8.17 Directory structure

8.17.1 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

8.17.2 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

data formats, models, and system components. These chapters are intended to provide deeper understanding of individual modules in support of both using PEcAn for science and development of the PEcAn toolbox.