NEWS.md

In NOAA-EDAB/Rpath: R implementation of Ecopath with Ecosim

Rpath 0.9.1

• New function documentation added

Rpath 0.9.0

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.

Rpath 0.0.1.3

Major Changes

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

Rpath 0.0.1.2

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.

Rpath 0.0.1.1

• Fixed mixotroph diet calculations and MTI calculation.

Rpath 0.0.1.0

• Acknowledgement of package submission along with manuscript

Rpath 0.0.0.917

• Fixed bug with adjust.fishing so one value can be applied over a range of sim.years

Rpath 0.0.0.916

• Fixed bug with original scenario file and stanza files being overwritten by C code.

Rpath 0.0.0.915

• Fixed bug with egg stanza calculation where the Wmat matrix was indexed wrong inthe calculation.

Rpath 0.0.0.9014

• 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.

Rpath 0.0.0.9013

• Fixed indexing issue with rsim.step and issue with rsim.run modifying initial rsim.scenario data table.

Rpath 0.0.0.911

• 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)

Rpath 0.0.0.906

• Added gear specific catch tracking and new extract.node function.

Rpath 0.0.0.905

• Caught up with Kerim's edits.

Rpath 0.0.0.904

• Data.table package updated and created a few bugs that have been solved.

Rpath 0.0.0.903

• 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

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.

NOAA-EDAB/Rpath documentation built on June 5, 2024, 9:03 p.m.