module photosynthesis: the function 'fitA' is my initial attempt to generalize Sunny's code for fitting FvCB model. It takes 3 arguements, the gas exchange data, the covariate data, and a list of model settings. That list includes 5 components: the fixed effects model for alpha (a.fixed) and Vcmax (V.fixed), the random effects for these (a.random, V.random), and the number of MCMC interations (n.iter). 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. However, at this instant I haven't tested this since I don't have a good covariates file from Sharma yet and still need to write the code that matches between fluxes and covariates. 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.

There is also a function read.Licor that parses text-exported Licor files into the format expected by the function. The file test.fitA.R has an example of using this function and merging a bunch of Licor files together.
fitA: added a bit of documentation. Increased the default MCMC to 5000

read.Licor: Modified to have "sep" as an arguement (default is TAB) and to have ellipsis arguement that is passed to read.table.
photosynthesis: small fixes to get the module to compile as part of PEcAn.all
Merge branch 'master' of github.com:PecanProject/pecan
Merge pull request #143 from mdietze/master

Photosynthesis Module