First CRAN realease candidate

.Rbuildignore

@@ -5,3 +5,4 @@
 ^README\.Rmd$
 ^\.github$
 ^checks$
+^cran-comments\.md$

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: georefdatar
-Title: Geosciences Reference Data Sets in R
-Version: 0.6.2.9000
+Title: Geosciences Reference Datasets in R
+Version: 0.6.4
 Authors@R: 
     person("Gerald", "Schuberth-Hlavač", email= "[email protected]",
       role = c("aut", "cre"))
-Description: The package includes reference data sets commonly used in 
-  geosciences, such as the standard atomic weights of elements, a periodic 
-  table, a mineral list, reservoir reference datasets (continental crust, 
-  mantle, basalts, etc.), decay constants, and isotopic ratios frequently used 
-  in geochronology. Additionally, the package provides functions for basic 
-  queries of atomic weights and mineral lists. All datasets have complete 
-  references, making them citable.
+Description: Reference datasets commonly used in geosciences. Such as the 
+  standard atomic weights of elements, a periodic table, a mineral list and 
+  their abbreviations, reservoir reference datasets (continental crust, mantle, 
+  basalts, etc.), decay constants and isotopic ratios frequently used in 
+  geochronology. Additionally, the package provides functions for basic queries 
+  of atomic weights and the mineral list. All datasets have complete references,
+  making them citable.
 License: MIT + file LICENSE
 URL: https://github.com/abuseki/georefdatar
 BugReports: https://github.com/abuseki/georefdatar/issues

R/IUPAC__Standard_atomic_weights_of_the_elements.R

@@ -2,7 +2,7 @@
 #'
 #' A data set containing the standard atomic weights of the elements as
 #' recommended by the [International Union of Pure and Applied Chemistry
-#' (IUPAC)](https://www.iupac.org) and [Commission on Isotopic Abundances and
+#' (IUPAC)](https://iupac.org) and [Commission on Isotopic Abundances and
 #' Atomic Weights (CIAAW)](https://www.ciaaw.org).
 #'
 #' This is table 1 of \insertCite{Prohaska2022}{georefdatar}. The (foot)notes in
@@ -24,7 +24,7 @@
 #' figures. Unless such precision cannot be attained due to the variability of
 #' isotopic composition in normal materials or due to the limitations of the
 #' measurement capability.}
-#' \item{abrStdAW::±}{A +/− value as a simplified measure of the reliability of
+#' \item{abrStdAW::±}{A plus-minus-value as a simplified measure of the reliability of
 #' the abridged values.}
 #' \item{Note}{The collected footnotes of the table. Notes are resolved to the
 #' sentences associated with them. If there is more than one note, the notes are

R/Minerals.R

@@ -1,10 +1,20 @@
 #' List of Minerals
 #'
-#' IMA approved list of minerals. Retrieved from _RRUFF_ \insertCite{Lafuente_2015;textual}{georefdatar}.
-#'
-#' @format A data frame with `r nrow(mins)` minerals and their names, symbols and chemistry.\cr
+#' [International Mineralogical Association (IMA)](https://mineralogy-ima.org/)
+#' Commission on New Minerals, Nomenclature and Classification (CNMNC)
+#' approved list of minerals, names and abbreviations
+#' \insertCite{Warr_2021}{georefdatar}.\cr
+#' Retrieved from [RRUFF](https://rruff.info/)
+#' \insertCite{Lafuente_2015}{georefdatar}.
+#'
+#' @format A data frame with `r nrow(mins)` minerals and their names, symbols
+#' (abbreviations) and chemistry.\cr
 #' `r paste(names(mins), collapse= ', ')`
 #'
+#' @seealso
+#'   [IMA approved minerals on RRUFF](https://rruff.info/ima/)
+#'
+#'   [IMA–CNMNC approved mineral symbols](https://rruff.info/rruff_1.0/uploads/MM85_291.pdf), \insertCite{Warr_2021}{georefdatar}
 #'
 #' @references{
 #'   \insertRef{Lafuente_2015}{georefdatar}
@@ -37,9 +47,9 @@
 #' minSearch('Pyh$', ignore.case = FALSE)
 #'
 minSearch <- function(pattern, ignore.case= TRUE) {
-  res <- unique(c(
-    grep(pattern, georefdatar::mins$Symbol, ignore.case = ignore.case),
-    grep(pattern, georefdatar::mins$Name, ignore.case = ignore.case)
+  res <- base::unique(c(
+    base::grep(pattern, georefdatar::mins$Symbol, ignore.case = ignore.case),
+    base::grep(pattern, georefdatar::mins$Name, ignore.case = ignore.case)
   ))
 
   georefdatar::mins[res, ]
@@ -65,5 +75,5 @@ minSearch <- function(pattern, ignore.case= TRUE) {
 #' minsForChemistry('Mn.*\\(SiO4\\)$')
 #'
 minsForChemistry <- function(pattern, ignore.case= FALSE) {
-  georefdatar::mins[grep(pattern, georefdatar::mins$Chemistry, ignore.case = ignore.case), ]
+  georefdatar::mins[base::grep(pattern, georefdatar::mins$Chemistry, ignore.case = ignore.case), ]
 }

