leaf-level.yaml

description: "A collection of sources which provide leaf-level data for
photosynthesis. Where possible, column meanings and units are included in the
metadata for each source."

sources:

  Lin2015:
    args:
      csv_kwargs:
        dtype:
          Funtype: str
          Date: str
          LAI: str
          LWPpredawn: float
          LightSource: str
          SWC: float
          SWP: float
          Totalheight: str
          sampleheight: float
        encoding: ISO-8859-1
        na_values: -9999.0
      urlpath: https://bitbucket.org/gsglobal/leafgasexchange/raw/23ee6bce1d3927b36eb868ecaea8f41aed7a33ec/WUEdatabase_2015-11-20_All_opt_full_params_bitbucket.csv
    description: "Column definitions may be found in the [README](https://bitbucket.org/gsglobal/leafgasexchange/src/master/)"
    driver: intake.source.csv.CSVSource 
    metadata: {}

  Anderegg2018:
    args:
      csv_kwargs:
        dtype:
          PARin: float64
          Comments: str
          OriginalFile: str
        na_values: -9999.0
      urlpath: https://figshare.com/ndownloader/files/10920236
    description: "This database accompanies the publication 'Anderegg, et al.
    (2018) Woody plants optimise stomatal behaviour relative to hydraulic risk.
    Ecology Letters. For more details, please see the
    [entry](https://figshare.com/articles/dataset/AllData_EcologyLetters_Figshare_v1_3-18_csv/6066449/1)
    on figshare. As per a private communication, the data columns were selected
    to match the meaning and units of the Lin2015 data and are replicated here
    in the metadata. However, some columns in this dataset are not found in the
    version of Lin2015 we point to here. In this case we have provided a guess
    at meanings and units based on orders of magnitude." 
    driver: intake.source.csv.CSVSource
    metadata:
      BLCond:
        note: not used, all NaN's
      canopyposition:
        options: top, Top, None
      Ci:
        name: CO2 concentration inside the leaf
        units: ppm
      CO2S:
        name: CO2 concentration at leaf surface
        units: ppm
      Comments:
        name: Measurement comments
      Cond:
        name: Stomatal conductance
        units: mol m-2 s-1
      Datacontrib:
        name: Data contributor
      Date:
        name: Date collected
      fitgroup:
        name: Measurement comments
      Funtype:
        options: temperate evergreen, Temperate conifer, Temperate evergreen, None
      GrowthCa:
        options: ambient, Ambient, None
      Growthcond:
        name: Growth condition
      GrowthTair:
        options: ambient, None
      Instrument:
        options: Licor 6400(2cm_ Fluo), Licor 6400, None
      LAI:
        name: Leaf area index
        options: 1.2, 1.9, 2.8
      latitude:
        name: Site latitude
        units: degrees_north
      Leafspan:
        options: evergreen, deciduous
      LightSource:
        name: not used, all Nan's
      Location:
        name: Site description
      longitude:
        name: Site longitude
        units: degrees_east
      LWP:
        name: Leaf Water Potential
        units: MPa
      LWPpredawn:
        name: Predawn Leaf Water Potential
        units: MPa
      opt:
        name: Growing under ambient or stressed condition, or reference of data
        options: opt, Feeney et al. 1998, Kolb & Stone 2000, Koepke & Kolb 2013, Xu & Baldochhi 2003, Chmura et al. 2016, Anderegg 2011, Resco et al. 2009, Arango-Velez et al. 2011, Choat 2006, Wolfe et al. 2016, Li et al. 2015, Sherman et al. 2004, Meinzer et al. 2004
      OriginalFile:
        options: deAngelis macchia species.xls, None
      PARin:
        name: Photosynthetically active radiation in cuvette
        units: 1e-6 mol m-2 s-1
      Pathway:
        options: C3, C4, CAM
      Patm:
        name: Atmospheric pressure
        units: kPa
      Photo:
        name: Photosynthetic rate
        units: 1e-6 mol m-2 s-1
      Plantform:
        options: tree, shrub, grass, crop, savanna
      Reference:
        name: Reference of the data, note some of this information is in 'opt'
        options: Martin-StPaul et al 2012, Limousin et al. 2013 PCE, None
      RH:
        name: Relative humidity
        units: '%'
      sampleheight:
        name: not used, all NaN's
      Season:
        name: not used, all NaN's
      Species:
        name: Species name
      SWC:
        name: Soil water content
        units: '?'
      SWP:
        name: not used, all NaN's
      Tair:
        name: Air temperature
        units: degC
      Time:
        name: Measurement time
      Tleaf:
        name: Leaf temperature
        units: degC
      Totalheight:
        name: '?'
        options: 5.8 , 4.15, 3.15,  nan
      Treatment:
        options: Ambient, Dry site of Gradient, Intermediate site of the gradient, Irrigation, OTC CO2_amb, Wet site of the Gradient, None
      Tregion:
        options: arctic, boreal, temperate, tropical
      Trmmol:
        name: Leaf transpiration
        units: 1e-3 mol m-2 s-1
      Type:
        options: gymnosperm, angiosperm, None
      VPD:
        name: Vapour pressure deficit
        units: kPa
      Wregion:
        options: arid, semi-arid, dry sub-humid, humid
      Wregion2:
        name: Moisture index
        units: '1'
        note: the order of magnitude of this data added in from other sources (see the 'opt' column) is 2x greater


