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README.md

Rpath

This is the repository for Rpath - the R version of the Ecopath with Ecosim model

The initial files are the code sent by Kerim to Sean on March 31, 2014 (ecopath_sim_r_v0_04_toSean_31_03_14.zip) Files have been renamed to drop the version number and take advantage of this VCS

Beta version notes:

v0.0.0.916 - Fixed bug with original scenario file and stanza files being overwritten by C code.

v0.0.0.915 - Fixed bug with egg stanza calculation where the Wmat matrix was indexed wrong inthe calculation.

v0.0.0.9014 - Updated adjustment functions. Renamed parameter "year" to "sim.year". Removed the "gear" parameter from adjust fishing as it is a group and there is never a group/fleet combo that needs to be specified.

v0.0.0.9013 - Fixed indexing issue with rsim.step and issue with rsim.run modifying initial rsim.scenario data table.

v0.0.0.911 - ecosim scenario objects now parameterized with a vector of years for labeling, e.g. years=c(1970,2017), not a single number of years.

  • rsim.run will run for the years specified (e.g. years=c(2013,2014) will save outputs in those two year slots). Haven't carried this change over to the multistep function.
  • labeling in the fishing/forcing matrices (columns labelled by species, rows labeled by years (for annual matrices, no labeling for monthly rows)
  • the addition of force_bybio (biomass forced to stay at input value)

v0.0.0.906 - Added gear specific catch tracking and new extract.node function.

v0.0.0.905 - Caught up with Kerim's edits.

v0.0.0.904 - Data.table package updated and created a few bugs that have been solved.

v0.0.0.903 - Fixed issue with consumption calculations due to the addition of diet import in the diet matrix.

Did not keep good track of notes prior to version 0.0.0.9003 - My Bad