Primary production data
- Biomass or carbon accumulation by primary producers (plants, usually)
- Variable: Gross or net primary production, aboveground or belowground
- Units: g biomass · m-2 · day-1 or g C · m-2 · day-1
Working with the long-term data of the Jornada Basin
A guided tour & hands-on workshop
A little background
- Jornada Basin has been an intensive research site for a long time.
- Jornada Experimental Range (JER), established in 1912
- Jornada Basin LTER (JRN), established in 1982
- Many other programs collect, or have collected, data in the Jornada Basin.
Here are a few…
Data collection, management, and use have evolved
- People, their studies and research priorities turn over
- Funding for programs can be unsteady
- As researchers, we’re not always perfect about data management
- Open data is a relatively new priority
- Managing and curating Jornada data is a continual work in progress…
The Jornada NPP study
A non-destructive ANPP method for drylands
- 1m2 long-term quadrats installed at 15 Jornada sites in 1989
- Field datasets:
- Replicate species harvests (dimensions & biomass)
- Plant dimensions (only) collected in long-term quadrats
- Allometric method to estimate biomass
- Huenneke, Clason, and Muldavin described the method in [
Used in numerous JRN pubs & cross-site syntheses
- NPP sites anchor many other Jornada studies
- Meteorology, soil profile characterization, soil water/temperature, plant traits, aerial photos, terrain/elevation models, phenology, animal studies, short-term grad student projects
- Validating new research methods (UAV/Remote sensing, models)
Jornada ANPP data
- Jornada NPP study sites (15 sites)
- Ecotone project (Bestelmeyer - 5 sites)
- Global change experiment (Sala - 1 site, slightly different method)
- Variable names differ, same units, same temporal resolution
- Red = 15 NPP sites; Orange = Ecotone, Green = GlobalChange
Jornada permanent quadrats
- Plant type, cover, and density measured since 1915
- Yearly to 1970s, break until early 90s, resuming at 5-year frequency
- 122 locations across the Jornada Experimental Range
Useful for assessing long-term vegetation change
- such as grass-shrub transitions
- Also, potentially useful for biodiversity research
Jornada quadrat cover data
- Jornada permanent quadrats (122, starting 1915)
- Ecotone quadrats (5, starting 2005)
- SMES (2, starting 1995)
- Different variable names, different units, different temporal resolution, different treatments
- Red = Perm Quads; Orange = Ecotone, Green = SMES
More plant cover data…
- Gibbens 2005 vegetation maps
- Line-point intercept data from multiple projects
- Jornada LTER transect knb-lter-jrn.210119001
- SMES knb-lter-jrn.210086001
- ConMod pilot knb-lter-jrn.210308002
Meteorology data
- Data collected from weather stations, including air temperature and RH, wind speed/direction, and precipitation.
NPP and Cross-scale weather stations
- Collecting continuously since 2013, multiple frequencies
- Data are regularly quality assured and sent to EDI
- There are some estimated/gapfilled precipitation datasets (since 1989) too
Soil water at NPP sites
Soil moisture data
- NPP and CSIS sites have automated soil profile sensors (VWC, T, EC) since 2013
- Long-term neutron probe data since 1989 (NPP sites and more)
- Many experiments have their own instrumentation or probe data
What are spatial data & GIS?
- (Geo)spatial data: Any data with location or geographic coordinates attached to the observation
- Geographic information systems (GIS): Integrated computer hardware and software that store, manage, analyze, edit, output, and visualize geographic data
Why do we care at the Jornada?
- Drylands are spatially heterogeneous
- We work in a large area
- We want to place our research in landscape context
The Jornada Spatial Data Catalog
- There are well over 1000 datasets
- Study & measurement locations
- Instrumentation, fences, roads, boundaries, buildings
- Physical geography
- Vegetation and soil survey products
- Remote sensing data
- Model outputs
- Only a small amount of datasets have been published or made accessible
How is it managed?