  Saunders2021:
    args:
      urlpath: https://github.com/altazietsman/ML-stomatal-conductance-models/blob/master/Input%20Data/df.xlsx?raw=true
    description: "This dataset, along with Anderegg2018, was used in the
    publication 'Saunders, et al. (2021) Machine learning models perform better
    than traditional empirical models for stomatal conductance when applied to
    multiple tree species across different forest biomes'. See their github
    [repository](https://github.com/altazietsman/ML-stomatal-conductance-models)
    for more details."
    driver: intake_excel.intake_excel.ExcelSource
    metadata:
      Cond:
        name: Stomatal conductivity
        units: mol m-2 s-1
      ETR:
        name: '?'
        units: '?'
      E_apparent:
        name: '?'
        units: '?'
      Patm:
        name: Atmospheric pressure
        units: kPa
      PhiPS2:
        name: '?'
        units: '?'
      RH:
        name: elative humidity
        units: '%'
      SWC:
        name: Soil water content
        units: m3 m-3
      Species:
        options: UXG, GXC
      Tair:
        name: Air temperature
        units: degC
      Tleaf:
        name: Leaf temperature
        units: degC
      VPDleaf:
        name: Vapor pressure deficit at leaf
        units: kPa
      date_time:
        name: Record timestamp
      soil:
        name: Duplicate of SWC
      solar:
        name: Incoming solar irradiance
        units: W m-2
      wind:
        name: All zeroes


  Han2022:
    driver: intake.source.csv.CSVSource
    args:
      csv_kwargs:
        dtype:
          Fm: float64
          Fm': float64
          Fo: float64
          Fs: float64
          Tleaf: float64
        names:
        - Species name
        - Tleaf
        - LeafReplicateNumber
        - PARi
        - CO2R
        - Ci
        - Anet
        - Fm'
        - Fs
        - VpdL
        - Press
        - OxygenPress
        - Fo
        - Fm
        skiprows: 1
      urlpath: 
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Andropogon_gerardii.csv?sequence=4&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Broadleaf_deciduous_liana_tropical.csv?sequence=5&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Broadleaf_deciduous_shrub_temperate.csv?sequence=6&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Broadleaf_deciduous_tree_boreal.csv?sequence=7&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Broadleaf_deciduous_tree_temperate.csv?sequence=8&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Broadleaf_deciduous_tree_tropical.csv?sequence=9&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Broadleaf_evergreen_tree_tropical.csv?sequence=10&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/C3_Crop.csv?sequence=11&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/C3_Grass.csv?sequence=12&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/C4_Crop.csv?sequence=13&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/C4_Grass.csv?sequence=14&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Cornus_racemosa_Cuyzam.csv?sequence=15&isAllowed=y
      - https://ecommons.cornell.edu/bitstream/handle/1813/110978/Needleaf_evergreen_tree_boreal.csv?sequence=16&isAllowed=y
      path_as_pattern: 'https://ecommons.cornell.edu/bitstream/handle/1813/110978/{PFT}.csv?sequence={sequence}&isAllowed=y'
    description: "Data from: The Physiological Basis for Estimating
    Photosynthesis from Chlorophyll a Fluorescence. Please cite as: Jimei Han,
    Lianhong Gu, Yongjiang Zhang, Ying Sun. (2022) Data from: The Physiological
    Basis for Estimating Photosynthesis from Chlorophyll a Fluorescence.
    [dataset] Cornell University eCommons Repository.
    https://doi.org/10.7298/q3hb-zq56"
    metadata:
      Species: 
        name: species
      Tleaf: 
        name: leaf temperature
        units: degC
      LeafReplicateNumber: 
        name: replicate number for individual leaf
        units: '1'
      PARi: 
        name: photosynthetically active radiation
        units: 1e-6 mol m-2 s-1
      CO2R: 
        name: reference CO2 concentration
        units: 1e-6 mol mol-1
      Ci:
        name: intercellular CO2 concentration
        units: 1e-6 mol mol-1
      Anet: 
        name: net photosynthesis
        units: 1e-6 mol m-2 s-1
      Fm': 
        name: maximum chlorophyll a fluorescence under light
        units: mV
      Fs: 
        name: steady-state chlorophyll a fluorescence under light
        units: mV
      VpdL: 
        name: leaf-to-air vapour pressure deficit
        units: kPa
      Press: 
        name: air pressure
        units: kPa
      OxygenPress:
        name: the pressure of oxygen
        units: kPa
      Fo: 
        name: minimum chlorophyll a fluorescence under fully dark-adapted conditions
        units: mV 
      Fm:
        name: maximum chlorophyll a fluorescence under fully dark-adapted conditions
        units: mV