https://github.com/isoverse/clumpedr
Clumped isotope data analysis in R
https://github.com/isoverse/clumpedr
analysis clumped data isotope processing r stable stable-isotopes
Last synced: 4 months ago
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Clumped isotope data analysis in R
- Host: GitHub
- URL: https://github.com/isoverse/clumpedr
- Owner: isoverse
- License: gpl-3.0
- Created: 2019-01-30T05:56:58.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2025-06-05T14:17:00.000Z (about 1 year ago)
- Last Synced: 2025-09-04T21:48:52.746Z (9 months ago)
- Topics: analysis, clumped, data, isotope, processing, r, stable, stable-isotopes
- Language: R
- Homepage: http://clumpedr.isoverse.org/
- Size: 1.49 MB
- Stars: 9
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
# clumpedr
[](https://doi.org/10.5281/zenodo.10638816)
[](https://cran.r-project.org/package=clumpedr)
[](https://github.com/isoverse/clumpedr/blob/master/LICENSE.md)
[](https://github.com/isoverse/clumpedr/releases)
[](https://mybinder.org/v2/gh/isoverse/clumpedr/main)
[](https://github.com/isoverse/clumpedr/actions/workflows/check-standard.yaml)
Clumpedr aims to facilitate analysis of clumped isotope data. It builds on [isoreader](https://github.com/isoverse/isoreader) which is used to import raw data files from the mass spectrometer, and most of the important data processing parts are based on Huntington et al. 2009 and Daëron et al. 2016.
Clumpedr includes dataprocessing steps such as:
- exclusion of failed cycles, based on a sudden drop of pressure
- simple background corrections using the mass 47.5 cup
- linear intensity matching of reference gas mass 44 to the sample gas, and
application of this shift to all other masses
- calculation of delta values
- default calculations use the Brand et al., 2010 pararameters.
- calculation of big delta values, Δ₄₇
- summarize per sample
- per-run correction and calculation of the empirical reference frame
## Installation
clumpedr is currently in development, and thus has not been released on [CRAN](https://CRAN.R-project.org) yet. Therefore, install it using:
```r
devtools::install_github("isoverse/clumpedr")
```
If this doesn't work, make sure you have `devtools` installed (`install.packages("devtools")`).
For the development version, use:
```r
devtools::install_github("isoverse/clumpedr", ref = "dev")
```
## Explanation
See the data processing vignette called clumped for an extensive example on how
to use clumpedr!
```r
vignette("clumped")
```
## Contributing
Contributions to improving the clumped data processing package are more than welcome! If something doesn't work the way you expect and you don't know how to fix it, write an issue. If you do know how to fix it, feel free to write a pull request!
## References
- Huntington, K. W., Eiler, J. M., Affek, H. P., Guo, W., Bonifacie, M., Yeung, L. Y., Thiagarajan, N., ..., Methods and limitations of 'clumped' CO₂ isotope (Δ₄₇) analysis by gas-source isotope ratio mass spectrometry, Journal of Mass Spectrometry, 44(9), 1318–1329 (2009). http://dx.doi.org/10.1002/jms.1614
- Daëron, M., Blamart, D., Peral, M., & Affek, H. P., Absolute isotopic abundance ratios and the accuracy of Δ₄₇ measurements, Chemical Geology, 442(), 83–96 (2016). http://dx.doi.org/10.1016/j.chemgeo.2016.08.014
## See also
- clumpedr is part of the [isoverse](https://www.isoverse.org/)
- Use [`isoreader`](https://github.com/isoverse/isoreader) to read in raw measurement
- [`seasonalclumped`](https://github.com/nielsjdewinter/seasonalclumped) can be used to reconstruct temperature and salinity variations from seasonal oxygen and clumped isotope records.
- [`isogeochem`](https://github.com/davidbajnai/isogeochem) can be used to calculate equilibrium Δ₄₇ and Δ₄₈ values, carbonate growth temperatures, isotopic fractionation factors and more.
- [`D47crunch`](https://github.com/mdaeron/D47crunch) is the Python processing code to process clumped data from δ₄₇ values. It features a pooled regression for the empirical transfer function and many other features.
- [`clumpedcalib`](https://github.com/japhir/clumpedcalib) Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping.
- [`clumped-processing`](https://github.com/UtrechtUniversity/clumped-processing) Clumped isotope measurement processing script for Thermo Fisher MAT 253 plus isotope ratio mass spectrometer with the Kiel IV used at Utrecht University.