Lots of changes, apparently ... Note previous commit missed files.
Latest change: addition of generic Xtable handler functions
(GenericXtableSetAttributes(), TabularXtableHeader(), and the longtable
version of that one, which is LongtableXtableHeader()).
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Both \Rfun{ConvertRefPotEC()} and \Rfun{ConvertRefPot()} \emph{need} to be rewritten to allow for different concentrations of each reference electrode!
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Both \Rfun{ConvertRefPotEC()} and \Rfun{ConvertRefPot()} \emph{need} to be rewritten to allow for different concentrations of each reference electrode!
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GenericXtableSetAttributes <- function(xtobject,
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nxtnames = NULL,
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nxtdigits = NULL,
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nxtdisplay = NULL,
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nxtalign = NULL,
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caption = "nxtcaption",
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label = "tab:nxtlabel") {
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#' @title Set the attributes for a generic xtable
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#'
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#' @description
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#' Sets attributes for the passed xtable object
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#'
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#' @details
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#' Sets names, digits, display, and align for the passed xtable object
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#'
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#' @param xtobject the xtable(table)
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#' @param nxtnames vector of names (column names)
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#' @param nxtdigits vector of digits (0 if column is non-numeric, numeric of desired number of digits otherwise)
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#' @param nxtdisplay vector of display format [see formatC(format=...)]
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#' @param nxtalign vector of LaTeX align (e.g., "l", "c", "r", "S[table-format=1.1]", ...)
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#' @examples
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#' GenericXtableSetAttributes(xtable(yourtable), nxtdigits = c(0, 2, 2, 4))
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#' @author Taha Ahmed <taha@@chepec.se>
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#' @return xtable
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# remember to put all names inside "{}" if you use siunitx
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if (!is.null(nxtnames)) {names(xtobject) <- nxtnames}
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# the prepended column due to "row.names"
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if (!is.null(nxtdigits)) {digits(xtobject) <- c(0, nxtdigits)}
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if (!is.null(nxtdisplay)) {display(xtobject) <- c("s", nxtdisplay)}
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if (!is.null(nxtalign)) {align(xtobject) <- c("l", nxtalign)}
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caption(xtobject) <- caption
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label(xtobject) <- label
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#
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return (xtobject)
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}
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LongtableXtableHeader <- function(xtobject, caption.text, caption.label) {
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# this function uses the \booktabs package
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# should NOT be used together with booktabs = TRUE
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ltxt.header <-
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paste(paste("\\caption{", caption.text, "}", sep = "", collapse = ""),
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paste("\\label{", caption.label, "}\\\\ ", sep = "", collapse = ""),
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"\\toprule ",
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attr(xtobject, "names")[1],
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paste(" &", attr(xtobject, "names")[2:length(attr(xtobject, "names"))], collapse = ""),
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"\\\\\\midrule ",
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"\\endfirsthead ",
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paste("\\multicolumn{",
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ncol(xtobject),
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"}{c}{{\\tablename\\ \\thetable{} -- continued from previous page}}\\\\ ",
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sep = ""),
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"\\toprule ",
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attr(xtobject, "names")[1],
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paste("&", attr(xtobject, "names")[2:length(attr(xtobject, "names"))], collapse = ""),
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"\\\\\\midrule ",
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"\\endhead ",
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"\\midrule ",
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paste("\\multicolumn{",
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as.character(ncol(xtobject)),
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"}{r}{{Continued on next page}}\\\\ ",
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sep = "", collapse = ""),
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"\\bottomrule \\endfoot ",
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"\\bottomrule \\endlastfoot ",
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collapse = "")
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return(ltxt.header)
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}
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TabularXtableHeader <- function(xtobject, names.custom = NULL) {
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# use names.custom to make more complicated headers, e.g. multiple-row
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# should be used together with booktabs = TRUE
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if (is.null(names.custom)) {
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txt.header <-
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paste(attr(xtobject, "names")[1],
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paste(" &", attr(xtobject, "names")[2:length(attr(xtobject, "names"))], collapse = ""),
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"\\\\\n")
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} else {
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txt.header <- names.custom
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}
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return(txt.header)
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}
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##################################################
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#################### eV2nm #######################
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##################################################
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eV2nm <- function(eV) {
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# Converts energy in eV to wavelength in nm
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#
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# Define some constants needed for the calculations
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Plancks.constant <- 4.135667516E-15 # \electron\volt\per\second
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speed.of.light <- 299792458 # \meter\per\second
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nm <- Plancks.constant * 1E9 * speed.of.light / eV
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return(nm)
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}
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##################################################
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#################### nm2eV #######################
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##################################################
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nm2eV <- function(nm) {
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# Converts wavelength in nm to energy in eV
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#
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# Define some constants needed for the calculations
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Plancks.constant <- 4.135667516E-15 # \electron\volt\per\second
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speed.of.light <- 299792458 # \meter\per\second
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eV <- Plancks.constant * 1E9 * speed.of.light / nm
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return(eV)
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}
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thth2d <- function(thth, wavelength = 1.540562) {
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# This function applies Bragg's law to calculate d-spacings from thth (n = 1)
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# Wavelengths:
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# Ag-Ka1 wavelength=0.5594075
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# Ag-Ka2 wavelength=0.563798
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# Ag-Kb1 wavelength=0.497069
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# Ag-Kb2 wavelength=0.497685
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# Co-Ka1 wavelength=1.788965
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# Co-Ka2 wavelength=1.792850
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# Co-Kb1 wavelength=1.620790
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# Cr-Ka1 wavelength=2.289700
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# Cr-Ka2 wavelength=2.293606
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# Cr-Kb1 wavelength=2.084870
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# Cu-Ka1 wavelength=1.540562
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# Cu-Ka2 wavelength=1.544398
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# Cu-Kb1 wavelength=1.392218
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# Fe-Ka1 wavelength=1.936042
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# Fe-Ka2 wavelength=1.939980
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# Fe-Kb1 wavelength=1.756610
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# Ge-Ka1 wavelength=1.254054
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# Ge-Ka2 wavelength=1.258011
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# Ge-Kb1 wavelength=1.057300
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# Ge-Kb2 wavelength=1.057830
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# Mo-Ka1 wavelength=0.709300
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# Mo-Ka2 wavelength=0.713590
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# Mo-Kb1 wavelength=0.632288
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# Mo-Kb2 wavelength=0.632860
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# Ni-Ka1 wavelength=1.657910
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# Ni-Ka2 wavelength=1.661747
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# Ni-Kb1 wavelength=1.500135
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# Zn-Ka1 wavelength=1.435155
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# Zn-Ka2 wavelength=1.439000
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# Zn-Kb1 wavelength=1.295250
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# Usage:
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# thth : vector with thth values in degrees
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# wavelength : radiation wavelength in Ångström
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return (wavelength / (2 * sin(as.radians(thth))))
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}
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#####################################
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############# trapz #################
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#####################################
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trapz <- function(x, y) {
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## Description:
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## Performs a trapezoidal integration (approximate numerical integration
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## of the area under the curve defined by the x and y coordinate pairs.
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## See Wikipedia for more info on trapezoidal integration.
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## Usage:
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## trapz(x, y)
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## Arguments:
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## x: vector (of length n)
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## y: vector (of length n)
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## Return value:
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## vector of length (n - 1)
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#
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idx <- 2:length(x)
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return (as.double((x[idx] - x[idx - 1]) * (y[idx] + y[idx - 1])) / 2)
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}
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