README.md

In rebeccalpowell/grassmapr: Predict C3/C4 Grass Distribution

grassmapr

The grassmapr package has two related objectives: (i) to predict the spatial distribution of terrestrial C3 and C4 grass cover – using input climate layers and crossover temperature - and (ii) to model plant stable carbon ((\delta)13C) isoscapes by applying isotopic endmembers to plant functional type cover layers. The user may optionally include other (i.e., non-grass) vegetation layers (e.g., % woody cover, % crop, etc.).

Background

The primary driver of (\delta)13C spatial variation in terrestrial plant tissue is the greater isotopic fractionation in C3 plants compared to C4 plants. The physiologically based crossover temperature model explains the turnover from C3 to C4 plants along gradients of temperature (Ehleringer et al. 1997, Collatz et al. 1998, Still et al. 2003).

The grassmapr package combines the crossover temperature model with gridded climate and land-cover data to predict the relative abundance of C3 and C4 vegetation distribution. Isotopic endmember values are then applied to map plant (\delta)13C, resulting in a spatially continuous representation, or isoscape. These layers are useful for understanding grass biogeography (e.g., Powell et al.  2012, Griffith et al. 2015) and for studies seeking to identify the movement of animals (e.g., Hobson 1999, Bowen & West 2008).

Note that (\delta)13C also varies with photosynthetic subtype in C4 plants and with rainfall and water availability in woody C3 plants (Cerling & Harris 1999, Diefendorf et al. 2010, Kohn 2010). Currently, grassmapr functions neglect these secondary sources of spatial variation.

Installation

The grassmapr package is hosted on GitHub. You can install the latest released version using devtools1:

install.packages("devtools")
devtools::install_github(repo = "rebeccalpowell/grassmapr")

Example usage

For a detailed guide to using grassmapr, see the vignette included with package installation. Examples of commented scripts are provided in the main-level folder. Data included in these examples are installed with the grassmapr package.

License

The grassmapr package is free and open source software; you may redistribute and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This package is distributed without any warranty, without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

Citation

To cite package grassmapr in publications, use:

Powell, R. L. et al. 2019. grassmapr, an R package to predict C3/C4 grass distributions and model terrestrial (\delta)13C isoscapes. https://github.com/rebeccalpowell/grassmapr

References

Bowen, G. J. and West, J. B. 2008. Isotope landscapes for terrestrial migration research. – In: Hobson, K. A. and Wassenaar, L. I. (eds.), Tracking Animal Migration with Stable Isotopes. Academic, pp. 79-105.

Cerling, T. E. and Harris, J. M. 1999. Carbon isotope fractionation between diet and bioapatite in ungulate mammals and implications for ecological and paleoecological studies. – Oecologia 120: 347-363.

Collatz, G. J. et al. 1998. Effects of climate and atmospheric CO2 partial pressure on the global distribution of C4 grasses: present, past, and future. – Oecologia 114: 441-454.

Diefendorf, A. F. et al. 2010. Global patterns in leaf (\delta)13C discrimination and implications for studies of past and future climate. – Proc. Natl. Acad. Sci. 107: 5738–43.

Ehleringer, J. R. et al. 1997. C4 photosynthesis, atmospheric CO2, and climate. – Oecologia 112: 285-299.

Griffith, D. M. et al. 2015. Biogeographically distinct controls on C3 and C4 grass distributions: merging community and physiological ecology. – Global Ecol. Biogeogr. 24: 304-313.

Hobson, K. A. 1999. Tracing origins and migration of wildlife using stable isotopes: a review. – Oecologia 120: 314-326.

Kohn, Matthew J. 2010. Carbon isotope compositions of terrestrial C3 plants as indicators of (paleo) ecology and (paleo) climate. – Proc. Natl. Acad. Sci. 107: 19691–19695.

Powell, R. L. et al. 2012. Vegetation and soil carbon-13 isoscapes for South America: integrating remote sensing and ecosystem isotope measurements. – Ecosphere 3: 109.

Still, C. J. et al. 2003. Global distribution of C3 and C4 vegetation: carbon cycle implications. – Global Biogeochem. Cycles 17: 1006.

1 Package devtools is available from GitHub: https://github.com/r-lib/devtools, or from CRAN: https://cran.r-project.org/web/packages/devtools/index.html

rebeccalpowell/grassmapr documentation built on June 20, 2019, 8:07 p.m.