length,
# unless the user supplied them (only necessary for > 1)
# unless the user supplied them (only necessary for length > 1)
if ( arglength > 1 ) {
# handle two cases:
# 1. user did not touch concentration, temperature and electrolyte args.
@ -327,7 +327,7 @@ as.SHE <- function(potential,
identical ( electrolyte , formals ( as.SHE ) $ electrolyte ) ) {
# case 1
# message("NOTE: default concentration and temperature values used for all potentials and scales.")
message ( paste0 ( " D efault concentration (", formals ( as.SHE ) $ concentration , " ) , temperature (", formals ( as.SHE ) $ temperature , " C) used for all supplied potential and scale values.") )
message ( paste0 ( " The d efault concentration (", formals ( as.SHE ) $ concentration , " ) and temperature (", formals ( as.SHE ) $ temperature , " C) will be assumed for all your potential/ scale values.") )
concentration <- rep ( concentration , arglength )
temperature <- rep ( temperature , arglength )
electrolyte <- rep ( electrolyte , arglength )
@ -340,7 +340,7 @@ as.SHE <- function(potential,
## we can now safely assume that length(<args>) == arglength
# place args into a single dataframe
# this way, we can correlate columns to each other by row
df <-
df args <-
data.frame ( potential = potential ,
scale = common :: RefCanonicalName ( scale ) ,
electrolyte = electrolyte ,
@ -348,139 +348,155 @@ as.SHE <- function(potential,
temperature = temperature ,
stringsAsFactors = FALSE )
# add column to keep track of vacuum scale
df $ vacuum <- as.logical ( FALSE
# dfargs$vacuum <- as.logical(FALSE
# add column to hold calc potential vs SHE
df $ SHE <- as.numeric ( NA )
dfargs $ SHE <- as.numeric ( NA )
## From here on, ONLY access the arguments via this dataframe
## That is, use dfargs$electrolyte, NOT electrolyte
# SHE scale special considerations
# 1. concentration is constant
if ( any ( df $ scale == common :: RefCanonicalName ( " SHE" ) ) ) {
df $ concentration [which ( df $ scale == common :: RefCanonicalName ( " SHE" ) ) ] <- " "
df $ electrolyte [which ( df $ scale == common :: RefCanonicalName ( " SHE" ) ) ] <- " "
# 1. concentration is constant for SHE
if ( any ( df args $ scale == common :: RefCanonicalName ( " SHE" ) ) ) {
df args $ concentration [which ( df args $ scale == common :: RefCanonicalName ( " SHE" ) ) ] <- " "
df args $ electrolyte [which ( df args $ scale == common :: RefCanonicalName ( " SHE" ) ) ] <- " "
}
# AVS scale special considerations
# 1. concentration is meaningless
# 2. direction is opposite of electrochemical scales, requiring change of sign
if ( any ( df $ scale == common :: RefCanonicalName ( " AVS" ) ) ) {
# concentration is meaningless for AVS (no electrolyte)
# so for those rows, we'll reset it
df $ concentration [which ( df $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- " "
df $ electrolyte [which ( df $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- " "
df $ vacuum [which ( df $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- TRUE
# 1. concentration is meaningless for AVS
if ( any ( dfargs $ scale == common :: RefCanonicalName ( " AVS" ) ) ) {
# concentration is meaningless for AVS (no electrolyte) so for those rows, we'll reset it
dfargs $ concentration [which ( dfargs $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- " "
dfargs $ electrolyte [which ( dfargs $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- " "
