A Simulated Data Set

Image credit: David LeBauer. Simulated growth of Sorghum genotypes; green is most productive and red line is least.

A Simulated Data Set

By David LeBauer; ARPA-E TERRA Reference Data and Computing Team Comment

A simulated dataset

We need feedback on data products that you will need access to. To obtain feedback prior to the pipeline being in place, we have simulated data that a sensor might observe, along with data sets containing some of the underlying environmental drivers and physiological traits.

Note that these data sets contain numerical artifacts, quasi-principled error terms, and liberal re-application of core concepts for the purposes of developing these datasets.

All of these simulated datasets are released with an unrestrive copyright. This means you can copy, modify, ans share the data. Please keep in mind that the data sets are not production quality - they have been developed solely to receive feedback.

A note on variable names

I have used the variable names currently used in BETYdb.org/variables, along with names inspired by the more standardized naming Climate Forecasting conventions. However, this is a very early pre-release, and we welcome comments on how such data should be formatted and accessed can be discussed in issue #18.

Design of Simulation Experiment

Sorghum lines grown at each of three sites along a N-S transect in Illinois over five years (2021-2025).

Time Span (2021-2025)

These are historic data, but the years have been changed to emphasize the point that these are not real data. The years have been chosen to select climate extremes. Two years were dry, two were wet, and one was average.

year drought index
2021 wet
2022 dry
2023 normal
2024 wet
2025 dry

Sites

These are approximate locations used to query the meteorological and soil data used in the simulations.

site name latitude longitude
north 42.0 -88.5
central 40.0 -88.5
south 37.0 -88.5

Each site has four replicate fields: A, B, C, D. This simulated dataset assumes each field within a site has similar, but different meteorology (e.g., as if they were all in the same county).

Meteorology

variable_id name standard_name units description
  Tmin   C Daily max temperature
  Tmax   C Daily min temperature
  Tavg   C Daily mean temperature
  precipitation precipitation_flux mm/d Daily precipitation

Genotypes

Two-hundred and twenty-seven lines were grown at each site. Each line is identified by a unique integer in the range [9915:10141]

Phenotypes

The phenotypes associated with each genotype is in the file phenotypes.csv.

These ‘phenotypes’ are used as input parameters to the simulation model. We often refer to these as ‘traits’ (as opposed to biomass or growth rates, which are states and proceses). In this example, we assume that ‘phenotypes’ are time-invariant.

variable_id name standard_name units Description
  genotype     genetically and phenotypically distinct line
  Vmax   umol m-2 s-1 maximum carboxylation of Rubisco according to the Collatz model
38 cuticular_cond conductance_of_fully_closed_stomata umol H2O m-2 s-1 leaf conductance when stomata fully closed
15 SLA specific_leaf_area m2 kg-1 Specific Leaf Area
39 quantum_efficiency mole_ratio_of_carbon_dioxide_to_irradiance_in_leaf fraction see Farqhuar model
18 LAI leaf_area_index m2 leaf m-2 ground Leaf Area Index
31 c2n_leaf mass_ratio_of_carbon_to_nitrogen_in_leaf ratio C:N ratio in leaves
493 growth_respiration_coefficient respiration_coefficient_for_growth mol CO2 / mol net assimilation amount of CO2 released due to growth per unit net photosynthesis
7 leaf_respiration_rate_m2 respiration_rate_per_unit_area_in_leaf umol CO2 m-2 s-1 Not really ““dark respiration”” Often this is respiration that occurs in the light. Date and time fields ““should”” identify pre-dawn (nightime/dark) leaf resp vs the Rd that comes from a A-Ci or A-PPFD curve
4 Vcmax rubisco_carboxylation_rate_in_leaf_assuming_saturated_rubp umol CO2 m-2 s-1 maximum rubisco carboxylation capacity
404 stomatal_slope.BB stomatal_slope_parameter_assuming_ball_berry_model ratio slope parameter for Ball-Berry Model of stomatal conductance
5 Jmax electron_transport_flux_in_thylakoid_assuming_saturated_light umol photons m-2 s-1 maximum rate of electron transport
492 extinction_coefficient_diffuse extinction_coefficient_for_diffuse_light_in_canopy   canopy extinction coefficient for diffuse light

Simulated Sensor Data

This dataset includes what a sensor might observe, daily for five years during the growing season.

variable_id name standard_name units Description
  sitename     Name of site
  plotid     experimental replicate plot
  year      
  date   YYYY-MM-DD  
  Stem stem_biomass_content   Mg / ha
  Leaf leaf_biomass_content   Mg / ha
  Root root_biomass_content   Mg / ha
  Rhizome rhizome_biomass_content   Mg / ha
18 LAI leaf_area_index ratio Leaf Area Index is the ratio of leaf area to ground area
  NDVI normalized_difference_vegetation_index ratio commonly used vegetation index
  Height canopy_height m  

How to obtain data and give feedback:

Please provide feedback. Please provide feedback by leaving a comment below, commenting on the issue in our GitHub repository, emailing me, dlebauer@illinois.edu, or visiting the TerraRef Reference Data chatroom.

  • If you do something cool, please send comments and figures!
  • I also can provide similar data at hourly or higher frequency as well as other processes and environmental drivers, Data are located on Box: https://uofi.box.com/sorghum-simulation

Data on BETYdb

These data have been uploaded to a test instance of our database, BETYdb. and can be accessed in the following ways:

  1. web interface: search + download
    • go to http://terraref.ncsa.illinois.edu/bety-test and search for “Sorghum” in the search box
    • click “Download Results”
  2. API:
    • basic search: http://terraref.ncsa.illinois.edu/bety-test/search?search=sorghum
    • Draft API Documentation: https://terraref.ncsa.illinois.edu/bety-test/api/docs
  3. SQL Dump: https://terraref.ncsa.illinois.edu/bety-test/dump/bety.tar.gz
  4. Other Methods: https://pecan.gitbooks.io/betydb-data-access/content/introduction.html

csv files: Data on Box

  • observations.csv: simulated observations including biomass, LAI, NDVI, height, (aka ‘phenotypes’)
  • phenotypes.csv: physiological traits such as photosynthetic parameters, SLA, leaf angle, etc. associated w/ genotype (assumed time invariant)
  • met.csv: daily temperature and precipitation summaries
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