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Update README.md for published manuscript
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sarahshi committed Jul 30, 2024
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PyIRoGlass is a Bayesian MCMC-founded Python algorithm, written in the open-source language Python3, for determining $\mathrm{H_2O}$ and $\mathrm{CO_2}$ species concentrations in the transmission FTIR spectra of basaltic to andesitic glasses. We leverage a database of naturally degassed melt inclusions and back-arc basin basalts to delineate the fundamental shape and variability of the baseline underlying the $\mathrm{CO_{3}^{2-}}$ and $\mathrm{H_2O_{m, 1635}}$ peaks, in the mid-infrared region. PyIRoGlass employs Bayesian inference and Markov Chain Monte Carlo sampling to fit all probable baselines and peaks, solving for best-fit parameters and capturing covariance to offer robust uncertainty estimates.

## Preprint
Find the [preprint on EarthArXiv](https://eartharxiv.org/repository/view/6193/) on for a more detailed description of the development and validation of the method.
## Manuscript
Find the [PyIRoGlass manuscript](https://doi.org/10.30909/vol.07.02.471501) published at Volcanica on for a more detailed description of the development and validation of the method. If you use this package in your work, please cite:

```console
Shi, S., Towbin, W. H., Plank, T., Barth, A., Rasmussen, D., Moussallam, Y., Lee, H. J. and Menke, W. (2024) “PyIRoGlass: An open-source, Bayesian MCMC algorithm for fitting baselines to FTIR spectra of basaltic-andesitic glasses”, Volcanica, 7(2), pp. 471–501. doi: 10.30909/vol.07.02.471501.
```

```
@article{Shietal2024,
doi = {10.30909/vol.07.02.471501},
url = {https://doi.org/10.30909/vol.07.02.471501},
year = {2024},
volume = {7},
number = {2},
pages = {471-501},
author = {Shi, Sarah C. and Towbin, W. Henry and Plank, Terry and Barth, Anna and Rasmussen, Daniel and Moussallam, Yves and Lee, Hyun Joo and Menke, William},
title = {PyIRoGlass: An open-source, Bayesian MCMC algorithm for fitting baselines to FTIR spectra of basaltic-andesitic glasses},
journal = {Volcanica}
}
```

## Documentation
Read the [documentation](https://pyiroglass.readthedocs.io/en/latest/) for a run-through of the PyIRoGlass code.
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