The current version of the MSEtool package is available
for download from CRAN.
addMPsPM objects when
nsim<15LinInterp_cpp when searching for values on
boundsSplot and empirical MP Empnsim argument to Simulate as an
override to OM@nsim. Useful for generating
Hist object with 2 sims when all historical values are
identical across simulationsBAM2OM to create OM from Beaufort Assessment
Model (BAM) outputmultiMSE which
can be a function of the state dynamics in either the current year or
previous yearmultiMSEmultiMSEmultiMSEspawn_time_frac argument to
iSCAM2OMmultiMSE can be time-varying if
entries in the MOM@SexPars$Herm list is an array with
dimensions nsim, maxage+1, nyears+proyearsMOM@cpars$control <- list(HermEq = FALSE) sidesteps
the first-year equilibrium age and sex distribution calculation from the
hermaphroditic age schedulecpars$control options in
help("validcpars")dynGet then get to find
the MPs in the R session (see function getMP).
dynGet finds functions that are defined inside the function
call stack but not available in the global environment.plot_SS2MOM for latest version of
r4ssMMSE@SB_SBMSY for MMSE
objectsOMdoccpars$qs to OM produce by
SS2OMSS2OM does not return
cpars$DataretL when retA passed
in cparsspawn_time_frac used in
multiMSECalc_Residuals when not estimating beta
parameterpopdyn.R to include
discard mortalitySubCpars for MOM objectsOM@h) to exceed 1 for Ricker
stock-recruit relationship (the simulated steepness value in the Data
object will be
Data@steep = rlnorm(OM@nsim, log(StockPars$hs - 0.2), sdconv(1, Obs@hbiascv)) + 0.2 - 0.5 * sdconv(1, Obs@hbiascv)^2.Assess2OM utilizes spawn_time_fracSS2OM when empirical weight-at-age is not
availableL95 calculation when all age classes are
mature (defaults to 1.5)OM.Rmdcpars$spawn_time_frac (default is beginning of year
spawn_time_frac=0). Need to check timing on order of
operations if this is used together with MICE features!Data@Vuln_CAL in generating CAL samples.
Data@Vuln_CAA is not currently implementedCAL_nsamp and other sample size data
across stocks in MOMMSE@Hist now includes slots AtAge and
TSdata when extended=FALSEMSE@N slot to include age and area
dimensions.MMSE@N slot to include age and area
dimensions.extended argument to multiMSE to
report N-at-age in MMSE@Misc$extended$NMOM@SexPars$share_par = FALSE argument
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$SSBfrom) and/or movement-at-age between stocks
(SexPars$Herm).SS2OM when empirical weight-at-age is not
availableL95 calculation when all age classes are
mature (defaults to 1.5)OM.Rmdplot.DataMisc information to PPD for
MMSEdevtools from Suggests and replace with
remotesSS2MOM_plots plotsSS2DataSSMOM2OMSS2OM in
SSinternalSS2MOM_plotsL95array when Mat_age
passed in through cparsSS2OM when
report=TRUEparallel=TRUE in runMSE and
multiMSE. To run MPs in parallel, specify a named list with
the name of the MP(s) assigned as TRUE. For
example,parallel=list(AvC=TRUE).summary.MMSE generic functionLag_Data function 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_Data for more
information.MOM) to
(multiHist)Real.Data.Map to cpars. This allows
mapping of simulated data across stocks in MOMs where the
real data is not stock-specific; e.g., cases where MOM
includes male and female stocks but the real data in
cpars$Data is not sex-specificrunMSE can use the split-apply-combine technique to run
projections in parallel with argument parallel = "sac".
Implementation details and notable issues are documented in the help doc
?runMSE. This is the fastest method for running simulations
but may not be suitable for all operating models and it may be more
difficult to troubleshoot errors.ASAP2DataAssess2OMmultiHist object (now
only returns biological information for fleet=1)gettaxa function for species that are found in
FishBase database but not in FishLife databasejoinData, joinHist,
joinMSE, and addMPs functionsrunMSE calculates vulnerable biomass from fishery
weight at age cpars$Wt_age_C if provided.0.5 * VBiomass (a legacy feature which is now removed). The
constraint is updated to 0.999 * Biomass.OM completeness and default values for
some parametersmultiMSEparallel in runMSE can takes a
named list of MPsWHAM2OM and ASAP2OM to
import assessments into operating modelsAssess2MOM to 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.Assess2OM supports Ricker stock-recruit
relationship.MMPsOM@cpars$Len_age is provided.MOM (introduced in
3.4.0)Data@Misc$StockPars (slot N_P,
SSB_P, etc.) during closed-loopusethis for console messagesmakeRel and makeMOM with
methods for developing MICE relationships, e.g., density-dependent
M.multiMSE uses
Wt_age_C for catch fraction calculations.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.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.rfishbaseAwatea2OM to import MCMC output from an Awatea
assessment model to openMSESS2MOM and SS2OM is one. The issue was
noticeable when the autocorrelation is high.plot_mov for plotting movement matrices.ProjectMOM and multiMSE now drop the
multiHist object from the MMSE object unless
argument dropHist=FALSESSMOM2OM where selectivity was NA when
fishing mortality was 0silent option to SS2Datacpars$Fec_age)SSMOM2OM where it was generating
redundant rec devsplot_SS2MOM to compare MOM dynamics with SS3
predictionscpars$Wt_age_CHist@Ref$ByYearcontrol$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)multiMSEpopdynOneTScppAddInd in the
projection yearsStock,
Fleet, and Obs objects (many thanks to Sarah
Valencia).XL2Data for importing data from
CSVI_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_betaOM@Ksd was not implemented correctly (5e6e8c6).new('Data',..) (issue #33)cpars$beta and cpars$Esd issue (issue
#34)This is a new major release of the MSEtool package. It
is not backwards compatible with previous versions of
MSEtool or DLMtool.
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)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.DLMtool had recruitment to
age-1).Data object now includes
age-0 (i.e., all age data must be length maxage+1)