ezsperry

This package is an R wrapper around the C version of Sperry's stomatal optimization model, found in this 2017 paper and this 2019 paper, among others.

installation

devtools::install_github("rileyleff/ezSperry-beta")

import

library("ezsperry")

quickstart examples

Run with defaults:

# import the package
library(ezsperry)

# create new model with default parameters and data
foo = new_sperry_model()

# run the model and save output to a variable
bar = run_sperry(foo)

# take a gander at the outputs
plot(bar$posi, bar$tree_e, t = "l")

Run with custom params:

library(ezsperry)
foo = new_sperry_model()
foo@Parameters@Photosynthesis@jmax = 110
foo@Parameters@Photsynthesis@vmax = 60
foo@Parameters@weibull[1,'root'] = 1.25 # "b" parameter in weibull curve for root tissue
foo@Parameters@Options@rain = TRUE
bar = run_sperry(foo)

Inspect data/params:

library(ezsperry)
foo = new_sperry_model()
str(foo)

how the wrapper works

Calling new_sperry_model() instantiates a custom S4 object that contains parameters, input data, and an empty slot for outputs.

Calling run_sperry() parses the inputs and parameters, then passes them to John Sperry's C program. This program has been lightly modified to accept R Objects as inputs. After the model runs in C, it captures the outputs and brings 'em back over to R.

Sperry_Model S4 Object Structure

Slot @Parameters

Slot @data

The slot @data contains a dataframe, with columns as follows:

column name	what it is	unit	data type	optional?	notes
Year	year	years	int	no	i.e. 1997
Day	day of year	days	int	no	i.e. Feb 19th = 50
Hour	hour of day	hours	int	no	i.e. 3pm = 15
Solar	solar radiation	W/square meter	float	no
Rain	total rainfall in last hour	mm	float	yes	inclusion can be switched on/off in @Parameters@Options
Wind	average hourly wind speed	meters/second	float	no	height of wind measurement set in @Parameters@Stand@height_above_soil
Tair	average hourly air temperature	celsius	float	no
Tsoil	average hourly soil temperature	celsius	float	no
D	vapor pressure deficit	MD (kPa)	float	no
Jmax_optional	hourly measurements of jmax	umol m-2 s-1 at 25C	float	yes	overrides model's internal jmax calculation, overrides temperature effects on jmax. requires @Parameters@Options@weibin_mode = TRUE
Vmax_optional	hourly measurements of vmax	umol m-2 s-1 at 25C	float	yes	overrides model's internal vmax calculation, overrides temperature effects on vmax. requires @Parameters@Options@weibin_mode = TRUE
Lai_optional	hourly measurements of LAI	dimless	float	yes	overrides model's internal LAI calculation. requires @Parameters@Options@weibin_mode = TRUE
Swc_optional	hourly measurements of SWC	dimless	float	yes	overrides model's internal soil water content calculation. requires @Parameters@Options@alex_mode = TRUE

It's getting late, I'll add the Params & Output descriptions tomorrow, sorry for the delay.

how the model works

See the paper(s) linked at the top