# dfargs$vacuum[which(dfargs$scale == common::RefCanonicalName("AVS"))] <- TRUE
}
# 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 ) {
# now just work our way through df args , line-by-line to determine potential as SHE
# all necessary conditions should be recorded right here in df args
for ( p in 1 : dim ( df args ) [1 ] ) {
# # WE ARE NOW WORKING ROW-BY-ROW THROUGH THE SUPPLIED ARGUMENTS IN dfargs
# Step-wise matching:
# + first, we subset against electrode scale. If dataset only has one row, done. Else,
# + we subset against either conc.string or conc.num. Stop if zero rows in dataset (error), otherwise proceed.
# Our "dataset" is the literature data supplied via the argument as.SHE.data
this.data.scale <- subset ( as.SHE.data , electrode == dfargs $ scale [p ] )
# subset.scale <- subset(as.SHE.data, electrode == dfargs$scale[p]
if ( dim ( this.data .scale) [1 ] > 1 ) {
# continue matching, now against conc.string or conc.num
if ( is.character ( df $ concentration [p ] ) ) {
subset.concentration <-
subset ( subset.scale , conc.string == df $ concentration [p ] )
if ( is.character ( dfargs $ concentration [p ] ) ) {
this.data.concentration <-
# subset.concentration <-
subset ( this.data.scale , conc.string == dfargs $ concentration [p ] )
} else {
subset.concentration <-
subset ( subset.scale , conc.num == df $ concentration [p ] )
this.data.concentration <-
# subset.concentration <-
subset ( this.data.scale , conc.num == dfargs $ 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()." )
if ( dim ( this.data.concentration ) [1 ] == 0 ) {
stop ( paste0 ( " Failed to find any matching entries in dataset for " ,
paste ( dfargs [p , ] , collapse = " " , sep = " " ) ) )
}
# Note: it's ok at this point if the resulting d f contains more than one row as
# Note: it's ok at this point if the resulting d ataset 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
this.SHE.data <- this.data.concentration
# 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
# just housekeeping again
this.SHE.data <- this.data.scale
# subset.SHE.data <- subset.scale
}
# 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 )
## Electrolyte
# == We would like to transparently handle the following scenario:
# || if the user did not specify electrolyte solution (which we can check by using formals())
# || but the dataset (after subsetting against scale and concentration above) still contains
# || more than one electrolyte
# >> Approach: we'll specify a "fallback" electrolyte, KCl (usually that's what the user wants)
# >> and inform/warn about it
# KCl is a good assumption, as we always have KCl
# for the cases where an electrode system has more than one electrolyte
fallback.electrolyte <- " KCl(aq)"
if ( length ( unique ( this.SHE.data $ electrolyte ) ) > 1 ) {
if ( formals ( as.SHE ) $ electrolyte == " " ) {
warning ( paste0 ( " More than one electrolyte " ,
" available for E(" , dfargs $ scale [p ] , " ) in dataset. " ,
" I'll assume you want " , fallback.electrolyte , " ." ) )
this.SHE.data <-
subset ( this.SHE.data , electrolyte == fallback.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 ) {
stop ( " Your choice of electrolyte does not match any data!" )
}
this.SHE.data <-
subset ( this.SHE.data , electrolyte == dfargs $ electrolyte [p ] )
# but stop if the resulting dataframe contains no rows
if ( dim ( this.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 ( any ( subset.SHE.data $ electrolyte != electrolyte ) ) {
warning ( paste0 ( " The requested electrolyte: " ,
ifelse ( any ( 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 ) )
