Description
Geosciences Reference Datasets.
Description
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.
README.md
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