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first draft of an isoverse cheatsheet

We've got a first draft of a cheatsheet for the three main isoverse packages (isoreader, isoprocessor, isoviewer). Any suggestions/feedback/ideas on how to improve the cheatsheet, what else to add, how to clarify what the functions do, etc. are most welcome:

isoorbi version 1.3. released

Hi all,

It's been a while with a formal release but we're excited for isoorbi version 1.3 to be available on CRAN now. This version is chalk-full of new features that make it easier to process and visualize IRMS data from Orbitraps. Check it out at isoorbi.isoverse.org! A paper on the new functionality and Orbitrap-based IRMS measurements in general is also in revision and the SI is already available here.

isoreader 1.2.7 now on CRAN

Isoreader 1.2.7 is now available on CRAN and can be installed with:

install.packages("isoreader")

For the most recent development version, as always, you can install directly from GitHub:

# installs the development tools package if not yet installed
if(!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
devtools::install_github("isoverse/isoreader")

isoreader 1.2.0 and isoprocessor 0.6.6

Hi all,

We just released a few important updates to isoreader (new version 1.2.0) and isoprocessor (new version 0.6.6) that address breaking changes caused by the recently released version 3.0 of the tibble package that powers the data frames in the isoverse. Please upgrade to the new versions as soon as possible and file a bug report for isoreader / isoprocessor if you still encounter errors:

# key dependency updates
remove.packages(c("rlang", "dplyr", "tibble", "vctrs", "tidyr", "xml2"))
install.packages(c("rlang", "dplyr", "tibble", "vctrs", "tidyr", "xml2"))

# isoverse
remove.packages(c("isoprocessor", "isoreader"))
devtools::install_github("isoverse/isoreader")
devtools::install_github("isoverse/isoprocessor")

New Functionality

The new version of isoreader also implements some important new functionality:

• possibility to specify the number of cores used in parallel processing (iso_read_continuous_flow(parellel = TRUE, parallel_cores = 3))
• possibility to turn off linux datetime warnings (iso_turn_datetime_warnings_off())
• the handling of cache files and reread functions. This is a bigger update that will allow more flexibility with cached files going forward (e.g. they can be copied from a processing computer along with the data files to provide other users with faster reads) and will make reading cached files and storage (.rds) files faster. You will get warnings about your old cache and storage files being out of date but as soon as you run iso_reread_outdated_files(iso_files) on your iso file collection to update to the latest version, this will disappear and your reads will become faster. You only need to do this once and then not again for the foreseeable future.
• expanded re-read functions including iso_reread_changed_files(iso_files), iso_reread_problem_files(iso_files), and iso_reread_all_files(iso_files) to make it easier to update previously read files

Thanks all for your help reporting these issues and thanks for your patience with the bug fixes during these unusual times.

List of issue tracker items addresssed in these releases:

• isoverse/isoreader#110
• isoverse/isoreader#112
• isoverse/isoreader#114
• isoverse/isoreader#115
• isoverse/isoprocessor#85
• isoverse/isoprocessor#86

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isoreader published in JOSS

Hi all,

The isoreader package is now published in the Journal of Open Source Software!

Please cite this paper in your publications if you use isoreader for data processing:

String citation: Kopf et al., (2021). Isoreader: An R package to read stable isotope data files for reproducible research. Journal of Open Source Software, 6(61), 2878, https://doi.org/10.21105/joss.02878

Bibtex entry:

@article{Kopf2021,
  doi = {10.21105/joss.02878},
  url = {https://doi.org/10.21105/joss.02878},
  year = {2021},
  publisher = {The Open Journal},
  volume = {6},
  number = {61},
  pages = {2878},
  author = {Sebastian Kopf and Brett Davidheiser-Kroll and Ilja Kocken},
  title = {Isoreader: An R package to read stable isotope data files for reproducible research},
  journal = {Journal of Open Source Software}
}

Thank you!