Switch from single to double operators in ecosim.cpp
Added examples to all functions
Updated documentation/website
Added package hex
Added a bibliography file
Created issue templates
Added contributors guideline and code of conduct
Rpath 0.9.1
New function documentation added
Rpath 0.9.0
Added Ecosense routines and vignettes
Added example ecosystems
Added Unit Tests
Fixed bug in stanza month calculations that affected some species
Rpath 0.8.0
Added bioenergetic code
adjust functions can now supply values by individual months rather than by years
Rpath 0.7.0
Added CI workflows
Added/updated documentation (pkgdown)
Stanza changes
Rpath 0.6.0
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.
Rpath 0.5.1
Fixed mixotroph diet calculations and MTI calculation.
Rpath 0.5.0
Initial Release
Acknowledgement of package submission to CRAN along with manuscript (see release notes)
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.
Fixed issue with consumption calculations due to the addition of diet import in the diet matrix.
