Bumped version number. Cleaned up Rd files.

Added info and links to README.

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: common
 Type: Package
 Title: chepec common
-Version: 0.0.0.9012
+Version: 0.0.1.9000
 Description: Commonly used functions and scripts.
 Authors@R: person("Taha", "Ahmed", email = "taha@chepec.se", role = c("aut", "cre"))
 License: GPL-3
+Encoding: UTF-8
 LazyData: TRUE
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 Imports:
    stats,
    knitr,

NAMESPACE

@@ -1,31 +1,22 @@
 # Generated by roxygen2: do not edit by hand
 
-export(AVS2SHE)
 export(Celsius2Kelvin)
-export(ConvertRefPot)
 export(ExtractSampleIdString)
 export(GenericXtableSetAttributes)
 export(Kelvin2Celsius)
 export(LoadRData2Variable)
 export(LongtableXtableHeader)
-export(OxygenSolubilityWater)
 export(ProvideSampleId)
-export(RefCanonicalName)
-export(SHE2AVS)
 export(SubfigureGenerator)
 export(SubstrateHistory)
 export(TabularXtableHeader)
-export(VapourPressureWater)
-export(as.SHE)
 export(as.degrees)
 export(as.radians)
-export(from.SHE)
 export(int2padstr)
 export(is.wholenumber)
 export(molarity2mass)
 export(numbers2words)
 export(pascal2torr)
-export(potentials.as.SHE)
 export(roundup)
 export(simpleCap)
 export(siunitx.uncertainty)

README.md

@@ -2,6 +2,10 @@
 
 Includes common numerical functions and some LaTeX-specific functions.
 
+Note that the package is named `common`, despite the repository having a different name.
+
+[This repository is mirrored on my Gitea](https://git.chepec.se/taha/common).
+
 
 
 ## NOTE: the electrochemical reference electrode functions

man/AVS2SHE.Rd

@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/unit-converters-electrochemical.R
-\name{AVS2SHE}
-\alias{AVS2SHE}
-\title{AVS -> SHE}
-\usage{
-AVS2SHE(avs)
-}
-\arguments{
-\item{avs}{Potential in AVS scale}
-}
-\value{
-potential in SHE scale (numeric)
-}
-\description{
-Converts from absolute vacuum scale (AVS) to SHE scale
-}

man/ConvertRefPot.Rd

@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/unit-converters-electrochemical.R
-\name{ConvertRefPot}
-\alias{ConvertRefPot}
-\title{Convert from one electrochemical scale to another}
-\usage{
-ConvertRefPot(argpotential, argrefscale, valuerefscale)
-}
-\arguments{
-\item{argpotential}{potential (numeric)}
-
-\item{argrefscale}{input reference scale (char string)}
-
-\item{valuerefscale}{output reference scale (char string)}
-}
-\value{
-potential in output reference scale (numeric)
-}
-\description{
-Convert from one electrochemical scale to another
-}

man/ConvertRefPotEC.Rd

@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/unit-converters-electrochemical.R
-\name{ConvertRefPotEC}
-\alias{ConvertRefPotEC}
-\title{ConvertRefPotEC}
-\usage{
-ConvertRefPotEC(argpotential, argrefscale, valuerefscale)
-}
-\arguments{
-\item{argpotential}{potential (numeric)}
-
-\item{argrefscale}{input reference scale (character string)}
-
-\item{valuerefscale}{output reference scale (character string)}
-}
-\value{
-potential in output reference scale (numeric)
-}
-\description{
-This function does the heavy lifting.
-Converts from an electrochemical reference scale into another.
-SHE:     standard hydrogen electrode
-Ag/AgCl: silver silver-chloride electrode (3M KCl)
-SCE:     saturated calomel electrode
-}

