georefdatar – Geosciences Reference Datasets in R

The goal of georefdatar is to provide regularly used reference data sets for geoscience for use with R.

Up to now these are:

• periodic table of the elements
• standard atomic weights of the elements, as recommended by IUPAC
• table of minerals – with name, symbol (abbreviation) and chemistry
• well known and widely used geochemical data of reservoirs like the primitive mantle, the continental crust, basalts, …
• tables of decay constants and isotopic rations frequently used in geochronology
• color codes of the International Chronostratigraphic Chart
• Sets of elements regularly used in geochemistry, e. g. REE, HREE, PGE, …
• some functions for basic queries of the periodic table of the elements and the list of minerals are also included.

All datasets are fully referenced, and a BibTeX file containing the references is included.

Installation

You can install the development version of georefdatar from GitHub with:

# install.packages("devtools")
devtools::install_github("abuseki/georefdatar")

Example

• To get the classic primitive mantle data of Sun and McDounough (1989) one can use:

  library(georefdatar)
  
  PM__Sun_McDounough__1989[,c('Cs','Rb','Ba','Th','U','Nb','K','La','Ce','Pb','Pr','Sr','P','Nd','Zr','Sm','Eu','Ti','Dy','Y','Yb','Lu')]

  ##       Cs    Rb    Ba    Th     U    Nb   K    La    Ce    Pb    Pr   Sr  P
  ## 1 0.0079 0.635 6.989 0.085 0.021 0.713 250 0.687 1.775 0.071 0.276 21.1 95
  ##      Nd   Zr    Sm    Eu   Ti    Dy    Y    Yb    Lu
  ## 1 1.354 11.2 0.444 0.168 1300 0.737 4.55 0.493 0.074

  or using dplyr:

  library(georefdatar)
  library(dplyr)
  
  PM__Sun_McDounough__1989 %>% select(Cs, Rb, Ba, Th, U, Nb, K, La, Ce, Pb, Pr, Sr, P, Nd, Zr, Sm, Eu, Ti, Dy, Y, Yb, Lu)

  ## # A tibble: 1 × 22
  ##       Cs    Rb    Ba    Th     U    Nb     K    La    Ce    Pb    Pr    Sr     P
  ##    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
  ## 1 0.0079 0.635  6.99 0.085 0.021 0.713   250 0.687  1.78 0.071 0.276  21.1    95
  ## # ℹ 9 more variables: Nd <dbl>, Zr <dbl>, Sm <dbl>, Eu <dbl>, Ti <dbl>,
  ## #   Dy <dbl>, Y <dbl>, Yb <dbl>, Lu <dbl>

• Query the list of minerals:

  • by names or symbols given as a regular expression:

    library(georefdatar)
    
    minSearch('Pyrr.*')

    ## # A tibble: 1 × 3
    ##   Symbol Name       Chemistry
    ##   <chr>  <chr>      <chr>    
    ## 1 Pyh    Pyrrhotite Fe7S8

    minSearch('^Ms$')

    ## # A tibble: 1 × 3
    ##   Symbol Name      Chemistry          
    ##   <chr>  <chr>     <chr>              
    ## 1 Ms     Muscovite KAl2(Si3Al)O10(OH)2

  • by chemistry as a regular expression:

    library(georefdatar)
    
    minsForChemistry('\\(SiO4\\)3$')

    ## # A tibble: 18 × 3
    ##    Symbol Name            Chemistry            
    ##    <chr>  <chr>           <chr>                
    ##  1 Alm    Almandine       Fe2+3Al2(SiO4)3      
    ##  2 Adr    Andradite       Ca3Fe3+2(SiO4)3      
    ##  3 Cdr    Calderite       Mn2+3Fe3+2(SiO4)3    
    ##  4 Erg    Eringaite       Ca3Sc2(SiO4)3        
    ##  5 Eul    Eulytine        Bi4(SiO4)3           
    ##  6 Glm    Goldmanite      Ca3V3+2(SiO4)3       
    ##  7 Grs    Grossular       Ca3Al2(SiO4)3        
    ##  8 Krr    Knorringite     Mg3Cr2(SiO4)3        
    ##  9 Maj    Majorite        Mg3(MgSi)(SiO4)3     
    ## 10 Mzr-Y  Menzerite-(Y)   (CaY2)Mg2(SiO4)3     
    ## 11 Mom    Momoiite        Mn2+3V3+2(SiO4)3     
    ## 12 Mmt    Morimotoite     Ca3(TiFe2+)(SiO4)3   
    ## 13 Prp    Pyrope          Mg3Al2(SiO4)3        
    ## 14 Sps    Spessartine     Mn2+3Al2(SiO4)3      
    ## 15 Tks    Trikalsilite    K2NaAl3(SiO4)3       
    ## 16 Tme    Trimerite       CaBe3Mn2+2(SiO4)3    
    ## 17 Uv     Uvarovite       Ca3Cr2(SiO4)3        
    ## 18 Wbh    Wayneburnhamite Pb9Ca6(Si2O7)3(SiO4)3

• Query atomic mass from the periodic table of the elements:

  aw('H')

  ## [1] 1.008

  aw('H')*2 + aw('O')

  ## [1] 18.015

  # Si wt% in muscovite
  round(3*aw('Si') / (aw('K')+3*aw('Al')+3*aw('Si')+12*aw('O')+2*aw('H')) * 100, 2)

  ## [1] 21.15