The code works up to hdf5save function.
Merge branch 'master' of github.com:PecanProject/pecan
h5 output works, working on fixing the base year
Merge pull request #138 from mdietze/master

updates to met2CF.csv
Merge branch 'master' of github.com:PecanProject/pecan
Conversion from .nc to .h5 works. Checking the output. There are some missing months in output.
Merge pull request #139 from apourmok/master

met2model.ED2 conversion works
drop schema instead of database
force encoding to be UTF-8
The function works and gives the output. Checked the output and they are correct. The problem with dimension of matrix is solved in general form so it can read in files with different time step.
Added optional overwrite function in case the user wants to overwrite existing files in Outfolder.
Overwriting option added as part of the function.
Merge pull request #142 from apourmok/master

The function works and gives correct output.
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.