• New function documentation added

Major Changes

  • Added Ecosense routines and vignettes
  • Added example ecosystems
  • Added Unit Tests
  • Fixed bug in stanza month calculations that affected some species
  • Changed versioning to reflect near-release status.

Major Changes

  • Added bioenergetic code
  • adjust functions can now supply values by individual months rather than by years

Major Changes

  • Added BAB to multistanzas
  • adjust.scenario can be applied to multiple groups at once rather than one at a time.
  • Changed variable names to align with manuscript
    • BB to Biomass
    • CC to Catch
    • GS to Unassim
    • Catch to Landings
    • Recruits from r to R
    • WWa to QageS
    • surv to survive_L
    • B to Biomass in Pedigree param list
    • All “byx” functions to “ForcedX”
    • EFFORT to ForcedEffort
    • CATCH and FRATE to ForcedCatch and ForcedFRate
  • Change default values of scramble flags from 1 to 0. Zero indicating the flag is off, 1 indicating it is on.
  • Fixed mixotroph diet calculations and MTI calculation.
  • Acknowledgement of package submission along with manuscript
  • Fixed bug with adjust.fishing so one value can be applied over a range of sim.years
  • Fixed bug with original scenario file and stanza files being overwritten by C code.
  • Fixed bug with egg stanza calculation where the Wmat matrix was indexed wrong inthe calculation.
  • 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.
  • Fixed indexing issue with rsim.step and issue with rsim.run modifying initial rsim.scenario data table.
  • 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)
  • Added gear specific catch tracking and new extract.node function.
  • Caught up with Kerim’s edits.
  • Data.table package updated and created a few bugs that have been solved.
  • 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

The initial files were 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.