MSEtool v3.4.0

MSEtool 3.4.0

New additions

• new functions makeRel and makeMOM with methods for developing MICE relationships, e.g., density-dependent M.
• depletion optimization in multiMSE uses Wt_age_C for catch fraction calculations.
• argument parallel in runMSE can now be MP-specific by specifying a logical vector of length(MPs). This is useful to apply slow-running MPs in parallel, while avoiding the parallel overhead time for fast-running MPs.

Fixes

• fix bug in re-calculation of MSY refs points when selectivity parameters change (introduced in last version)
• fix indexing in multiMSE when growth and natural mortality are time-varying. Internal code in HistMICE, qestMICE, popdynMICE and popdynOneMICE was updated for better readability, i.e., removing obsolete/redundant code and better references for array dimensions.

Minor changes

• add progress bar when knitting OM.rmd in Shiny
• edits to make compatible with latest version of rfishbase