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R

# common.R
# General-purpose functions
# Taha Ahmed, Jan 2011
# CONTENTS
# >>>> int2padstr
# >>>> It2charge
# >>>> ProvideSampleId
# >>>> ConvertRefPot
# >>>> Celsius2Kelvin
# >>>> Kelvin2Celsius
# >>>> as.radians
# >>>> as.degrees
# >>>> molarity2mass
##################################################
################## int2padstr ####################
##################################################
int2padstr <- function (ii, pchr, w) {
## Description:
## Converts an integer or a vector of integers to
## a string padded with characters.
## Usage:
## int2padstr(ii, pchr, w)
## Arguments:
## ii: integer or vector of integers
## pchr: a padding character (e.g., "0")
## w: width of the return string (an integer)
## Make sure to set the width longer than
## or equal to the length of the biggest integer.
## For example, if the integers (ii) are
## in the range 1 - 100, set w to at least 3.
## Value:
## A character string or a vector of character strings
gsub(" ", pchr, formatC(ii, format="s", mode="character", width = w))
}
##################################################
################### It2charge ####################
##################################################
It2charge <- function (time, current) {
## Description:
## Calculates cumulative charge, differentials, etc. from
## amperometric data (current and time).
## __Intended to be used from within other functions (CHI.R)__
## Usage:
## It2charge(time, current)
## Arguments:
## time: a vector with time data.
## current: a vector of the same length as time, with current data.
## May be either currents or current densities, no matter.
## Value:
## Returns a dataframe with columns:
## timediff, dIdt, charge, sumcharge
#
# Calculate the time vector difference
timediff <- c(time[1], diff(time))
# timediff times the current gives the charge,
# since the time vector can be considered as
# the cumulative time, while we need to multiply
# the current with the time elapsed since the last
# current measurement (the timediff).
charge <- current * timediff
dIdt <- current / time
# Return value
ff <- data.frame(timediff = timediff,
dIdt = dIdt, charge = charge,
sumcharge = cumsum(charge))
return(ff)
}
##################################################
################ ProvideSampleId #################
##################################################
ProvideSampleId <- function (fullpathwithfilename) {
### OBS! Only very rudimentary error-checking.
### If the filename is formatted as \w*-\w*-\w*, we use the middle segment,
### otherwise we use the whole string (excluding the extension)
# Extract the name of the parent directory of the datafilename argument
substrateid <- basename(dirname(fullpathwithfilename))
# Extract the name of the method from the filename-part
# First split the filename over all hyphens
nameparts <- strsplit(basename(fullpathwithfilename), "-")[[1]]
# If the number of nameparts exceed 3, save the whole filename as methodid, otherwise use the middle part
if (length(nameparts) > 3) {
# We need to lose the file extension from the last namepart
nameparts[length(nameparts)] <- strsplit(nameparts[length(nameparts)], "\\.")[[1]][1]
methodid <- paste(nameparts, collapse = "-")
} else {
methodid <- nameparts[2]
}
# Make an informative sampleid
sampleid <- paste(substrateid, methodid, sep = "-")
#
return(sampleid)
}
##################################################
################# ConvertRefPot ##################
##################################################
ConvertRefPot <- function(argpotential, argrefscale, valuerefscale) {
# Converts from some reference potential scale into another
# SHE: standard hydrogen electrode scale
# Ag/AgCl: silver silver-chloride electrode scale
# SCE: standard calomel scale
#
##### 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)
}
##################################################
############### Celsius2Kelvin ###################
##################################################
Celsius2Kelvin <- function(Celsius) {
# Converts temperature from Celsius to Kelvin
#
# Check and correct for values below -273.15
if (Celsius < -273.15) {
# If Celsis is less than absolute zero, set it to absolute zero
Celsius <- -273.15
}
Kelvin <- Celsius + 273.15
return(Kelvin)
}
##################################################
############### Kelvin2Celsius ###################
##################################################
Kelvin2Celsius <- function(Kelvin) {
# Converts temperature from Kelvin to Celsius
#
# Check and correct for negative values
if (Kelvin < 0) {
# If Kelvin is less than zero, set it to zero
Kelvin <- 0
}
Celsius <- Kelvin - 273.15
return(Celsius)
}
##################################################
################# as.radians #####################
##################################################
as.radians <- function(degrees) {
# Converts from degrees to radians
radians <- degrees * (pi / 180)
return(radians)
}
##################################################
################# as.degrees #####################
##################################################
as.degrees <- function(radians) {
# Converts from radians to degrees
degrees <- radians * (180 / pi)
return(degrees)
}
##################################################
############### molarity2mass ####################
##################################################
molarity2mass <- function(formulamass, volume, molarity) {
# Calculates the required mass of
# the substance to be dissolved.
# ARGS: formulamass - formula mass of the substance (in gram per mole)
# volume - volume of the final solution (in liters)
# molarity - molarity (in moles per liter)
# VALUE: mass of substance (in grams)
#
mass <- formulamass * volume * molarity
# Unit check:
# [g * mol-1] * [liter] * [mole * liter-1] = [g]
return(mass)
}