NEWS.md
In pzylstra/frame_r: Fire Research and Modelling Environment

NEWS

Removed public function ffm_db_connect (returned a DBI connection object) and replaced it with a private helper function used by ffm_db_load and ffm_db_summary.

Fixed bug in ffm_run when parameters are incomplete.

Function readLegacyParamFile has been deprecated. New code should now use ffm_read_legacy_params.
Added function ffm_write_params to write parameters to file as a CSV-format table. This is just a simple wrapper that calls write.csv with appropriate default arguments and optionally checks parameters before writing.

Functions ffm_run and ffm_run_command now attempt to deal with embedded spaces in paths and file names.

Removed dependency on the rScala package. Function ffm_run is now a simple function (rather than an S3 generic). It passes simulation parameters and details of the output database to the external Scala application via a temporary file and system call. When the function is run with an existing output file specified, users can select between adding simulation results to the existing database as new replicates, or discarding previous results.
Updated Java JAR files for version 0.2 of the Scala application and its dependencies.
Added function ffm_check_java to check that Java version 1.8 (aka Java 8) or higher is installed and accessible from the command line. This check is run the first time that ffm_run is called during a session.
Added function ffm_check_params to test whether all required parameters have been provided for the simulation.
The data frame DefaultSpeciesParams has been removed from the package to avoid clashes with default data provided by the user. A data frame of default parameter values can now be passed to function ffm_run which will call ffm_complete_params. Alternatively, the user can call ffm_complete_params directly before running the simulation.
Function ffm_complete_params now allows for species to appear in more than one stratum and, where this is the case, each species occurrence is considered separately. Default values for a given parameter may now be specified for just a subset of the species included in the defaults data frame, with others having NA values.
Functions to work with the copy of DefaultSpeciesParams previously included in the package, such as ffm_find_species and ffm_species_known have been removed.