Add Goldschmidt's classification

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: georefdatar
 Title: Geosciences Reference Datasets
-Version: 0.6.5.9001
+Version: 0.6.5.9002
 Authors@R: 
     person("Gerald", "Schuberth-Hlavač", email= "abuseki@synapticgap.com",
       role = c("aut", "cre"))
@@ -18,7 +18,7 @@ URL: https://github.com/abuseki/georefdatar
 BugReports: https://github.com/abuseki/georefdatar/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends: 
     R (>= 2.10)
 LazyData: true

NEWS.md

@@ -1,14 +1,19 @@
 # georefdatar (development version)
 
+## georefdatar 0.6.5.9002
+
+Added the Goldschmidt's classification of the elements
+(litho-, chalco-, sidero- and atmophile) to the element sets.
+
 ## georefdatar 0.6.5.9001
 
-* Changed the mineral list from using the RRUFF list to using the list in the 
-  supplementary material of Warr (2021).\
-  The Warr (2021) list also includes group names. This makes it more  practical 
-  for use in a general earth science context, where one often wants to or needs 
-  to refer to a group of minerals. E.g. amphibol, biotite, pyroxene, ...\
-  In the RRUFF list these groups are not mentioned because the are not minerals,
-  strictly speaking.
+Changed the mineral list from using the RRUFF list to using the list in the 
+supplementary material of Warr (2021).\
+The Warr (2021) list also includes group names. This makes it more  practical 
+for use in a general earth science context, where one often wants to or needs 
+to refer to a group of minerals. E.g. amphibole, biotite, pyroxene, ...\
+In the RRUFF list these groups are not mentioned because the are not minerals,
+strictly speaking.
 
 # georefdatar 0.6.5
 

R/elementSets.R

@@ -98,3 +98,62 @@
 #' @describeIn PGE Pd-PGE subgroup
 #' @format character vector with `r length(PPGE)` elements.
 "PPGE"
+
+
+
+#' Goldschmidt's classification of the elements
+#'
+#' @description
+#' Sets containing the elements classified after Goldschmidt.
+#'
+#' @details
+#' The geochemical behavior of the elements is controlled by many factors (e.g.
+#' ionic radius, volatility, redox, ...). Therefore, the elements can be
+#' classified in several ways. A common classification scheme is that developed
+#' by _V. M. Goldschmidt_, which is based on the affinity of elements to form
+#' different types of compounds. The Elements are characterized as:
+#'
+#' 1. **lithophile** (rock-loving): elements with a strong affinity for forming
+#' oxides and silicate minerals.
+#' 1. **chalcophile**  (copper-loving): elements with a strong affinity for
+#' forming sulfides.
+#' 1. **siderophile**  (iron-loving): elements with a strong affinity to form
+#' metals or solid solutions in metals.
+#' 1. **atmophile**  (air-loving): elements that exist either uncombined or as
+#' highly volatile compounds.
+#'
+#'
+#' @references
+#' \insertRef{Marshall1999}{georefdatar}
+#' @importFrom Rdpack reprompt
+#'
+#' @examples
+#' # List the atmophile elements
+#' Atmophile
+#'
+#' # Show the electron configuration of the atmophile elements
+#' pte[pte$Symbol %in% Atmophile, c("Symbol", "ElectronConfiguration")]
+#'
+#' @name Goldschmidt
+NULL
+
+#' @rdname Goldschmidt
+#' @order 1
+#' @format `Lithophile`: character vector with `r length(Lithophile)` elements.
+"Lithophile"
+
+#' @rdname Goldschmidt
+#' @order 2
+#' @format `Chalcophile`: character vector with `r length(Chalcophile)` elements.
+"Chalcophile"
+
+#' @rdname Goldschmidt
+#' @order 3
+#' @format `Siderophile`: character vector with `r length(Siderophile)` elements.
+"Siderophile"
+
+#' @rdname Goldschmidt
+#' @order 4
+#' @format `Atmophile`: character vector with `r length(Atmophile)` elements.
+"Atmophile"
+

data-raw/elementSets.R

@@ -1,4 +1,4 @@
-## code to prepare `elemSet` dataset goes here
+# code to prepare `elemSet` dataset goes here
 
 ## REE
 Lanthanides <- c('La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu')
@@ -23,3 +23,24 @@ usethis::use_data(REM, overwrite = TRUE)
 usethis::use_data(PGE, overwrite = TRUE)
 usethis::use_data(IPGE, overwrite = TRUE)
 usethis::use_data(PPGE, overwrite = TRUE)
+
+
+## Goldschmidt
+t <- readxl::read_xlsx('data-raw/GeochemClass__EncyGeoChem__Tab_G4.xlsx')
+# Add Symbol to element name since we want the symbols for the elements and not
+# their names
+t$Symbol <- unlist(lapply(t$Element, function(e) {pte[pte$Name==e,]$Symbol}))
+
+# Build the element sets
+Atmophile <- subset(t, t$Goldschmidt=="Atmophile" |
+                       t$Goldschmidt=="Atmophile/Lithophile")$Symbol
+Chalcophile <- subset(t, t$Goldschmidt=="Chalcophile")$Symbol
+Lithophile <- subset(t, t$Goldschmidt=="Lithophile" |
+                        t$Goldschmidt=="Atmophile/Lithophile")$Symbol
+Siderophile <- subset(t, t$Goldschmidt=="Siderophile")$Symbol
+
+# save the data
+usethis::use_data(Atmophile, overwrite = TRUE)
+usethis::use_data(Chalcophile, overwrite = TRUE)
+usethis::use_data(Lithophile, overwrite = TRUE)
+usethis::use_data(Siderophile, overwrite = TRUE)

inst/WORDLIST

@@ -9,6 +9,7 @@ CPKHexColor
 CaO
 Chondrite
 Chronostratigraphic
+chronostratigraphic
 ElectronAffinity
 ElectronConfiguration
 Electronegativity
@@ -62,3 +63,7 @@ IUPAC
 CNMNC
 CIAAW
 CMD
+Warr
+Goldschmidt
+pyroxene
+amphibole

tests/testthat/test-elementSets.R

@@ -1,4 +1,4 @@
-test_that("elementSets works", {
+test_that("REE and Co works", {
 
   expect_true(all(
     length(Lanthanides) == 15,
@@ -33,3 +33,24 @@ test_that("elementSets works", {
   )
 
 })
+
+
+test_that("Goldscmidt works", {
+  expect_setequal(Atmophile,
+                  c('H', "He", "N", "Ne", "Ar", "Kr", "Xe", "Rn", "C", "O")
+                  )
+  expect_setequal(Chalcophile,
+                  c('S', 'Cu', 'Zn', 'Ga', 'As', 'Se', 'Ag', 'Cd', 'In', 'Sb',
+                    'Te', 'Hg', 'Tl', 'Pb', 'Bi')
+                  )
+  expect_setequal(Lithophile,
+                  c('Li', 'Be', 'B', 'C', 'O', 'F', 'Na', 'Mg', 'Al', 'Si', 'P',
+                    'Cl', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Br', 'Rb',
+                    'Sr', 'Y', 'Zr', 'Nb', 'I', 'Cs', 'Ba', 'La', 'Ce', 'Pr',
+                    'Nd', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb',
+                    'Lu', 'Hf', 'Ta', 'Th', 'U')
+                  )
+  expect_setequal(Siderophile, c('Fe', 'Co', 'Ni', 'Ge', 'Mo', 'Ru', 'Rh', 'Pd',
+                                 'Sn', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au')
+                  )
+})