# dataset contains only one unique electrolyte
# again, check if electrolyte in arg matches the one in dataset
# if it does, great, if it does not, print a message and use it anyway
if ( unique ( this.SHE.data $ electrolyte ) == dfargs $ electrolyte [p ] ) {
this.SHE.data <-
subset ( this.SHE.data , electrolyte == dfargs $ electrolyte [p ] )
} else {
subset.SHE.data <-
subset ( subset.SHE.data , electrolyte == electrolyte )
# whatever electrolyte the user supplied does not match what's left in the datasubset
# but at this point the user is probably better served by returning the electrolyte we have
# along with an informative message (that's the only reason for the if-else below)
electrolytes.in.subset <-
unique ( subset ( as.SHE.data , electrode == dfargs $ scale [p ] ) $ electrolyte )
if ( dfargs $ electrolyte [p ] == " " ) {
message (
paste0 ( ' Electrolyte "" (empty string) not in dataset for E(' ,
dfargs $ scale [p ] , ' ). ' ,
' These electrolytes are: ' ,
paste ( electrolytes.in.subset , collapse = ' , or ' ) , ' .' ,
" I'll assume you want " , fallback.electrolyte , " ." )
)
} else {
message ( paste0 ( " Electrolyte " , dfargs $ electrolyte [p ] , " not in dataset for E(" ,
dfargs $ scale [p ] , " ). " ,
" These electrolytes are: " ,
paste ( electrolytes.in.subset , collapse = " , or " ) , " ." ,
" I'll assume you want " , fallback.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 ] ) ) {
if ( ! any ( his .SHE.data$ temp == df args $ temperature [p ] ) ) {
# sought temperature was not available in dataset, check that it falls inside
# 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 ) ) ) {
if ( ( dfargs $ temperature [p ] <= max ( this.SHE.data $ temp ) ) && ( dfargs $ temperature [p ] >= min ( this.SHE.data $ temp ) ) ) {
# within dataset range, do linear interpolation
lm.subset <- stats :: lm ( SHE ~ temp , data = subset.SHE.data )
lm.subset <- stats :: lm ( SHE ~ temp , data = his .SHE.data)
# interpolated temperature, calculated based on linear regression
# (more accurate than simple linear interpolation with approx())
pot.interp <-
lm.subset $ coefficients [2 ] * df $ temperature [p ] + lm.subset $ coefficients [1 ]
lm.subset $ coefficients [2 ] * df args $ temperature [p ] + lm.subset $ coefficients [1 ]
### CALC POTENTIAL vs SHE
df $ SHE [p ] <-
ifelse ( df $ vacuum [p ] ,
pot.interp - df $ potential [p ] ,
pot.interp + df $ potential [p ] )
df args $ SHE [p ] <-
ifelse ( df args$ scale [p ] == " AVS" ,
pot.interp - df args $ potential [p ] ,
pot.interp + df args $ potential [p ] )
}
} else {
# requested temperature does exist in dataset
### CALC POTENTIAL vs SHE
df $ SHE [p ] <-
ifelse ( df $ vacuum [p ] ,
subset ( subse t.SHE.data, temp == df $ temperature [p ] ) $ SHE - df $ potential [p ] ,
subset ( subse t.SHE.data, temp == df $ temperature [p ] ) $ SHE + df $ potential [p ] )
df args $ SHE [p ] <-
ifelse ( df args$ scale [p ] == " AVS" ,
subset ( his .SHE.data, temp == df args $ temperature [p ] ) $ SHE - df args $ potential [p ] ,
subset ( his .SHE.data, temp == df args $ temperature [p ] ) $ SHE + df args $ potential [p ] )
}
}
return ( df $ SHE )
return ( df args $ SHE )
}
@ -509,27 +525,29 @@ from.SHE <- function(potential,
temperature = 25 ,
as.SHE.data = potentials.as.SHE ( ) ) {
# make this work for arbitrary-length vectors of potential and scale
# make sure potential and scale args have the same length
# 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
# potential and scale vectors supplied by user could have arbitrary length
# just make sure potential and scale args have the same length (or length(scale) == 1)
if ( length ( potential ) == 0 | length ( scale ) == 0 ) {
stop ( " Arguments potential or scale cannot be empty!" )
stop ( " Potential or scale arguments cannot be empty!")
