intercellular.CO2 {bigleaf}R Documentation

Bulk Intercellular CO2 Concentration


Bulk canopy intercellular CO2 concentration (Ci) calculated based on Fick's law given surface conductance (Gs), gross primary productivity (GPP) and atmospheric CO2 concentration (Ca).


  Ca = "Ca",
  GPP = "GPP",
  Gs = "Gs_mol",
  Rleaf = NULL, = FALSE,
  constants = bigleaf.constants()



Data.Frame or matrix with all required columns


Atmospheric or surface CO2 concentration (umol mol-1)


Gross primary productivity (umol CO2 m-2 s-1)


Surface conductance to water vapor (mol m-2 s-1)


Ecosystem respiration stemming from leaves (umol CO2 m-2 s-1); defaults to 0

if Rleaf is provided, should missing values be treated as NA (TRUE) or set to 0 (FALSE, the default)?


DwDc - Ratio of the molecular diffusivities for water vapor and CO2 (-)


Bulk intercellular CO2 concentration (Ci) is given by:

Ci = Ca - (GPP - Rleaf)/(Gs/1.6)

where Gs/1.6 (mol m-2 s-1) represents the surface conductance to CO2. Note that Gs is required in mol m-2 s-1 for water vapor. Gs is converted to its value for CO2 internally. Ca can either be atmospheric CO2 concentration (as measured), or surface CO2 concentration as calculated from surface.CO2.


Ci -

Bulk canopy intercellular CO2 concentration (umol mol-1)


The equation is based on Fick's law of diffusion and is equivalent to the often used equation at leaf level (ci = ca - An/gs). Note that GPP and Gs have a different interpretation than An and gs. Gs comprises non-physiological contributions (i.e. physical evaporation) and is confounded by physical factors (e.g. energy balance non-closure). GPP does not account for dark respiration and is further subject to uncertainties in the NEE partitioning algorithm used. Leaf respiration can be provided, but it is usually not known at ecosystem level (as a consequence, Ci is likely to be slightly underestimated) This function should be used with care and the resulting Ci might not be readily comparable to its leaf-level analogue and/or physiological meaningful.


Kosugi Y. et al., 2013: Determination of the gas exchange phenology in an evergreen coniferous forest from 7 years of eddy covariance flux data using an extended big-leaf analysis. Ecol Res 28, 373-385.

Keenan T., Sabate S., Gracia C., 2010: The importance of mesophyll conductance in regulating forest ecosystem productivity during drought periods. Global Change Biology 16, 1019-1034.


# calculate bulk canopy Ci of a productive ecosystem
# note the sign convention for NEE

[Package bigleaf version 0.8.2 Index]