isocalcR

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The goal of isocalcR is to provide a suite of user-friendly, open source functions for commonly performed calculations when working with stable isotope data. A major goal of isocalcR is to help eliminate errors associated with data compilation necessary for many standard calculations, as well as to provide the scientific community with a reliable, easily accessible resource for reproducible work. Part of this effort includes best practices of data usage, as the user is not required to download atmospheric CO2 or atmospheric δ13CO2 data for the workhorse calculations, but instead relies on published, peer-reviewed, and recommended publicly available data (Belmecheri and Lavergne, 2020). isocalcR is not meant to replace an understanding of the underlying physiological mechanisms related to these calculations, but instead to streamline the process. At present, calculations for years 0 C.E. - 2019 C.E. will work, with 2020 available for the development version.

Installation

You can install the released version of isocalcR from CRAN with:

install.packages("isocalcR")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("justinmathias/isocalcR")

Functionality

isocalcR Function Description
d13C.to.D13C Calculate leaf carbon isotope discrimination (∆13C) given plant tissue δ13C signature (‰)
d13C.to.Ci Calculate leaf intercellular CO2 concentration (ppm) given plant tissue δ13C signature (‰)
d13C.to.CiCa Calculate the ratio of leaf intercellular CO2 to atmospheric CO2 concentration (ppm) given plant tissue δ13C signature (‰)
d13C.to.diffCaCi Calculate the difference between atmospheric CO2 concentration (ppm) and leaf intercellular CO2 concentration (ppm) given plant tissue δ13C signature (‰)
d13C.to.iWUE Calculate leaf intrinsic water use efficiency (µmol CO2 mol H2O-1) given plant tissue δ13C signature (‰)


Examples

Calculate leaf intrinsic water use efficiency from leaf δ13C:

library(isocalcR) #Load the package
d13C.to.iWUE(-27, 2015, 300, 25) #Calculate iWUE from leaf organic material with a δ13C signature of -27 ‰ for the year 2015, 300 meters above sea level at 25°C.
#> [1] 94.4544

Data for atmospheric CO2 and atmospheric δ13CO2 for the period 0 C.E. to 2019 C.E. can be loaded and viewed. Data are from Belmecheri and Lavergne (2020).

data(CO2data)
head(CO2data)
#>   yr     Ca d13C.atm
#> 1  0 277.63    -6.41
#> 2  1 277.63    -6.41
#> 3  2 277.64    -6.41
#> 4  3 277.64    -6.41
#> 5  4 277.65    -6.41
#> 6  5 277.66    -6.41

Literature cited

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.

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.

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.