custom.calc: custom.calc

View source: R/custom.calc.R

custom.calcR Documentation



Calculates D13C, Ci, CiCa, diffCaCi, or iWUE with user specified values of d13C.plant, d13CO2.atm, atmospheric CO2, temperature, and elevation. The user can also specify whether to calculate each physiological index using the 'simple', 'photorespiration', or 'mesophyll' formulation in all calculations where Ci is computed. Method defaults to 'simple' assuming 'leaf' tissue and incorporates an apparent fractionation by Rubisco, b, of 27 permille (Cernusak and Ubierna 2022). If 'wood' tissue is supplied as an argument in the 'simple' method, the apparent fractionation by Rubisco, b, is updated to 25.5 permille (Cernusak and Ubierna 2022).


  frac = 0,
  outvar = "D13C",
  Ca = NULL,
  elevation = NULL,
  temp = NULL,
  method = "simple",
  tissue = "leaf"



Measured plant tissue carbon isotope signature, per mille (‰)


Atmospheric d13CO2, per mille (‰)


Post-photosynthetic fractionation factor, defaults to 0 assuming leaf material, user should supply reasonable value if from wood (generally -1.9 - -2.1)


Variable of interest to calculate from the following: D13C, Ci, CiCa, diffCaCi, or iWUE. Defaults to D13C.


Atmospheric CO2 concentration (ppm).


Elevation (m.a.s.l.) of the sample, necessary to account for photorespiration processes


Leaf temperature (°C)


Method to calculate iWUE (simple, photorespiration, or mesophyll). Defaults to 'simple'. See Lavergne et al. 2022, Ma et al. 2021, Gong et al. 2022.


Plant tissue of the sample (i.e. leaf or wood) used only during calculations using the simple formulation. Defaults to 'leaf'.


One of the specified outvars: D13C (permille), Ci (ppm), CiCa (unitless), diffCaCi (ppm), or iWUE (micromol CO2 per mol H2O). Defaults to 'D13C'.


Badeck, F.-W., Tcherkez, G., Nogués, S., Piel, C. & Ghashghaie, J. (2005). Post-photosynthetic fractionation of stable carbon isotopes between plant organs—a widespread phenomenon. Rapid Commun. Mass Spectrom., 19, 1381–1391.

Belmecheri, S. & Lavergne, A. (2020). Compiled records of atmospheric CO2 concentrations and stable carbon isotopes to reconstruct climate and derive plant ecophysiological indices from tree rings. Dendrochronologia, 63, 125748.

Bernacchi, C.J., Singsaas, E.L., Pimentel, C., Portis Jr, A.R. & Long, S.P. (2001). Improved temperature response functions for models of Rubisco-limited photosynthesis. Plant, Cell Environ., 24, 253–259.

Craig, H. (1953). The geochemistry of the stable carbon isotopes. Geochim. Cosmochim. Acta, 3, 53–92.

Cernusak, L. A. & Ubierna, N. Carbon Isotope Effects in Relation to CO2 Assimilation by Tree Canopies. in Stable Isotopes in Tree Rings: inferring physiological, climatic, and environmental responses 291–310 (2022). doi:10.1007/978-3-030-92698-4_9.

Davies, J.A. & Allen, C.D. (1973). Equilibrium, Potential and Actual Evaporation from Cropped Surfaces in Southern Ontario. J. Appl. Meteorol., 12, 649–657.

Farquhar, G., O’Leary, M. & Berry, J. (1982). On the relationship between carbon isotope discrimination and the intercellular carbon dioxide concentration in leaves. Aust. J. Plant Physiol., 9, 121–137.

Frank, D.C., Poulter, B., Saurer, M., Esper, J., Huntingford, C., Helle, G., et al. (2015). Water-use efficiency and transpiration across European forests during the Anthropocene. Nat. Clim. Chang., 5, 579–583.

Gong, X. Y. et al. Overestimated gains in water‐use efficiency by global forests. Glob. Chang. Biol. 1–12 (2022) doi:10.1111/gcb.16221.

Lavergne, A. et al. Global decadal variability of plant carbon isotope discrimination and its link to gross primary production. Glob. Chang. Biol. 28, 524–541 (2022).

Ma, W. T. et al. Accounting for mesophyll conductance substantially improves 13C-based estimates of intrinsic water-use efficiency. New Phytol. 229, 1326–1338 (2021).

Tsilingiris, P.T. (2008). Thermophysical and transport properties of humid air at temperature range between 0 and 100°C. Energy Convers. Manag., 49, 1098–1110.

Ubierna, N. & Farquhar, G.D. (2014). Advances in measurements and models of photosynthetic carbon isotope discrimination in C3 plants. Plant. Cell Environ., 37, 1494–1498.


custom.calc(d13C.plant = -27, d13C.atm = -8.7)

isocalcR documentation built on March 31, 2023, 7:25 p.m.