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# The bigleaf R package

**bigleaf** is an R package for the 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.
All calculations are based on a 'big-leaf' representation of the vegetation and return representative bulk ecosystem/canopy variables.

## Citation

Knauer J, El-Madany TS, Zaehle S, Migliavacca M (2018) Bigleafâ€”An R package for the calculation of physical and physiological ecosystem properties from eddy covariance data. PLoS ONE 13(8): e0201114. https://doi.org/10.1371/journal.pone.0201114

## Installation

The bigleaf R package is on CRAN and can be installed using:

install.packages("bigleaf")

The development version can be directly installed from this bitbucket repository:

library(devtools) install_bitbucket("juergenknauer/bigleaf")

## Usage

Most functions work by providing a data.frame or matrix which contains all required variables: For example, surface conductance for the spruce forest in Tharandt, Germany (DE-Tha) can be calculated with the following commands:

DE_Tha_June_2014$Ga <- aerodynamic.conductance(DE_Tha_June_2014,Tair="Tair",pressure="pressure",wind="wind",ustar="ustar")[,"Ga_h"] surface.conductance(DE_Tha_June_2014,Tair="Tair",pressure="pressure",Rn="Rn",VPD="VPD",LE="LE",Ga="Ga") surface.conductance(DE_Tha_June_2014,Tair="Tair",pressure="pressure",Rn="Rn",VPD="VPD",LE="LE",Ga=0.1)

Here, DE_Tha_June_2014 denotes the input data.frame. Note that input variables can be provided as column names of the input data.frame (as argument Ga in line 2 above), or alternatively, as vectors with the same length as the input data.frame or of length 1 (as argument Ga in line 3 above). If variables are provided in the default column names (as above), the command can be shortened to:

surface.conductance(DE_Tha_June_2014)

Important: please ensure that all input variables are in the correct units as described on the help pages.

Please report bugs or issues here

## Package content

The package provides the following functionalities:

### Data filtering

- data quality filter
- filter based on meteorological variables (radiation, precipitation, ustar, temperature, etc.)
- growing season filter (based on daily GPP)

### Meteorological variables

- air density
- virtual temperature
- pressure from altitude
- psychrometric constant
- latent heat of vaporization
- saturation vapor pressure
- slope of saturation vapor pressure curve

### Aerodynamic properties

- aerodynamic conductance (different versions) for momentum, water, heat, and CO2
- Canopy boundary-layer conductance (Rb and kB-1 parameter; empirical and physically-based models)
- Monin-Obhukov length
- stability parameter zeta
- stability correction functions (different versions)
- roughness length for momentum (z0m) and heat (z0h)
- decoupling coefficient 'omega'
- Reynolds number
- wind speed at a given height from the logarithmic wind profile equation

### Surface conditions

- vapor pressure, specific humidity, and VPD at the big-leaf surface
- CO2 concentration at the big-leaf surface
- aerodynamic surface temperature
- radiometric surface temperature

### Evapotranspiration (ET) and water-use efficiency (WUE)

- potential ET (Priestley-Taylor and Penman-Monteith equations)
- imposed and equilibrum ET
- WUE, inherent WUE, underlying WUE

### Physiological variables

- canopy conductance (inverted Penman-Monteith equation)
- bulk intercellular CO2 concentration (Ci)
- bulk photosynthetic capacity (Vcmax25 and Jmax25)
- stomatal slope parameter g1 (USO, Ball&Berry, Leuning models)
- stomatal sensitivity to VPD
- ecosystem light response, light-use efficiency

### Energy balance

- energy balance closure (EBR and slope method)
- biochemical energy
- energy-use efficiency

### Unit conversions

- conductance conversion from m s-1 to mol m-2 s-1 and vice versa
- conversions between humidity measures (vapor pressure, specific humidity, relative humidity, and VPD)
- conversion between latent heat flux (W m-2) and evapotranspiration (kg m-2 s-1)
- conversion between radiation in W m-2 and umol m-2 s-1
- carbon fluxes from umol m-2 s-1 to g m-2 day-1

## Contact

For questions, remarks, and suggestions please contact jknauer@bgc-jena.mpg.de