NEWS

Rpath 1.2.0

Changed to log integration smoother instead of linear smoother for catch output calculations for better catch output accuracy, especially during rapid biomass changes. This may change previous catch outputs by a few percent. This does not change the biomass removed in a model step, but changes the output catch values.
Applying biomass forcing via ForceBio to multistanza groups has no current effect, but the model was reporting forced outputs without actually changing biomass. Attempting to force multistanza groups with ForceBio now results in an error.

Added functionality to fit rsim runs to observed biomass and catch data, using optim().
Added plotting functions designed to show fit results.
Added spawning-stock biomass outputs for multistanza groups.
Added output diagnostics options to rsim.run(), including output of derivative parts for selected species, and more detailed multistanza outputs of weight and numbers.
Added more informative warning/error messages to some functions.

Added ability to import .eiixml files via the create.rpath.from.eiixml() function
Added balance functionality to estimate P/B from input Biomass and EE, also allowing a missing Q/B to be estimated from input PC and the estimated P/B
Corrected accounting for single-stage interdetrital flows during balance
Behavior change: if all of P/B, Q/B, and PC are supplied as inputs for a group, recalculate PC during balance to ensure internal model consistency (instead of leaving PC unchanged and possibly inaccurate)
Improved error messages in rpath() balance routine to help diagnose models that are missing parameters
Improved warning message content in check.rpath.params() to aid diagnosis
Modified rpath.stanzas() so it no longer produces errors when called with a model that has no multistanza groups (instead it returns the model unchanged)
Added Western Bering Sea model .eiixml and EwE output csv files as an import example
Added Convert_EwE_to_Rpath vignette to describe .eiixml import process
Tested eiixml input routines on over 150 models available via EcoBase with most producing consistent results between Rpath and EwE; some remaining balancing differences between Rpath and EwE are noted in the Convert_EwE_to_Rpath vignette
Fixed some table ordering issues with stanza inputs
Documentation fixes

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.

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.