NEONiso (development version)

NEONiso 0.8.0

• Added an HDF5 abstraction layer (R/hdf5_utils.R) that supports both hdf5r (CRAN) and rhdf5 (Bioconductor) backends. Both packages are now listed as suggested dependencies rather than hard imports, and the backend is selected automatically at runtime based on availability.
• Removed the dependency on the caret package. Cross-validation in estimate_calibration_error() is now performed using base R, which reduces the package’s dependency footprint. Note that Rsquared is no longer included in the cross-validation output (R-squared is still reported from the model fit itself).
• Various performance improvements to calibration regression routines:
  • Data frames in fit_carbon_regression() and fit_water_regression() are now pre-allocated to the correct size rather than a fixed 200,000 rows.
  • Time vectors are constructed once outside the calibration loop instead of being grown element-by-element inside it.
  • Formula objects and the calibration half-width are hoisted out of the loop to avoid repeated construction.
  • Model summaries are cached to avoid redundant recomputation.
• Simplified convert_POSIXct_to_NEONhdf5_time() to use format() instead of manual string construction with individual lubridate accessor functions.
• Output file writing functions (setup_output_file, write_carbon_*, write_water_*) now accept an open file identifier, reducing redundant file open/close operations during calibration output. The rhdf5::h5closeAll() calls in the main calibration functions have been replaced with targeted h5_close() calls.
• Now requires neonUtilities >= 2.3.0 (previously >= 2.1.1).
• Expanded the test suite with new test files for HDF5 utility functions, HDF5 round-trip operations, and regression snapshot tests.

NEONiso 0.7.2

• Fixes a bug that causes the manage_local_ec_archive function to miss a large set of files that are on the remote server.

NEONiso 0.7.1

• Substantial upgrades to package documentation.

• The name “Bowling_2003” in methods and functions has been deprecated in favor of “gainoffset.” This change was made primarily to improve clarity of what the methods actually do. Code that uses the old “Bowling_2003” nomenclature will continue to work until at least version 0.8.0, but will issue a deprecation warning. # NEONiso 0.7.0

• calibrate_carbon_bymonth and calibrate_water_bymonth have been removed. Use calibrate_carbon and calibrate_water instead.

• terrestrial_relocatable_sites() has been renamed terrestrial_gradient_sites() to comply with a similar change made by NEON.

• Patch to hard-coded 9 minute interval to comply with switch to 6 minute averaging interval for isoCo2 product, following ATM ISO TWG recommendations.

NEONiso 0.6.4

• Small patch adding a minimum number of observations argument to the calibrate_carbon functions.

NEONiso 0.6.3

• Small patch to address change requested by CRAN. Issue with package documentation introduced in ROxygen 7.0.0: https://github.com/r-lib/roxygen2/issues/1491.

NEONiso 0.6.2

• This will be the last release that has the *_by_month functions! They have deprecated for about a year, and will be removed before next release. Use calibrate_carbon (mature) or calibrate_water (experimental).
• Adds an argument to manage_local_EC_archive that allows checking out specific releases (e.g., RELEASE-2023) instead of release + provisional. To check out all data, set to NULL.
• Exports get_Rstd, a helper function to return the heavy-to-light isotope ratio of the relevant international standard.
• Allows use of the useFasttime argument in dependency neonUtilities::stackEddy, for neonUtilities >= 2.3.0. stackEddy(useFasttime = TRUE) is ~3x faster on large datasets than stackEddy(useFasttime = FALSE), which improves performance significantly when trying to work on larger timeseries in the NEON archives.
• Adds new cross-validation error metrics to linear regression calibration method for carbon. Note that these metrics are still to be considered experimental and may continue to change.

NEONiso 0.6.1

• Exports new helper function for getting sites with water isotopes, water_isotope_sites().
• The reference_corrections vignette was blank in the previous release - it is updated in this release (#81)
• Makes select functions used internally consistent with upcoming changes to tidyselect (h/t Hadley Wickham)

NEONiso 0.6.0

• An experimental calibration routine for water isotopes has been added. It does have some known issues (e.g., no correction is made for concentration dependence of the analyzers yet), and any data produced from this function should be considered provisional.
• Added capability to plot data used in carbon calibration regression in order to help identify periods where calibration parameters seem to be okay, but quality of calibrated data is degraded.
• Added cross-validation error estimates to carbon calibration routines.
• The calibrate_carbon_bymonth() function has been marked as deprecated, but will be removed no earlier than version 0.7.0 or the end of 2022. The more flexible calibrate_carbon() function should be used.
• A bug that generated non-nonsensical CO2 and d13C values has been fixed (#72).
• The calibrate_carbon() function now also provides calibrated values for reference material measurement. These are useful for determining calibration error when one of the reference materials is omitted from the calibration (e.g., generate calibration relationships to the high and medium standards, then estimate error as the difference between calibrated measurement and known reference values).
• Reduced the number of tests that run on CRAN to minimize compute resources requested.
• Made a function that corrects a few mismatched reference values more visible, and added a few more instances where reference data needs to be corrected.

NEONiso 0.5.3

• Small maintenance release that addresses a NOTE on CRAN.

NEONiso 0.5.2

• Fixes a bug where an rhdf5 function was not being imported properly, generating warnings and errors on CRAN.
• Updates manage_local_ec_archive to avoid a scenario that was creating duplicate files, thereby being more efficient with drive space.

NEONiso 0.5.1

• This update takes advantage of upgrades to the stackEddy function in neonUtilities 2.1.1, which allows the calibration routines to run more efficiently on NEON’s HDF5 files. For example, calibrate_carbon(), runs ~2x faster if neonUtilities 2.1.1 is used instead of earlier versions.

NEONiso 0.5.0

• Adds the calibrate_carbon() function, which can be used to generate monthly output files or can be used to bundle all of the months of data available for an individual site into a single file. In the long-term, calibrate_carbon() will be the ‘workhorse’ function for NEON’s carbon data, and calibrate_carbon_bymonth will be deprecated in a future release.

NEONiso 0.4.0

• This is the initial release on CRAN.