} else if ( length ( potential ) != length ( scale ) ) {
# stop, unless length(scale) == 1 where we will assume it should be recycled
if ( length ( scale ) == 1 ) {
message ( " Arg ument <scale> has unit length. Recycling it to match length of <potential>. ")
message ( " Arg <scale> has unit length. We'll recycle 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." ) )
stop ( " Length of <potential> and <scale> must be equal OR <scale> may be unit length." )
}
}
arglength <- length ( potential )
# make the args concentration, temperature and electrolyte this same length,
# unless the user supplied them (only necessary for > 1)
# unless the user supplied them (only necessary for length > 1)
if ( arglength > 1 ) {
# handle two cases:
# 1. user did not touch concentration, temperature or electrolyte 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 or electrolyte, but still failed to
# ensure length equal to arglength. In this case, abort.
@ -538,7 +556,7 @@ from.SHE <- function(potential,
identical ( temperature , formals ( from.SHE ) $ temperature ) &
identical ( electrolyte , formals ( from.SHE ) $ electrolyte ) ) {
# case 1
message ( paste0 ( " D efault concentration (", formals ( from.SHE ) $ concentration , " ) , temperature (", formals ( from.SHE ) $ temperature , " C) used for all supplied potential and scale values.") )
message ( paste0 ( " The d efault concentration (", formals ( from.SHE ) $ concentration , " ) and temperature (", formals ( from.SHE ) $ temperature , " C) will be assumed for all your potential/ scale values.") )
concentration <- rep ( concentration , arglength )
temperature <- rep ( temperature , arglength )
electrolyte <- rep ( electrolyte , arglength )
@ -551,147 +569,154 @@ from.SHE <- function(potential,
## we can now safely assume that length(<args>) == arglength
# place args into a single dataframe
# this way, we can correlate columns to each other by row
df <-
df args <-
data.frame ( potential = potential , # vs SHE
scale = common :: RefCanonicalName ( scale ) , # target scale
electrolyte = electrolyte ,
concentration = concentration ,
temperature = temperature ,
stringsAsFactors = FALSE )
# # add column to keep track of vacuum scale
# df$vacuum <- as.logical(FALSE)
# # add column to hold calc potential vs target scale
# df$targetscale <- as.numeric(NA)
## Special considerations
# SHE scale independent of concentration, per definition
if ( any ( df $ scale == common :: RefCanonicalName ( " SHE" ) ) ) {
df $ concentration [which ( df $ scale == common :: RefCanonicalName ( " SHE" ) ) ] <- " "
df $ electrolyte [which ( df $ scale == common :: RefCanonicalName ( " SHE" ) ) ] <- " "
## From here on, ONLY access the arguments via this dataframe
## That is, use dfargs$electrolyte, NOT electrolyte (and so on)
# SHE scale special considerations
# 1. concentration is constant for SHE
if ( any ( dfargs $ scale == common :: RefCanonicalName ( " SHE" ) ) ) {
dfargs $ concentration [which ( dfargs $ scale == common :: RefCanonicalName ( " SHE" ) ) ] <- " "
dfargs $ electrolyte [which ( dfargs $ scale == common :: RefCanonicalName ( " SHE" ) ) ] <- " "
}
# AVS scale: concentration is meaningless (no electrolyte)
if ( any ( df $ scale == common :: RefCanonicalName ( " AVS" ) ) ) {
df $ concentration [which ( df $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- " "
df $ electrolyte [which ( df $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- " "
# AVS scale special considerations
# 1. concentration is meaningless for AVS
if ( any ( dfargs $ scale == common :: RefCanonicalName ( " AVS" ) ) ) {
# concentration is meaningless for AVS (no electrolyte) so for those rows, we'll reset it
dfargs $ concentration [which ( dfargs $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- " "
dfargs $ electrolyte [which ( dfargs $ scale == common :: RefCanonicalName ( " AVS" ) ) ] <- " "
}
for ( p in 1 : dim ( df ) [1 ] ) {
# First, subset against electrode scale. If as.SHE.data only contains one row
# for this electrode scale we are DONE. If not, proceed to subset against concentration
subset.scale <- subset ( as.SHE.data , electrode == df $ scale [p ] )
