README.md

In pvermees/simplex: Data Reduction Software for Secondary Ion Mass Spectrometry

simplex

simplex is an R package for SIMS data processing that takes into account the compositional nature of isotopic data. This means that only the relative abundances of the isotopes carry the useful information.

simplex can be used online, offline and from the command line. The easiest way to use the program is by visiting http://isoplotr.es.ucl.ac.uk/simplex/. If you would like to install your own online mirror of simplex, the please follow the instructions provided HERE. The remainder of this README page provides instructions for offline use, either using the browser-based Graphical User Interface, or the R command line.

Prerequisites

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

install.packages('remotes')

Installation

To install the current development version of simplex from Github, type:

remotes::install_github('tim-band/shinylight')
remotes::install_github('pvermees/isoplotr')
remotes::install_github('pvermees/simplex')

Graphical User Interface (GUI)

The easiest way to run simplex is to start its GUI in a browser tab, using the following R command:

simplex::simplex()

Command Line Interface (CLI)

Load the simplex package into memory:

library(simplex)

The process function groups all the main data reduction steps, including the drift correction, logratio calculation, and calibration:

dat <- read_data(f='SHRIMP.pd',m=method('GA-UPb'))
lr <- logratios(dat)
stand <- standard('Temora-t')
paired <- pairing(lr,stand=stand)
cal <- calibration(lr,stand=stand,pairing=paired,prefix="TEM")
result <- calibrate(cal,exterr=TRUE)
plot(result)

Extracting the results for 91500 zircon, saving the results as a .csv file and plotting in IsoplotR:

samp <- subset(result,prefix='915')
tab <- data2table(samp)
write.csv(tab,file='~/Desktop/91500.csv',row.names=FALSE)

Stable isotope analysis of oxygen data:

dat <- read_data(f='*.asc',m=method('IGG-O'))
lr <- logratios(dat)
stand <- standard('NBS28')
cal <- calibration(lr,stand=stand,prefix="NBS28")
Cameca_oxygen <- calibrate(cal,exterr=TRUE)
tab <- data2table(Cameca_oxygen)

Built-in help can be obtained at the command prompt:

?logratios

To view a full list of functions:

help(package='simplex')

Author

Pieter Vermeesch

License

This project is licensed under the GPL-3 License

pvermees/simplex documentation built on Sept. 2, 2023, 12:40 p.m.