README.md

In pvermees/GeoplotR: Toolbox for Geological Plots

GeoplotR

GeoplotR is an R package to classify geochemical data.

Web interface

GeoplotR can be run online, offline, and from the command line. The easiest way to get started with the program is via its web interface:

http://isoplotr.es.ucl.ac.uk/geoplotr/

Installation for offline use

You must have R installed on your system (see http://r-project.org). Additionally, to install GeoplotR from Github, you also need the remotes package. This can be installed by typing the following code at the R command line prompt:

install.packages('remotes')

after which GeoplotR can be installed as follows:

remotes::install_github('pvermees/GeoplotR')
remotes::install_github('pvermees/GeoplotRgui')

Note that the command line functionality and graphical user interface (GUI) are stored in two separate R packages. To start the GUI on your own computer:

GeoplotRgui::GeoplotRgui()

Command line

Advanced users can get access to all the functions in the GUI, and more, from the R console. To view the contents of the API:

help(package="GeoplotR")

Here are some command line examples:

1. Quadratic discriminant analysis of Ti-Zr-Y data:

library(GeoplotR) data(test,package='GeoplotR') TiZrY(Ti=wtpct2ppm(test[,'TiO2'],oxide='TiO2'), Zr=test[,'Zr'],Y=test[,'Y'],type='QDA',ternary=TRUE)

1. Total-Alkali-Silica diagram:

out <- TAS(Na2O=test[,'Na2O'],K2O=test[,'K2O'],SiO2=test[,'SiO2'])

Where out lists the classification of each sample in test.

1. Plot basalt compositions from Iceland and the Cascade Mountains on an A-F-M diagram, and mark the two-stage calc-alkaline/tholeiitic decision boundary of Vermeesch and Pease (Geochemical Perspective Letters, 2021) on it:

data(cath,package='GeoplotR') A <- cath[,'Na2O']+cath[,'K2O'] F <- cath[,'FeOT'] M <- cath[,'MgO'] AFM(A,F,M,ternary=TRUE,decision=TRUE, twostage=TRUE,pch=21,bg=cath[,'affinity']) legend('topleft',legend=c('Cascades','Iceland'), pch=21,pt.bg=c(1,2))

1. Plot the Iceland data in logratio space and visualise their Bowen-Fenner indices as a kernel density estimate:

data(cath,package='GeoplotR') TH <- (cath[,'affinity']=='th') A <- cath[TH,'Na2O']+cath[TH,'K2O'] F <- cath[TH,'FeOT'] M <- cath[TH,'MgO'] AFM(A,F,M,ternary=FALSE,decision=TRUE,twostage=TRUE)

Author

Pieter Vermeesch

License

This project is licensed under the GPL-3 License

pvermees/GeoplotR documentation built on Aug. 20, 2024, 4:45 a.m.