Physical and Physiological Ecosystem Properties from Eddy Covariance Data

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. Calculations assume the land surface to behave like a 'big-leaf' and return bulk ecosystem/canopy variables.


News

NEWS for Package 'bigleaf'

version 0.6.5 (2018-06-17)

  • Vignette "Tutorial on bigleaf" added

version 0.6.4 (2018-06-15)

  • bug fix to energy.closure(): G and S were previously always ignored in the calculation of the intercept and slope.

version 0.6.3 (2018-06-13)

  • rownames corrected in the example datasets (starting at 1 now)
  • second part of output in filter.data() function is only shown if at least one variable is actually filtered.
  • default values for several arguments changed (e.g. "Ga" to "Ga_h") to ensure internal consistency

version 0.6.2 (2018-06-11)

  • hard-coded conversion factors replaced by constants (e.g. g2kg, Pa2kPa, umol2mol, etc.) which were added to the bigleaf.constants() list.

version 0.6.1 (2018-04-18)

  • default names for 'formulation' arguments changed for clarity in surface.conductance() and decoupling(). "PenmanMonteith" is changed to "Penman-Monteith", "FluxGradient" to "Flux-Gradient", and "JarvisMcNaughton_1986" to "Jarvis&McNaughton_1986".

version 0.6.0 (2018-04-18)

  • function reference.ET() is now covered by potential.ET(). If 'approach=Penman-Monteith', potential ET is calculated according to the Penman-Monteith equation (as previously in reference.ET()). Argument 'Gs_pot' (formerly 'Gs_ref') is given in mol m-2 s-1 and defaults to 0.6 mol m-2 s-1.

version 0.5.2 (2018-04-10)

  • Gb output in aerodynamic.conductance and Gb functions renamed to Gb_h to clarify that values correspond to heat transfer. Same for Rb and kB.

version 0.5.1 (2018-04-09)

  • results of additional quantities (for which Sc is provided) are expressed as conductances instead of resistances in aerodynamic.conductance()
  • 'data' included as argument in radiometric.surface.temp()
  • calculation of 'nr_data' accounts for missing values in Gamma if model=Leuning (function stomatal.slope())

version 0.5.0 (2018-04-06)

  • wind.profile() function restructured. z0m can be provided or calculated from the logarithmic wind profile equation
  • reflectance of downwelling longwave radiation is now accounted for in the calculation of radiometric surface temperature (function radiometric.surface.temp())
  • variable 'LW_down' added to dataset DE_Tha_Jun_2014
  • argument 'calc.surface.CO2' removed from intercellular.CO2()

version 0.4.6 (2018-04-05)

  • important bugfix concerning several functions: all required arguments are passed to nested functions
  • argument 'N' in aerodynamic.conductance() now defaults to 2 as in Gb.Su()

version 0.4.5 (2018-03-16)

  • variables 'LW_up' (upward longwave radiation) and 'Reco' (ecosystem respiration) were added to all three example datasets
  • bug fix to 'surface.conditions' and 'pressure.from.elevation' regarding the 'Esat.formulation' argument. In 'Esat.formulation', this argument is not implemented and the default formulation is taken for all calculations.

version 0.4.4 (2018-03-13)

  • 'reference.ET': argument Gs renamed to Gs_ref

version 0.4.3 (2018-03-12)

  • Function 'bigleaf.constants' restructured in a way that allows changing the constants for each function call

version 0.4.2 (2018-03-12)

  • constants (a,b,c) from Allen et al. 1998 added as option to 'Esat.slope' (pull request from Rémi Vezy)
  • Argument 'Esat.formula' added to every function that calculates esat or slope of esat to allow consistency among functions.
  • 'light.response': argument "..." added to the nls function
  • 'stomatal.slope': argument "..." within each call of nls in the function

version 0.4.1 (2018-03-08)

  • aerodynamic.conductance: Ga_CO2 added to function output

version 0.4.0 (2018-03-08)

  • 'aerodynamic.conductance': Rb can be calculated for other quantities if the respective Schmidt number is provided. I.e. new arguments "Sc" and "Sc_name" as the value of the Schmidt number, and the name of the quantity for which Sc is provided, respectively.
  • 'bigleaf.constants': Prandtl number (Pr) and Schmidt number for CO2 (Sc_CO2) added
  • 'light.response': bug fix: +Reco replaced by -Reco (sign was reversed)

version 0.3.2 (2018-03-06)

  • rH.to.VPD: if statement vectorized (thanks to Rémi Vezy)
  • radiometric.surface.temp: Output renamed ("." replaced by "_")

version 0.3.1 (2018-02-09)

  • Monin.Obukhov.length: default arguments added

Reference manual

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install.packages("bigleaf")

0.7.0 by Juergen Knauer, a month ago


https://bitbucket.org/juergenknauer/bigleaf


Report a bug at https://bitbucket.org/juergenknauer/bigleaf/issues


Browse source code at https://github.com/cran/bigleaf


Authors: Juergen Knauer [aut, cre] , Soenke Zaehle [ctb] , Tarek El-Madany [ctb] , Mirco Migliavacca [ctb] , Thomas Wutzler [aut]


Documentation:   PDF Manual  


Task views: Hydrological Data and Modeling


GPL (>= 2) license


Imports robustbase, solartime

Suggests knitr, rmarkdown, testthat


Suggested by REddyProc.


See at CRAN