man/OxygenSolubilityWater.Rd

@@ -1,65 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/chemistry-tools.R
-\name{OxygenSolubilityWater}
-\alias{OxygenSolubilityWater}
-\title{Oxygen solubility in water}
-\usage{
-OxygenSolubilityWater(temperature)
-}
-\arguments{
-\item{temperature}{numeric, vector. In degrees Celsius.}
-}
-\value{
-a dataframe with the following columns:
-    + "temperature" same as the supplied temperature
-    + "g/cm-3" oxygen solubility expressed as gram per cubic cm
-    + "mg/L" ditto expressed as milligram per litre
-    + "mol/L" ditto expressed as moles per litre (molarity)
-    + "permoleculewater" number of O2 molecules per molecule of water
-   Note: mg/L is equivalent to ppm by weight (since water has approx
-   unit density in the temperature range 0-50 Celsius).
-}
-\description{
-Oxygen solubility in water  which is in contact with
-air saturated with water vapour, as a function of
-temperature and at a total pressure of 760 torr.
-}
-\details{
-Some background: as the temperature of a gasesous solution is raised the
-gas is driven off until complete degassing occurs at the boiling point
-of the solvent. This variation of solubility with temperature can be
-derived from thermodynamic first principles.
-But the variation of oxygen solubility in water cannot be represented by a
-simple relationship (derived from thermodynamic first principles), and so
-more complicated expressions which are fitted to empirical data have
-to be used.
-
-Hitchman, Measurement of Dissolved Oxygen, 1978 reproduce a table by
-Battino and Clever (1966) that presents experimental values of the
-so-called Bunsen absorption coefficient (this is the volume of gas, at 0 C
-and 760 torr, that, at the temperature of measurement, is dissolved in one
-volume of the solvent when the partial pressure of the gas is 760 torr)
-recorded by eleven research groups up until 1965. The standard error of the
- mean value is never greater +-0.5%. The mean values from this table are
-probably accurate enough for most applications.
-Hitchman notes that the data in this table can be fitted by two forms of
-equations: one form obtained from Henry's law (under the restriction that
-the partial pressure of the gas remains constant), and another form by
-describing the variation with temperature by fitting a general power series.
-The latter approach is used in this function.
-
-Hitchman chooses to fit a fourth degree polynomial, and found that the
-square of the correlation coefficient was 0.999996.
-
-For more background and detailed derivation of the formula used here,
-see section 2.2 (pp. 11) in Hitchman.
-
-This formula is strictly speaking only valid for 0 < T < 50 celsius.
-The function will return values outside this range, but with a warning.
-}
-\examples{
-\dontrun{
-OxygenSolubilityWater(22)
-OxygenSolubilityWater(c(2, 7, 12, 30))
-}
-}

man/RefCanonicalName.Rd

@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/unit-converters-electrochemical.R
-\name{RefCanonicalName}
-\alias{RefCanonicalName}
-\title{Get standardised name of reference electrode}
-\usage{
-RefCanonicalName(refname)
-}
-\arguments{
-\item{refname}{string or a vector of strings}
-}
-\value{
-vector with corresponding "canonical" name or empty string (if none found)
-}
-\description{
-Given a reference electrode label, this function returns its canonical name
-(as defined by this package).
-This function tries to match against as many variations as possible for each
-reference electrode.
-The entire point of this function is to decrease the mental load on the user
-by not requiring them to remember a particular label or name for each reference
-electrode, instead almost any sufficiently distinct label or string will still
-be correctly identified.
-}

man/SHE2AVS.Rd

@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/unit-converters-electrochemical.R
-\name{SHE2AVS}
-\alias{SHE2AVS}
-\title{SHE -> AVS}
-\usage{
-SHE2AVS(she)
-}
-\arguments{
-\item{she}{Potential in SHE scale}
-}
-\value{
-potential in AVS scale (numeric)
-}
-\description{
-Converts from SHE scale to absolute vacuum (AVS) scale
-}

man/VapourPressureWater.Rd

@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/chemistry-tools.R
-\name{VapourPressureWater}
-\alias{VapourPressureWater}
-\title{Vapour pressure of water}
-\usage{
-VapourPressureWater(temperature)
-}
-\arguments{
-\item{temperature}{numeric vector, in degrees Celsius}
-}
-\value{
-vapour pressure of water, in kilopascal
-}
-\description{
-Vapour pressure of water as a function of temperature
-This function returns the vapour pressure of water at the given
-temperature(s) from the common::vapourwater dataset.
-}
-\examples{
-\dontrun{
-VapourPressureWater(45)
-VapourPressureWater(c(20, 25, 45, 60))
-}
-}

