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The bigleaf R package

bigleaf is an R package for the calculation of physical (e.g. aerodynamic conductance, surface temperature) and physiological
(e.g. canopy conductance, water-use efficiency) ecosystem properties from eddy covariance data and accompanying meteorological measurements.
All calculations are based on a 'big-leaf' representation of the vegetation and return representative bulk ecosystem/canopy variables.

Citation

Knauer J, El-Madany TS, Zaehle S, Migliavacca M (2018) Bigleaf—An R package for the calculation of physical and physiological ecosystem properties from eddy covariance data.
PLoS ONE 13(8): e0201114. https://doi.org/10.1371/journal.pone.0201114

Installation

The bigleaf R package is on CRAN and can be installed using:

install.packages("bigleaf")

The development version can be directly installed from this bitbucket repository:

library(devtools)
install_bitbucket("juergenknauer/bigleaf")

Usage

Most functions work by providing a data.frame or matrix which contains all required variables:
For example, surface conductance for the spruce forest in Tharandt, Germany (DE-Tha) can be calculated with
the following commands:

DE_Tha_June_2014$Ga <- aerodynamic.conductance(DE_Tha_June_2014,Tair="Tair",pressure="pressure",wind="wind",ustar="ustar")[,"Ga_h"]
surface.conductance(DE_Tha_June_2014,Tair="Tair",pressure="pressure",Rn="Rn",VPD="VPD",LE="LE",Ga="Ga")
surface.conductance(DE_Tha_June_2014,Tair="Tair",pressure="pressure",Rn="Rn",VPD="VPD",LE="LE",Ga=0.1)

Here, DE_Tha_June_2014 denotes the input data.frame. Note that input variables can be provided as column names of the
input data.frame (as argument Ga in line 2 above), or alternatively, as vectors with the same length as the input data.frame
or of length 1 (as argument Ga in line 3 above). If variables are provided in the default column names (as above), the command can
be shortened to:

surface.conductance(DE_Tha_June_2014)

Important: please ensure that all input variables are in the correct units as described on the help pages.

Please report bugs or issues here

Package content

The package provides the following functionalities:

Data filtering

  • data quality filter
  • filter based on meteorological variables (radiation, precipitation, ustar, temperature, etc.)
  • growing season filter (based on daily GPP)

Meteorological variables

  • air density
  • virtual temperature
  • pressure from altitude
  • psychrometric constant
  • latent heat of vaporization
  • saturation vapor pressure
  • slope of saturation vapor pressure curve

Aerodynamic properties

  • aerodynamic conductance (different versions) for momentum, water, heat, and CO2
  • Canopy boundary-layer conductance (Rb and kB-1 parameter; empirical and physically-based models)
  • Monin-Obhukov length
  • stability parameter zeta
  • stability correction functions (different versions)
  • roughness length for momentum (z0m) and heat (z0h)
  • decoupling coefficient 'omega'
  • Reynolds number
  • wind speed at a given height from the logarithmic wind profile equation

Surface conditions

  • vapor pressure, specific humidity, and VPD at the big-leaf surface
  • CO2 concentration at the big-leaf surface
  • aerodynamic surface temperature
  • radiometric surface temperature

Evapotranspiration (ET) and water-use efficiency (WUE)

  • potential ET (Priestley-Taylor and Penman-Monteith equations)
  • imposed and equilibrum ET
  • WUE, inherent WUE, underlying WUE

Physiological variables

  • canopy conductance (inverted Penman-Monteith equation)
  • bulk intercellular CO2 concentration (Ci)
  • bulk photosynthetic capacity (Vcmax25 and Jmax25)
  • stomatal slope parameter g1 (USO, Ball&Berry, Leuning models)
  • stomatal sensitivity to VPD
  • ecosystem light response, light-use efficiency

Energy balance

  • energy balance closure (EBR and slope method)
  • biochemical energy
  • energy-use efficiency

Unit conversions

  • conductance conversion from m s-1 to mol m-2 s-1 and vice versa
  • conversions between humidity measures (vapor pressure, specific humidity, relative humidity, and VPD)
  • conversion between latent heat flux (W m-2) and evapotranspiration (kg m-2 s-1)
  • conversion between radiation in W m-2 and umol m-2 s-1
  • carbon fluxes from umol m-2 s-1 to g m-2 day-1

Contact

For questions, remarks, and suggestions please contact jknauer@bgc-jena.mpg.de