if ( dim ( subset.scale ) [1 ] > 1 ) {
# now just work our way through dfargs, line-by-line to determine potential as SHE
# all necessary conditions should be recorded right here in dfargs
for ( p in 1 : dim ( dfargs ) [1 ] ) {
## WE ARE NOW WORKING ROW-BY-ROW THROUGH THE SUPPLIED ARGUMENTS IN dfargs
# Step-wise matching:
# + first, we subset against electrode scale. If dataset only has one row, done. Else,
# + we subset against either conc.string or conc.num. Stop if zero rows in dataset (error), otherwise proceed.
# Our "dataset" is the literature data supplied via the argument as.SHE.data
this.data.scale <- subset ( as.SHE.data , electrode == dfargs $ scale [p ] )
# subset.scale <- subset(as.SHE.data, electrode == dfargs$scale[p])
if ( dim ( this.data.scale ) [1 ] > 1 ) {
# continue matching, now against conc.string or conc.num
if ( is.character ( df $ concentration [p ] ) ) {
subset.concentration <-
subset ( subset.scale , conc.string == df $ concentration [p ] )
if ( is.character ( df args $ concentration [p ] ) ) {
this.data .concentration <-
subset ( this.data .scale, conc.string == df args $ concentration [p ] )
} else {
subset.concentration <-
subset ( subset .scale, conc.num == df $ concentration [p ] )
this.data .concentration <-
subset ( this.data .scale, conc.num == df args $ 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()." )
if ( dim ( this.data.concentration ) [1 ] == 0 ) {
stop ( paste0 ( " Failed to find any matching entries in dataset for " ,
paste ( dfargs [p , ] , collapse = " " , sep = " " ) ) )
}
# Note: it's ok at this point if the resulting d f contains more than one row as
# Note: it's ok at this point if the resulting d ataset 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
this.SHE.data <- this.data .concentration
} else {
# just housekeeping again
subset.SHE.data <- subset .scale
this.SHE.data <- this.data .scale
}
# 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" ,
" We'll use the default electrolyte: " , default.electrolyte ) )
subset.SHE.data <-
subset ( subset.SHE.data , electrolyte == default.electrolyte )
## Electrolyte
# == We would like to transparently handle the following scenario:
# || if the user did not specify electrolyte solution (which we can check by using formals())
# || but the dataset (after subsetting against scale and concentration above) still contains
# || more than one electrolyte
# >> Approach: we'll specify a "fallback" electrolyte, KCl (usually that's what the user wants)
# >> and inform/warn about it
# KCl is a good assumption, as we always have KCl for the cases where
# an electrode system has more than one electrolyte
fallback.electrolyte <- " KCl(aq)"
if ( length ( unique ( this.SHE.data $ electrolyte ) ) > 1 ) {
if ( formals ( as.SHE ) $ electrolyte == " " ) {
warning ( paste0 ( " More than one electrolyte " ,
" available for E(" , dfargs $ scale [p ] , " ) in dataset. " ,
" I'll assume you want " , fallback.electrolyte , " ." ) )
this.SHE.data <-
subset ( this.SHE.data , electrolyte == fallback.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 ) {
stop ( " Your choice of electrolyte does not match any data!" )
}
this.SHE.data <-
subset ( this.SHE.data , electrolyte == dfargs $ electrolyte [p ] )
# but stop if the resulting dataframe contains no rows
if ( dim ( this.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 ( any ( subset.SHE.data $ electrolyte != electrolyte ) ) {
warning ( paste0 ( " The requested electrolyte: " ,
ifelse ( any ( 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 ) )
