R/cbk.ref.R

In misasa/chelyabinsk: Express geochemical datasets

#' @title Return element abundances of reference
#'
#' @description Return element abundances of reference.  The reference
#'   includes "Wasson.1988", "McDonough.1995", "Boynton.1989",
#'   "Palme.2014", and "Anders.1989".
#'
#' [1] Wasson, J. T., and Kallemeyn, G. W. (1988). Compositions of chondrites. Phil. Trans. Roy. Soc. London A, 325, 535-544.
#' [2] McDonough, W., and Sun, S. (1995). The composition of the earth. Chemical Geology, 120(3-4), 223-253.
#' [3] Janousek, V. et al. (2015). Geochemical Modelling of Igneous Processes--Principles And Recipes in R Language. Springer
#' [4] Palme, H., Lodders, K. and Jones, A. (2014) Solar System Abundances of the Elements, In Treatise on Geochemistry (Second Edition), edited by Heinrich D. Holland and Karl K. Turekian, Elsevier, Oxford, Pages 15-36.
#' [5] Anders, E., and Grevesse, N.. (1989). Abundances of the elements: Meteoritic and solar. Geochimica et Cosmochimica Acta, 53, 197-214.
#'
#' @param analysis A name of reference that is one of "Wasson.1988",
#'   "McDonough.1995", "Boynton.1989", "Palme.2014", and "Anders.1989".
#' @param property A numeric vector of element property with label
#'   that serves as sort key (default: NULL).  You can feed output from
#'   `cbk.periodic'.
#' @param tableunit Output unit that will be resolved by
#'   `cbk.convector'. (default: "none")
#' @return A pmlame of element abundances
#' @seealso \code{\link{cbk.periodic}}
#' @export
#' @examples
#' cbk.ref("Boynton.1989","ppm")
#' cbk.ref("Wasson.1988","ppm",cbk.periodic('atomicnumber'))
#' cbk.ref("Wasson.1988","ppm",cbk.periodic('volatility'))
#' cbk.ref("McDonough.1995","ppm",cbk.periodic('volatility'))
cbk.ref <- function(analysis,tableunit="none",property=NULL){
  ## foo        <- c(.31,.808,.122,.6,.195,.0735,.2590,.0474,.322,.0718,.21,0.0324,.209,.0322)
  ## names(foo) <- c("La","Ce","Pr","Nd","Sm","Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu")

  ## read as vector
  ## pmlame     <- read.table(cbk.path("ref.csv"),sep=",",header=T,row.names=1)
  ## pmlame     <- cbk.read.dflame(cbk.path("ref1-dflame0.csv"),tableunit)
  pmlame        <- cbk.read.dflame(cbk.path("ref1-dflame0.csv"),tableunit,verbose=FALSE)
  ## foo        <- as.numeric(pmlame)
  ## foo        <- as.numeric(pmlame[analysis,]) # conversion to numeric vector
  ## names(foo) <- names(pmlame)
  foo           <- pmlame[analysis,]

  ## filter
  ## bar        <- foo[is.finite(foo) & !is.nan(foo) & !is.na(foo)]
  blank         <- apply(foo, 2, function(x) all(is.na(x)))
  bar           <- foo[,!blank]

  ## sort when sort-key is provided
  if(!is.null(property)){
    ## bar         <- bar[names(property)]
    names.share <- intersect(names(property),names(bar))
    bar         <- bar[,names.share,drop=FALSE]
    ## bar         <- bar[,names(property),drop=FALSE]
  }

  return(bar)
}