- Somewhat decentralized and siloed
- There are some great USDA GIS staff
- The LTER produces lots of data
- Researchers often manage their own pile of GIS data
- Some data are restricted access
- We are working out improved coordination and access methods
- A data commons is one goal…
Data:
- Datasets in public repositories
- Real-time data
- Spatial data from the Jornada GeoPortal
- https://lter.jornada.nmsu.edu
The Jornada GeoPortal
- https://jornada-geoportal-nmsu.hub.arcgis.com/
- This is a new, under-construction system
- Based on ArcGIS Online (AGOL), provided by NMSU
- All previously available GIS layers are there now
- Restricted layers available on login (request access)
- Permissions management is important for spatial data
How data are categorized and made searchable
Online interaction with spatial data
- Maps, web apps, “StoryMaps”, etc.
- Here is a basic map of the Jornada’s spatial data
- With an account you can log in and create these yourself
Join the JornadaGIS_users group
- There is more data available to authenticated users!
- Steps to get access:
- Make an AGOL account - institutional or public
- Fill out the Jornada Spatial Data Agreement
- Submit your AGOL username in the form!
- I’ll add you to the group
- Keep in mind you are testing a new system…
- Help wanted making nice maps!
What is RAP?
- https://rangelands.app
- Allred et al. 2021, 2025, Jones et al. 2021
Tab 1: Core long-term data
- Long-term data underpinning JRN LTER’s core research themes. Most of this is in EDI.
Tab 2: Primary data catalog
- The full JRN LTER data catalog hosted by EDI repository. 366 datasets searchable by metadata fields here
Tab 3: Data in other repositories
- Search Jornada data holdings in other repositories (Dryad, NCBI, AmeriFlux). Includes citeable datasets & portals for partner networks. “Special” data types.
Tab 4: Spatial data
- Selected geospatial/GIS datasets available for download. This is a small fraction of available spatial data.
Tab 5: Data partnerships
- Data from other research networks & agencies operating in the Jornada Basin. Some of these are in Tab 3 also.
Jornada data in
Environmental Data Initiative repository (EDI)
- https://edirepository.org
- A “generalist” repository for LTER & other environmental data
- High quality, searchable metadata
- Most LTER datasets go here
- USDA datasets are increasingly going here too
- Searchable at EDI or Tab 2
DeX
- Profile, subset and plot tabular datasets in EDI
EDIutils R package
- EDIutils - an API client for the EDI repository
- https://docs.ropensci.org/EDIutils/
- Search/Access data in EDI
- Also has data management tools…
- There will be a quick demo….
Some data are special
- Specialized data is best archived with similar data
- Nucleotide sequencing & genomic data
- Eddy covariance (flux) data
- Imagery data
- Shared data formats, variables, methods, or metadata standards
- Archived in specialized data repositories
- This data is supported by the JRN LTER, so we provide access
- Searchable in Tab 3, but less metadata available
- PhenoCam
There is lots of other Jornada data
- We don’t directly manage ALL Jornada data
- NEON
- CZNet
- Remote sensing data (NASA, USGS, Sentinel, etc)
- NOAA & NRCS stations
- Collections data (specimens & physical samples)
- We usually provide access via links to other data portals
- “Data Partnerships” are listed in Tab 5 and some datasets/portals in Tab 3
- We can help - let us know what you are looking for!
The Interactive data viewer
- R Shiny app showing met station locations (NPP & CSIS) and providing access to “provisional” met data.
Interactive data viewer
- Met data current to yesterday
- Subset & download data
- No QA/QC (!), but links to published data available
- Good for general orientation and answering the question “Did it rain at my site yesterday?”
DataOne
- Metadata aggregator
- Many “member nodes”
- All LTER repositories (EDI, BCO-DMO, ADC)
- Dryad et al.
- Some fed agency data
- Standard tabular datasets
- No NCBI, AmeriFlux, etc
- Good for cross-site synthesis, challenging for site-specific data