# dataset contains only one unique electrolyte
# again, check if electrolyte in arg matches the one in dataset
# if it does, great, if it does not, print a message and use it anyway
if ( unique ( this.SHE.data $ electrolyte ) == dfargs $ electrolyte [p ] ) {
this.SHE.data <-
subset ( this.SHE.data , electrolyte == dfargs $ electrolyte [p ] )
} else {
subset.SHE.data <-
subset ( subset.SHE.data , electrolyte == electrolyte )
# whatever electrolyte the user supplied does not match what's left in the datasubset
# but at this point the user is probably better served by returning the electrolyte we have
# along with an informative message (that's the only reason for the if-else below)
electrolytes.in.subset <-
unique ( subset ( as.SHE.data , electrode == dfargs $ scale [p ] ) $ electrolyte )
if ( dfargs $ electrolyte [p ] == " " ) {
message (
paste0 ( ' Electrolyte "" (empty string) not in dataset for E(' ,
dfargs $ scale [p ] , ' ). ' ,
' These electrolytes are: ' ,
paste ( electrolytes.in.subset , collapse = ' , or ' ) , ' .' ,
" I'll assume you want " , fallback.electrolyte , " ." )
)
} else {
message ( paste0 ( " Electrolyte " , dfargs $ electrolyte [p ] , " not in dataset for E(" ,
dfargs $ scale [p ] , " ). " ,
" These electrolytes are: " ,
paste ( electrolytes.in.subset , collapse = " , or " ) , " ." ,
" I'll assume you want " , fallback.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 ] ) ) {
if ( ! any ( his .SHE.data$ temp == df args $ temperature [p ] ) ) {
# sought temperature was not available in dataset, check that it falls inside
# 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 ) ) ) {
if ( ( dfargs $ temperature [p ] <= max ( this.SHE.data $ temp ) ) && ( dfargs $ temperature [p ] >= min ( this.SHE.data $ temp ) ) ) {
# within dataset range, do linear interpolation
lm.subset <- stats :: lm ( SHE ~ temp , data = subset.SHE.data )
lm.subset <- stats :: lm ( SHE ~ temp , data = his .SHE.data)
# interpolated temperature, calculated based on linear regression
# (more accurate than simple linear interpolation with approx())
pot.interp <-
lm.subset $ coefficients [2 ] * df $ temperature [p ] + lm.subset $ coefficients [1 ]
# message("Calc potential using interp temperature")
lm.subset $ coefficients [2 ] * dfargs $ temperature [p ] + lm.subset $ coefficients [1 ]
### CALC POTENTIAL vs requested scale
if ( df $ scale [p ] == common :: RefCanonicalName ( " AVS" ) ) {
# message("Target scale is AVS")
df $ potentialvsscale [p ] <-
pot.interp - df $ potential [p ]
} else {
# message("Target scale is not AVS")
df $ potentialvsscale [p ] <-
df $ potential [p ] - pot.interp
}
dfargs $ potentialvsscale [p ] <-
ifelse ( dfargs $ scale [p ] == " AVS" ,
pot.interp - dfargs $ potential [p ] ,
dfargs $ potential [p ] - pot.interp )
}
} else {
# requested temperature does exist in dataset
### CALC POTENTIAL vs requested scale
# message("Calc potential using exact temperature match")
if ( df $ scale [p ] == common :: RefCanonicalName ( " AVS" ) ) {
# message("Target scale is AVS")
df $ potentialvsscale [p ] <-
subset ( subset.SHE.data , temp == df $ temperature [p ] ) $ SHE - df $ potential [p ]
} else {
# message("Target scale is not AVS")
df $ potentialvsscale [p ] <-
df $ potential [p ] - subset ( subset.SHE.data , temp == df $ temperature [p ] ) $ SHE
}
dfargs $ potentialvsscale [p ] <-
ifelse ( dfargs $ scale [p ] == " AVS" ,
subset ( this.SHE.data , temp == dfargs $ temperature [p ] ) $ SHE - dfargs $ potential [p ] ,
dfargs $ potential [p ] - subset ( this.SHE.data , temp == dfargs $ temperature [p ] ) $ SHE )
}
}
return ( df $ potentialvsscale )
return ( dfargs $ potentialvsscale )
}
