| Title: | PEcAn functions used for leaf-level photosynthesis calculations |
|---|---|
| Description: | The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. The PEcAn.photosynthesis package contains functions used in the Hierarchical Bayesian calibration of the Farquhar et al 1980 model. |
| Authors: | Mike Dietze [aut, cre], Xiaohui Feng [aut], Shawn Serbin [aut], Shashank Singh [aut], Chris Black [ctb], University of Illinois, NCSA [cph] |
| Maintainer: | Mike Dietze <[email protected]> |
| License: | BSD_3_clause + file LICENSE |
| Version: | 1.7.3.9000 |
| Built: | 2024-11-20 22:22:44 UTC |
| Source: | https://github.com/PecanProject/pecan |
estimate_mode
estimate_mode(x, adjust = 0.1)estimate_mode(x, adjust = 0.1)
x |
numeric values |
adjust |
passed to stats::density |
Mike Dietze
Xiaohui Feng
fitA
fitA(flux.data, cov.data = NULL, model = NULL)fitA(flux.data, cov.data = NULL, model = NULL)
flux.data |
data.frame of Licor data, concatenated by rows, and with a leading column 'fname' that is used to count the number of curves and match to covariates |
cov.data |
data.frame of covariate data. Column names used in formulas |
model |
list including at least 6 components: the fixed effects model for alpha (a.fixed) and Vcmax (V.fixed), the random effects for these (a.random, V.random), the variable used to match the gas-exchange and covariate data (match), and the number of MCMC interations (n.iter). Additional optional arguments: TPU = TRUE turns on TPU limitation; Temp == 'Bernacchi01' turns on the Bernacchi et al 2001 temperature correction. If this is turned on all parameters are estimated for 25C, otherwise no temperature correction is applied. Setting Temp = 'June2004' will turn on the June et al 2004 Funct Plant Biol temperature correction to Jmax. Note: these two corrections are not mutually exclusive, you can set Temp = c('June2004','Bernacchi2001') Right now the fixed effects are specified as a string using the standard R lm formula syntax, but without the LHS variable (e.g. '~ SLA + chl + SLA:chl'). The tilde is optional. For random effects, the two options right now are just 'leaf' for leaf-level random effects and NULL. 'model' has a default that sets all effects to NULL (fit one curve to all data) and n.iter=1000. |
Mike Dietze
Xiaohui Feng
Licor_QC
Licor_QC(dat, curve = c("ACi", "AQ"), tol = 0.05)Licor_QC(dat, curve = c("ACi", "AQ"), tol = 0.05)
dat |
data frame |
curve |
Whether to do Quality Control by examining the 'ACi' curve, the 'AQ' curve, or both |
tol |
Code automatically tries to separate ACi and AQ curves in the same dataset by detecting the 'reference' condition for light and CO2 respectively. This is the relative error around the mode in that detection. |
Mike Dietze
plot_photo
plot_photo(data, out, curve = c("ACi", "AQ"), tol = 0.05, byLeaf = TRUE)plot_photo(data, out, curve = c("ACi", "AQ"), tol = 0.05, byLeaf = TRUE)
data |
input data |
out |
fitted model output from |
curve |
Whether to do Quality Control by examining the 'ACi' curve, the 'AQ' curve, or both |
tol |
Code automatically tries to separate ACi and AQ curves in the same dataset by detecting the 'reference' condition for light and CO2 respectively. This is the relative error around the mode in that detection. |
byLeaf |
whether to plot fits on a leaf-by-leaf basis |
Mike Dietze
read_Licor
read_Licor(filename, sep = "\t", ...)read_Licor(filename, sep = "\t", ...)
filename |
name of the file to read |
sep |
file delimiter. defaults to tab |
... |
optional arguements forwarded to read.table |
Mike Dietze