Data Notifications

There have been many changes in NEON's microbial data products, as were detailed in an earlier Data Notification. This is an update on the status of NEON microbe data.

neonUtilities 2.4.2 is now available on CRAN! Read on to learn more about updates in this version.

The samples endpoint has been fixed and the update of NEON Biorepository records is underway.

We reduced the number of dilution subsamples per root core in table bbc_dilution from 10 to 3 at all terrestrial sites. This change was reviewed and approved by the NEON Plant Biomass and Productivity Technical Working Group, and was implemented on 2023-08-02, saving 70% of the labor associated with time-intensive sorting of dilution subsamples.

As of NEON’s 2024 Data Release, there have been modifications in the eddy covariance storage exchange (ECSE) workflow and bundled HDF5 files (DP4.00200.001).

NEON quantifies soil microbe biomass via measurement of phospholipid fatty acids (PLFA). The high-throughput PLFA method used involves addition of an internal standard to each sample, then PLFA concentrations are scaled by the recovery of that internal standard. For data collected prior to November 1, 2021, PLFAs were reported in unscaled format with extraction efficiency provided in order for users to conduct the scaling. After November 1, 2021, unscaled data are no longer ingested, and only data scaled to the internal standard are provided.

Due to an ordering error at NEON’s Southeast Domain (D03), aquatic biogeochemical samples that are required to be collected with GF/F grade filters

We have identified an issue with unusually high values for a subset of Dissolved Organic Carbon (DOC) concentrations published in Chemical properties

An error in the samples endpoint of the NEON API returned incorrect taxonomy data for a subset of sample types, impacting some NEON Biorepository collection records and potentially other users of the samples endpoint. This issue does not affect data products accessed via the NEON Data Portal, neonUtilities, or the data endpoint of the API.

In response to the issues identified in a previous post, NEON staff are currently developing code specifically designed to correct timestamps in data processing. The impacted data will undergo reprocessing and be published as provisional data as soon as the code is ready. We aim to release the corrected data in the 2025 data release.

To resolve apparent negative blank-corrected nitrate + nitrite N concentrations in some soil potassium chloride (KCl) extracts collected prior to 2022, a statistical correction using quantile regression can be applied to the data. This correction has been added as an optional function parameter in the neonNTrans R package def.calc.ntrans function.

As of November 1, 2023, Particulate Mass (DP1.00101.001) samples are no longer collected at NEON sites. NEON’s Particulate Mass data product (DP1.00101.001) provides the mass of PM10 (particulate matter 10 micrometers or less in diameter) collected on quartz filters biweekly at six NEON sites; these filters are archived and made available for further analysis from the NEON Biorepository.

Beginning in the 2024 field season, there will be a maximum of 4 bouts of small mammal sampling (DP1.10072.001) per year at all sites as well as a maximum of 6 mammal grids per site. We are also introducing a low intensity sampling regime of 1 bout per year at 3 sites (DSNY, LENO, BARR) with extremely low capture rates, diversity, and pathogen infection.

Recent improvements in DNA sequencing technology and laboratory protocols are producing data of overall better quality and greatly expanded size. As a result there have been a lot of changes in NEON's microbial data products, and data released in the coming year will include many updates and new, improved data.

NEON's fourth data release, RELEASE-2024, is now available for download!

Beginning in the 2023 field season, the Herbaceous clip harvest (DP1.10023.001) data product is no longer collected at 11 forested sites where herbaceous productivity is less than 10% of aboveground productivity.

neonUtilities 2.4.1 is now available on CRAN! Read on to learn more about updates in this version.

Photosynthetically active radiation (quantum line) (DP1.00066.001) has been reprocessed using NEON’s new instrument processing pipeline. Computation of skewness and kurtosis statistics has been updated in the new pipeline.

Primary precipitation (DP1.00006.001) has been reprocessed with an interim algorithm to better show spurious trace precipitation and improve quality flagging.

Data for the Litterfall and fine woody debris production and chemistry data product (DP1.10033.001) were published without data on total cover of qualifying vegetation (woody individual > 2M height). RELEASE-2024 and releases and provisional data thereafter include a new table 'ltr_vegetationCover' that provides cover of qualifying woody vegetation at the scale of the subplot for all deployed traps at all sites.

Certain AOP data products will be temporarily unavailable or in transition prior to RELEASE-2024. We recommend holding off on downloading AOP data during this transition period, or using the Contact Us form to request the status of any specific AOP data product(s), site(s), and year(s). This process is estimated to be complete by the end of January 2024.

Data previously published with incorrect soil water content measurement uncertainties have been reprocessed and republished.

We have discovered an 8-minute timestamp offset in data from all Picarro instruments, beginning 19 September 2023 and ending 30 November 2023. This issue only affects data collected by the instrument, not the valves that control switching measurement levels, which leads to incorrect partitioning of data to each measurement level and validation gas in data processing.

NEON recently discovered two issues with the way an external laboratory was storing samples and reporting quality assurance data for foliar chlorophyll. All impacted records have been flagged in the cfc_chlorophyll table in DP1.10026.001 Plant Foliar Traits.

It was discovered that some sensorDepth values recently published in the Water Quality (DP1.20288.001) data product are incorrect for some lake sites. We suggest users download the expanded data package with the more detailed quality flags to better identify affected data, and then substitute an approximate depth of 0.5 m.

Issues identified in the previous posts AOP Lidar Data Quality Notification and AOP Lidar Data Quailty Notification - Update have been resolved.

At the 32 sites where breeding landbird point counts are conducted in 9-point grids, two-thirds of counts have been reported with incorrect point IDs due to a transposition error when convertingnumeric point labels (1-9) into alphanumeric point IDs (A1-C3) during data ingest.

An error in many of the sensor calibration files means that the reported measurement uncertainty in the soil water content data product (DP1.00094.001) is lower than the actual measurement uncertainty for many locations.

The conductivity timeseries data in Reaeration and Salt-based discharge are being moved into individual files per sampling event. This affects the rea_conductivityFieldData and sbd_conductivityFieldData tables. Users of these data should update neonUtilities to version 2.4.0 or greater to ensure correct data stacking.

The Data Portal and the neonUtilities R package have been updated to default to downloading only data from the most recent Data Release. Provisional data, which are subject to change without notice, are still accessible, but are downloadable on an opt-in basis, rather than opt-out.