MSEtool 3.3.9999 - Development Version

Fixes

  • fix bug in re-calculation of MSY refs points when selectivity parameters change (introduced in last version)

Minor changes

  • add progress bar when knitting OM.rmd in Shiny

MSEtool 3.3.0

New additions

  • added Awatea2OM to import MCMC output from an Awatea assessment model to openMSE
  • reference points are now calculated assuming constant stock-recruit alpha and beta parameters. Previously, constant R0 and steepness was assumed. See (https://openmse.com/tutorial-reference-points/) for more details.

Fixes

  • fix minor bug in calculating SSB in first year when using OMs imported from SS3
  • fix minor bug when passing movement matrix in with cpars
  • fix minor bug so that the mean of sampled recruitment deviations in SS2MOM and SS2OM is one. The issue was noticeable when the autocorrelation is high.
  • add check for missing OM slots such as interval, pstar, nyears, etc

Minor changes

  • update plot_mov for plotting movement matrices.
  • ProjectMOM and multiMSE now drop the multiHist object from the MMSE object unless argument dropHist=FALSE

MSEtool 3.2.0

Fixes

  • fix issue in SSMOM2OM where selectivity was NA when fishing mortality was 0
  • remove debugging message that was stupidly left in last release

Minor changes

  • add silent option to SS2Data

New additions

  • add option to include fecundity-at-age used to calculate spawning biomass (cpars$Fec_age)

MSEtool 3.1.1

Fixes

  • patch bug in generation of size composition data (introduced in v3.1.0)
  • fix minor issue with SSMOM2OM where it was generating redundant rec devs

New additions

  • added plot_SS2MOM to compare MOM dynamics with SS3 predictions

MSEtool 3.1.0

New additions

  • Dynamic and equilibrium spawning potential ratio (SPR) are now calculated for the historical and projection years.
  • add option to include empirical weight-at-age for the catches with cpars$Wt_age_C
  • F_crash, F_med, and other reference points have been added to Hist@Ref$ByYear
  • can now optimize for depletion in terms of SB/SBMSY with control$D <- 'SBMSY'
  • option to simulate CAL data including removals (retained + discards) with OM@cpars$control$CAL="removals". Default is to simulate only retained catch-at-length.
  • option to apply TAC to all removals with OM@cpars$control$TAC="removals". Default is to for TAC to refer to retained catch (i.e., removals will be greater than TAC if there are discards)

Minor changes

  • add more informative messages when conditioning on real data
  • add conditioning on real data for multiMSE
  • MSY calculations now in C++ for significant speed increase

Fixes

  • fix the plus-group calculations in popdynOneTScpp
  • fix issue with simulated index in AddInd in the projection years

MSEtool 3.0.2

Updates

  • Help description has been updated for Stock, Fleet, and Obs objects (many thanks to Sarah Valencia).

Fixes

  • fix minor bugs in XL2Data for importing data from CSV

MSEtool 3.0.1

Minor Changes

  • Add I_beta, SpI_beta, and VI_beta for the individual indices. Defaults to use OM@beta for all, unless a real index is supplied, e.g., OM@cpars$Data@Ind, OM@cpars$Data@SpInd, or OM@cpars$Data@VInd, or if supplied in cpars, e.g., OM@cpars$I_beta

Fixes

  • fix bug where variability in von Bert K with OM@Ksd was not implemented correctly (5e6e8c6).
  • fix error with incorrect beta values when conditioning with real index (ie )
  • fix randomly occurring bug in C++ code that was causing crashes
  • fix issue with importing composition data with new('Data',..) (issue #33)
  • fix cpars$beta and cpars$Esd issue (issue #34)
  • fix issue with importing Data files from csv

MSEtool 3.0.0

This is a new major release of the MSEtool package. It is not backwards compatible with previous versions of MSEtool or DLMtool.

Major Changes

  • The most significant change in this version is that the MSEtool package now contains all code related to generating operating models, simulating fisheries dynamics, conducting management strategy evaluation, and examining the results (previously in the DLMtool package). This change was primarily done to better align the actual contents of the packages with the respective package names.
  • MSEtool now only has a set of reference management procedures (e.g., FMSYref)
  • The Data-Limited Methods Toolkit package now contains the collection of data-limited methods, and uses MSEtool V3+ as a dependency; i.e., installing and loading DLMtool will also install and load MSEtool and make all functions for generating OMs, conducting MSE, etc available.
  • The operating model has been updated and an age-0 age-class has been added to the population dynamics model; i.e., recruitment is now to age-0 (previously the OM in DLMtool had recruitment to age-1).
  • The catch-at-age (CAA) in the Data object now includes age-0 (i.e., all age data must be length maxage+1)