9.3 Directory structure

9.3.1 Overview of PEcAn repository as of PEcAn 1.5.3

pecan/
 +- base/          # Core functions
    +- all         # Dummy package to load all PEcAn R packages
    +- db          # Modules for querying the database
    +- logger      # Report warnings without killing workflows
    +- qaqc        # Model skill testing and integration testing
    +- remote      # Communicate with and execute models on local and remote hosts
    +- settings    # Functions to read and manipulate PEcAn settings files
    +- utils       # Misc. utility functions
    +- visualization # Advanced PEcAn visualization module
    +- workflow    # functions to coordinate analysis steps
 +- book_source/   # Main documentation and developer's guide
 +- CHANGELOG.md   # Running log of changes in each version of PEcAn
 +- docker/        # Experimental replacement for PEcAn virtual machine
 +- documentation  # index_vm.html, references, other misc.
 +- models/        # Wrappers to run models within PEcAn
    +- ed/         # Wrapper scripts for running ED within PEcAn
    +- sipnet/     # Wrapper scripts for running SIPNET within PEcAn
    +- ...         # Wrapper scripts for running [...] within PEcAn
    +- template/   # Sample wrappers to copy and modify when adding a new model
 +- modules        # Core modules
    +- allometry
    +- data.atmosphere
    +- data.hydrology
    +- data.land
    +- meta.analysis
    +- priors
    +- rtm
    +- uncertainty
    +- ...
 +- scripts        # R and Shell scripts for use with PEcAn
 +- shiny/         # Interactive visualization of model results
 +- tests/         # Settings files for host-specific integration tests
 +- web            # Main PEcAn website files

9.3.2 Generic R package structure:

see the R development wiki for more information on writing code and adding data.

 +- DESCRIPTION    # short description of the PEcAn library
 +- R/             # location of R source code
 +- man/           # Documentation (automatically compiled by Roxygen)
 +- inst/          # files to be installed with package that aren't R functions
    +- extdata/    # misc. data files (in misc. formats)
 +- data/          # data used in testing and examples (saved as *.RData or *.rda files)
 +- NAMESPACE      # declaration of package imports and exports (automatically compiled by Roxygen)
 +- tests/         # PEcAn testing scripts
   +- testthat/    # nearly all tests should use the testthat framework and live here