22.4 Meta Analysis

22.4.1 run.meta.analysis()

The meta-analysis code begins by distilling the trait.data to just the values needed for the meta-analysis statistical model, with this being stored in madata.Rdata. This reduced form includes the conversion of all error statistics into precision (1/variance), and the indexing of sites, treatments, and greenhouse. In reality, the core meta-analysis code can be run independent of the trait database as long as input data is correctly formatted into the form shown in madata.

The evaluation of the meta-analysis is done using a Bayesian statistical software package called JAGS that is called by the R code. For each trait, the R code will generate a [trait].model.bug file that is the JAGS code for the meta-analysis itself. This code is generated on the fly, with PEcAn adding or subtracting the site, treatment, and greenhouse terms depending upon the presence of these effects in the data itself.

Meta-analyses are run, and summary plots are produced.