SS2OMwhen empirical weight-at-age is not available
L95calculation when all age classes are mature (defaults to 1.5)
cpars$spawn_time_frac(default is beginning of year
spawn_time_frac=0). Need to check timing on order of operations if this is used together with MICE features!
Data@Vuln_CALin generating CAL samples.
Data@Vuln_CAAis not currently implemented
CAL_nsampand other sample size data across stocks in
MSE@Histnow includes slots
MSE@Nslot to include age and area dimensions.
MMSE@Nslot to include age and area dimensions.
multiMSEto report N-at-age in
MOM@SexPars$share_par = FALSEargument that turns off parameter mirroring of stock-recruit, depletion parameters; fleet parameters related to effort trends; and all observation/implementation parameters. This can be used to generalize a 2-sex MOM to a multi-stock model with shared spawning output (
SexPars$SSBfrom) and/or movement-at-age between stocks (
devtoolsfrom Suggests and replace with
multiMSE. To run MPs in parallel, specify a named list with the name of the MP(s) assigned as TRUE. For example,
Lag_Datafunction to be used internally in custom MPs to lag all time-series data by specified number of time-steps (or optionally only some data slots). See
?Lag_Datafor more information.
cpars. This allows mapping of simulated data across stocks in
MOMswhere the real data is not stock-specific; e.g., cases where
MOMincludes male and female stocks but the real data in
cpars$Datais not sex-specific
runMSEcan use the split-apply-combine technique to run projections in parallel with argument
parallel = "sac". Implementation details and notable issues are documented in the help doc
?runMSE. This is the fastest method for running simulations but may not be suitable for all operating models and it may be more difficult to troubleshoot errors.
multiHistobject (now only returns biological information for fleet=1)
gettaxafunction for species that are found in FishBase database but not in FishLife database
runMSEcalculates vulnerable biomass from fishery weight at age
0.5 * VBiomass(a legacy feature which is now removed). The constraint is updated to
0.999 * Biomass.
OMcompleteness and default values for some parameters
runMSEcan takes a named list of MPs
ASAP2OMto import assessments into operating models
Assess2MOMto generate a multi-fleet operating model, either for a 2-sex population where recruitment is predicted from female spawning output, or a single-sex population.
Assess2OMsupports Ricker stock-recruit relationship.
MOM(introduced in 3.4.0)
SSB_P, etc.) during closed-loop
usethisfor console messages
makeMOMwith methods for developing MICE relationships, e.g., density-dependent M.
Wt_age_Cfor catch fraction calculations.
runMSEcan 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.
multiMSEwhen growth and natural mortality are time-varying. Internal code in
popdynOneMICEwas updated for better readability, i.e., removing obsolete/redundant code and better references for array dimensions.
Awatea2OMto import MCMC output from an Awatea assessment model to openMSE
SS2OMis one. The issue was noticeable when the autocorrelation is high.
SSMOM2OMwhere selectivity was NA when fishing mortality was 0
SSMOM2OMwhere it was generating redundant rec devs
control$D <- 'SBMSY'
OM@cpars$control$CAL="removals". Default is to simulate only retained catch-at-length.
OM@cpars$control$TAC="removals". Default is to for TAC to refer to retained catch (i.e., removals will be greater than TAC if there are discards)
Obsobjects (many thanks to Sarah Valencia).
VI_betafor the individual indices. Defaults to use
OM@betafor all, unless a real index is supplied, e.g.,
OM@cpars$Data@VInd, or if supplied in cpars, e.g.,
OM@Ksdwas not implemented correctly (5e6e8c6).
cpars$Esdissue (issue #34)
This is a new major release of the
MSEtool package. It is not backwards compatible with previous versions of
MSEtoolpackage now contains all code related to generating operating models, simulating fisheries dynamics, conducting management strategy evaluation, and examining the results (previously in the
DLMtoolpackage). This change was primarily done to better align the actual contents of the packages with the respective package names.
MSEtoolnow only has a set of reference management procedures (e.g.,
MSEtoolV3+ as a dependency; i.e., installing and loading
DLMtoolwill also install and load
MSEtooland make all functions for generating OMs, conducting MSE, etc available.
DLMtoolhad recruitment to age-1).
Dataobject now includes age-0 (i.e., all age data must be length