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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
version <- as.character(packageVersion("isoprocessor"))
```
# isoprocessor <a href='http://isoprocessor.isoverse.org'><img src='man/figures/isoprocessor_logo_thumb.png' align="right" height="138.5"/></a>
[](https://cran.r-project.org/package=isoprocessor)
[](https://github.com/isoverse/isoprocessor/commits)
[](http://isoprocessor.isoverse.org/)
[](https://github.com/isoverse/isoprocessor/actions?workflow=R-CMD-check)
[](https://mybinder.org/v2/gh/isoverse/isoprocessor/binder?urlpath=rstudio)
[](https://mybinder.org/v2/gh/isoverse/isoprocessor/binder?urlpath=lab)
## About
This package provides broad functionality for IRMS data processing and reduction pipelines.
Existing functionality includes signal conversion (voltage to current and back), time scaling (continuous flow chromatograms), isotope ratio calculations, delta value calculations, as well as easy-to-use highly flexible data calibration and visualization pipelines for continuous flow data. Additional tools on O17 corrections, H3 factor calculation, peak detection, baseline correction, etc are in the works. All implemented functions are well documented and ready for use. However, since this package is still in active development some syntax and function names may still change.
## Installation
You can install the [isoprocessor](http://isoprocessor.isoverse.org/) package from GitHub using the `devtools` package. Note that while [isoprocessor](http://isoprocessor.isoverse.org/) uses some functions from [isoreader](http://isoreader.isoverse.org/), it does NOT require IRMS data to be read with [isoreader](http://isoreader.isoverse.org/), it can be used standalone with raw data obtained differently.
```{r gh-installation, eval = FALSE}
# installs the development tools package if not yet installed
if(!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
# installs the newest version of isoprocessor
devtools::install_github("isoverse/isoprocessor")
```
## Update
To update to a newer version of isoprocessor:
```{r update, eval = FALSE}
# installs the newest version of isoprocessor
devtools::install_github("isoverse/isoprocessor")
```
Troubleshooting note: depending on your workspace and operating system, you may have to re-start your R session, delete previous versions of these packages (`remove.packages("isoprocessor")`, `remove.packages("isoreader")`), and/or manually install some dependencies (e.g. the `digest` package tends to cause trouble: `remove.packages("digest"); install.packages("digest")`).
## Functionality
- for a full reference of all available functions, see the **[Function Reference](http://isoprocessor.isoverse.org/reference/)**
- for an example of how to work with continuos flow data, see the vignette on **[Continuous Flow](http://isoprocessor.isoverse.org/articles/continuous_flow.html)**
- for an example of how to work with dual inlet data, see the vignette on **[Dual Inlet](http://isoprocessor.isoverse.org/articles/dual_inlet.html)**
- for an example of how Thermo Isodat in particular calculates isotope ratios for standard continuous flow and dual inlet data, see the **[Isodat calculations notebook](http://isoprocessor.isoverse.org/articles/isodat_calculations.html)**
- additional vignettes on data reduction and calibration are in the works:
- example 1: **[bulk carbon isotope analysis](http://isoprocessor.isoverse.org/articles/ea_irms_example_carbon.html)**
- example 2: **[compound specific carbon isotope analysis](http://isoprocessor.isoverse.org/articles/gc_irms_example_carbon.html)**
## Open Source
[isoprocessor](http://isoprocessor.isoverse.org/) is and will always be fully open-source (i.e. free as in 'freedom' and free as in 'free beer') and is provided as is. The source code is released under GPL-2.
## isoverse <a href='http://www.isoverse.org'><img src='man/figures/isoverse_logo_thumb.png' align="right" height="138.5"/></a>
This package is part of the isoverse suite of data tools for stable isotopes. If you like the functionality that isoverse packages provide to the geochemical community, please help us spread the word and include an isoverse or individual package logo on one of your posters or slides. All logos are posted in high resolution in the main [isoverse repository](https://github.com/isoverse/isoverse/tree/master/man/figures).