R/PeriodicTable.R

@@ -7,7 +7,7 @@
 #' `r paste(names(pte), collapse= ', ')`
 #'
 #' @seealso [IUPAC_StdAW] for the standard atomic weights of the elements
-#' recommended by [IUPAC](https://www.iupac.org)
+#' recommended by [IUPAC](https://iupac.org)
 #'
 #' @references{
 #'   \insertRef{pubChemPTable}{georefdatar}

README.Rmd

@@ -4,7 +4,7 @@ output: github_document
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE, message = FALSE)
 ```
-# georefdatar -- Geosciences Reference Data Sets in R
+# georefdatar -- Geosciences Reference Datasets in R
 
 
 <!-- badges: start -->

README.md

@@ -1,5 +1,5 @@
 
-# georefdatar – Geosciences Reference Data Sets in R
+# georefdatar – Geosciences Reference Datasets in R
 
 <!-- badges: start -->
 

cran-comments.md

@@ -0,0 +1,8 @@
+# georefdatar 0.6.4
+
+* This is a new release.
+
+## R CMD check results
+
+0 errors | 0 warnings | 0 note
+

inst/REFERENCES.bib

@@ -80,7 +80,6 @@ @InCollection{Lafuente_2015
   month     = nov,
   pages     = {1--30},
   doi       = {10.1515/9783110417104-003},
-  url       = {https://rruff.info/about/downloads/HMC1-30.pdf},
 }
 
 @Article{Warr_2021,
@@ -92,7 +91,6 @@ @Article{Warr_2021
   pages     = {1--30},
   doi       = {10.1180/mgm.2021.43},
   publisher = {Mineralogical Society},
-  url       = {https://www.cambridge.org/core/journals/mineralogical-magazine/article/imacnmnc-approved-mineral-symbols/62311F45ED37831D78603C6E6B25EE0A},
 }
 
 @InCollection{Rudnick2003,
@@ -117,7 +115,6 @@ @InCollection{Rudnick2014
   isbn      = {978-0-08-098300-4},
   pages     = {1--51},
   doi       = {10.1016/B978-0-08-095975-7.00301-6},
-  url       = {https://www.sciencedirect.com/science/article/pii/B9780080959757003016},
 }
 
 @Article{Steiger1977,
@@ -142,7 +139,6 @@ @Article{Renne2011
   pages   = {5097--5100},
   volume  = {75},
   doi     = {10.1016/j.gca.2011.06.021},
-  url     = {https://www.sciencedirect.com/science/article/pii/S0016703711003498},
 }
 
 @Article{Renne2001,
@@ -180,7 +176,6 @@ @Article{Villa2015
   pages   = {382--385},
   volume  = {164},
   doi     = {10.1016/j.gca.2015.05.025},
-  url     = {https://www.sciencedirect.com/science/article/pii/S0016703715003208},
 }
 
 @Article{Hiess2012,
@@ -206,7 +201,6 @@ @Article{Lee2006
   pages   = {4507--4512},
   volume  = {70},
   doi     = {10.1016/j.gca.2006.06.1563},
-  url     = {https://www.sciencedirect.com/science/article/pii/S0016703706018679},
 }
 
 @Article{Cohen2013,
@@ -262,7 +256,7 @@ @Book{Rollinson1993
   year      = {1993},
 }
 
- 
+
 @TechReport{Prohaska2022,
   author      = {Prohaska, Thomas and Irrgeher, Johanna and Benefield, Jacqueline and Böhlke, John K. and Chesson, Lesley A. and Coplen, Tyler B. and Ding, Tiping and Dunn, Philip J. H. and Gröning, Manfred and Holden, Norman E. and Meijer, Harro A. J. and Moossen, Heiko and Possolo, Antonio and Takahashi, Yoshio and Vogl, Jochen and Walczyk, Thomas and Wang, Jun and Wieser, Michael E. and Yoneda, Shigekazu and Zhu, Xiang-Kun and Meija, Juris},
   institution = {IUPAC},

inst/WORDLIST

@@ -58,3 +58,7 @@ PPGE
 MREE
 eontheme
 eratheme
+IUPAC
+CNMNC
+CIAAW
+CMD

tests/testthat/test-Minerals.R

@@ -0,0 +1,9 @@
+test_that("test mineral search functions work", {
+  expect_equal(minSearch("Prp")$Name, "Pyrope")
+  expect_equal(minSearch("Pyrope")$Symbol, "Prp")
+  expect_equal(minSearch("Pyrope")$Chemistry, minSearch("Prp")$Chemistry)
+
+  expect_equal(minsForChemistry("^Ce\\(PO4\\)$")$Symbol, "Mnz-Ce")
+  expect_equal(minsForChemistry("^Ce\\(PO4\\)$")$Name, "Monazite-(Ce)")
+
+})