man/as.SHE.Rd

@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/unit-converters-electrochemical.R
-\name{as.SHE}
-\alias{as.SHE}
-\title{Convert from electrochemical or physical scale to SHE}
-\usage{
-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}
-
-\item{as.SHE.data}{dataframe with dataset}
-}
-\value{
-potential in SHE scale
-}
-\description{
-Convert an arbitrary number of potentials against any known electrochemical
-scale (or the electronic vacuum scale) to potential vs SHE.
-}

man/from.SHE.Rd

@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/unit-converters-electrochemical.R
-\name{from.SHE}
-\alias{from.SHE}
-\title{Convert from SHE scale to another electrochemical or physical scale}
-\usage{
-from.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 target scale}
-
-\item{electrolyte}{optional, specify electrolyte solution, e.g., "KCl(aq)". Must match one of the values in \code{\link{potentials.as.SHE}$electrolyte}}
-
-\item{concentration}{of electrolyte in mol/L, or as the string "saturated"}
-
-\item{temperature}{of system in degrees Celsius}
-
-\item{as.SHE.data}{by default this parameter reads the full dataset \code{\link{potentials.as.SHE}}}
-}
-\value{
-potential in the specified target scale
-}
-\description{
-Convert an arbitrary number of potentials vs SHE to another electrochemical
-scale (or the vacuum scale).
-The available target scales are those listed by \code{\link{potentials.as.SHE}}.
-}

man/numbers2words.Rd

@@ -4,8 +4,8 @@
 \alias{numbers2words}
 \title{numbers2words}
 \usage{
-numbers2words(x, billion = c("US", "UK"), and = if (billion == "US") "" else
+numbers2words(x, billion = c("US", "UK"), and = if (billion == "US") ""
-  "and")
+  else "and")
 }
 \arguments{
 \item{x}{number}

man/potentials.as.SHE.Rd

@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/unit-converters-electrochemical.R
-\name{potentials.as.SHE}
-\alias{potentials.as.SHE}
-\title{Potentials as SHE}
-\usage{
-potentials.as.SHE()
-}
-\value{
-tidy dataframe with the following columns
-   \tabular{ll}{
-   \code{electrode}     \tab reference electrode \cr
-   \code{electrolyte}   \tab electrolyte \cr
-   \code{conc.num}      \tab concentration of electrolyte, mol/L \cr
-   \code{conc.string}   \tab concentration of electrolyte, as string, may also note temperature at which conc \cr
-   \code{temp}          \tab temperature / degrees Celsius \cr
-   \code{SHE}           \tab potential vs SHE / volt \cr
-   \code{sid}           \tab set id, just for housekeeping inside this function \cr
-   \code{reference}     \tab BibTeX reference \cr
-   \code{dEdT}          \tab temperature coefficient / volt/kelvin \cr
-   }
-}
-\description{
-This function just outputs a tidy dataframe with potential vs SHE for
-different scales, electrolytes, concentrations, and temperatures.
-Using data from literature.
-}

man/vapourwater.Rd

@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{vapourwater}
-\alias{vapourwater}
-\title{Vapour pressure and other saturation properties of water}
-\format{A data frame with 189 rows and 4 variables:
-\describe{
-  \item{temperature}{temperature/celsius}
-  \item{pressure}{pressure/kilopascal}
-  \item{enthalpy}{enthalpy of vapourisation/kilojoule per kilogram}
-  \item{surfacetension}{surface tension/millinewton per metre}
-}}
-\source{
-Handbook of Chemistry and Physics, 94th ed., 6-10-90, Eric W. Lemmon.
-}
-\description{
-A dataset summarising vapour pressure, enthalpy of vapourisation,
-    and surface tension of water from 0.01 Celsius to 373.95 Celsius.
-    Data as accepted by the International Association for the Properties
-    of Water and Steam for general scientific use.
-    Source: CRC handbook, 94th ed., table 6-10-90, Eric W. Lemmon.
-}
-\author{
-Taha Ahmed
-}