-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
40 additions
and
83 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,93 +1,55 @@ | ||
| --- | ||
| output: github_document | ||
| --- | ||
| ```{r setup, include=FALSE} | ||
| knitr::opts_chunk$set(echo = TRUE, message = FALSE) | ||
|
|
||
| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
|
|
||
| ```{r, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| collapse = TRUE, | ||
| comment = "#>", | ||
| fig.path = "man/figures/README-", | ||
| out.width = "100%" | ||
| ) | ||
| ``` | ||
| # georefdatar -- Geosciences Reference Datasets in R | ||
|
|
||
| # georefdatar | ||
|
|
||
| <!-- badges: start --> | ||
| [](https://github.com/abuseki/georefdatar/actions/workflows/R-CMD-check.yaml) | ||
| [](https://CRAN.R-project.org/package=georefdatar) | ||
| [](https://choosealicense.com/licenses/mit/) | ||
| [](https://github.com/abuseki/georefdatar/actions/workflows/test-coverage.yaml) | ||
| <!-- badges: end --> | ||
|
|
||
| The goal of georefdatar is to provide regularly used reference data sets for | ||
| geoscience for use with _R_. | ||
| The goal of georefdatar is to ... | ||
|
|
||
| Up to now these are: | ||
| ## Installation | ||
|
|
||
| * periodic table of the elements | ||
| * standard atomic weights of the elements, as recommended by [IUPAC](https://iupac.org) | ||
| * 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](https://stratigraphy.org/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. | ||
| You can install the development version of georefdatar from [GitHub](https://github.com/) with: | ||
|
|
||
| All datasets are fully referenced, and a BibTeX file containing the references is included. | ||
| ``` r | ||
| # install.packages("devtools") | ||
| devtools::install_github("abuseki/georefdatar") | ||
| ``` | ||
|
|
||
| ## Installation | ||
| ## Example | ||
|
|
||
| You can install the version from [CRAN](https://cran.r-project.org/) with: | ||
| This is a basic example which shows you how to solve a common problem: | ||
|
|
||
| ``` r | ||
| install.packages("georefdatar") | ||
| ```{r example} | ||
| library(georefdatar) | ||
| ## basic example code | ||
| ``` | ||
|
|
||
| Or you can install the development version from [GitHub](https://github.com/) with: | ||
| What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so: | ||
|
|
||
| ``` r | ||
| # install.packages("devtools") | ||
| devtools::install_github("abuseki/georefdatar") | ||
| ```{r cars} | ||
| summary(cars) | ||
| ``` | ||
|
|
||
| ## Example | ||
| You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. | ||
|
|
||
| You can also embed plots, for example: | ||
|
|
||
| ```{r pressure, echo = FALSE} | ||
| plot(pressure) | ||
| ``` | ||
|
|
||
| * To get the classic primitive mantle data of Sun and McDounough (1989) one can use: | ||
|
|
||
| ```{r} | ||
| 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')] | ||
| ``` | ||
|
|
||
| or using `dplyr`: | ||
| ```{r} | ||
| 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) | ||
| ``` | ||
|
|
||
| * Query the list of minerals: | ||
| * by names or symbols given as a regular expression: | ||
| ```{r} | ||
| library(georefdatar) | ||
| minSearch('Pyrr.*') | ||
| minSearch('^Ms$') | ||
| ``` | ||
|
|
||
| * by chemistry as a regular expression: | ||
| ```{r} | ||
| library(georefdatar) | ||
| minsForChemistry('\\(SiO4\\)3$') | ||
| ``` | ||
|
|
||
| * Query atomic mass from the periodic table of the elements: | ||
| ```{r} | ||
| aw('H') | ||
| aw('H')*2 + aw('O') | ||
| # Si wt% in muscovite | ||
| round(3*aw('Si') / (aw('K')+3*aw('Al')+3*aw('Si')+12*aw('O')+2*aw('H')) * 100, 2) | ||
| ``` | ||
|
|
||
| In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters