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Description

Geosciences Reference Datasets.

Reference datasets commonly used in the geosciences. These include standard atomic weights of the elements, a periodic table, a list of minerals including their abbreviations and chemistry, geochemical data of reservoirs (primitive mantle, continental crust, mantle, basalts, etc.), decay constants and isotopic ratios frequently used in geochronology, color codes of the chronostratigraphic chart. In addition, the package provides functions for basic queries of atomic weights, the list of minerals, and chronostratigraphic chart colors. All datasets are fully referenced, and a BibTeX file containing the references is included.

georefdatar – Geosciences Reference Datasets in R

R-CMD-check

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
    
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Version

0.6.5

License

Unknown

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