fitA

fitA

fitA(flux.data, cov.data = NULL, model = NULL)

Arguments

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.

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.

Arguments

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