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Release Notes
kaydin edited this page Jun 5, 2024
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5 revisions
- New function documentation added
- 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.
- Added bioenergetic code
- adjust functions can now supply values by individual months rather than by years
- 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.