API for Blue-Matter/MSEtool
Management Strategy Evaluation Toolkit

Global functions
AAVE	Man page Source code
AAVY	Man page Source code
ASAP2Data	Man page Source code
ASAP2OM	Man page Source code
AddRealData	Source code
AddRealData_MS	Source code
Add_predictive	Source code
Albacore	Man page
Albacore_TwoFleet	Man page
Assess2MOM	Man page Source code
Assess2OM	Man page Source code
Atlantic_mackerel	Man page
Awatea2OM	Man page Source code
AwateaRead	Source code
AwateaSel	Source code
BAM2MOM	Man page Source code
BAM2OM	Man page Source code
BlankSelPlot	Man page Source code
Blow_opt	Man page Source code
Blue_shark	Man page
Bluefin_tuna	Man page
Bluefin_tuna_WAtl	Man page
Butterfish	Man page
CALsimp	Man page Source code
COSEWIC_Blow	Man page Source code
COSEWIC_Dplot	Man page Source code
COSEWIC_Hplot	Man page Source code
COSEWIC_Pplot	Man page Source code
COSEWIC_report	Man page Source code
COSEWIC_tab	Man page Source code
COSEWIC_tab_formatted	Man page Source code
CSRA	Man page Source code
CSRAfunc	Man page Source code
CalcAsymptoticDist	Man page Source code
CalcDistribution	Source code
CalcMPDynamics	Man page Source code
CalcMSYRefs	Source code
CalcSPRdyn	Source code
CalcSPReq	Source code
CalcUnfishedRefs	Source code
Calc_Residuals	Source code
Calc_Stats	Source code
CalculateQ	Man page Source code
Can	Man page Source code
Cant	Man page Source code
CheckDuplicate	Man page Source code
CheckMPs	Man page Source code
CheckOM	Man page Source code
CheckSelect	Source code
Check_custom_SRR	Source code
China_rockfish	Man page
Chk	Source code
ChkYrs	Man page Source code
Choose	Man page
ChooseEffort	Man page Source code
ChooseL5	Source code
ChooseLFS	Source code
ChooseM	Man page Source code
ChooseSelect	Man page Source code
ChooseVmaxlen	Source code
Cobia	Man page
CombineMMP	Man page Source code
Converge	Man page Source code
Cos_thresh_tab	Man page Source code
Cplot	Man page Source code
DFO_Dplot	Source code
DFO_Kobe	Source code
DFO_Kobe_TS	Source code
DFO_bar	Man page Source code
DFO_cbar	Source code
DFO_cosplot	Source code
DFO_hist	Man page Source code
DFO_plot	Man page Source code
DFO_plot2	Man page Source code
DFO_proj	Man page Source code
DFO_quant	Man page Source code
DFO_report	Man page Source code
DFO_spider	Man page Source code
DFO_tab	Man page Source code
DFO_tab_formatted	Man page Source code
DLMDataDir	Man page Source code
DLMdiag	Man page Source code
Data-class	Man page
Data-class-objects	Man page
Data2csv	Man page Source code
DataDescription	Man page
DataDir	Man page Source code
DataInit	Man page Source code
DataSlots	Man page
Data_xl	Man page Source code
DecE_Dom	Man page
DecE_HDom	Man page
DecE_NDom	Man page
Dom	Man page Source code
Emp	Man page
Example_datafile	Man page
Export_customMPs	Source code
FMSYref	Man page Source code
FMSYref50	Man page Source code
FMSYref75	Man page Source code
Fease	Man page Source code
Fit_Index	Source code
Fit_Index_MS	Source code
FlatE_Dom	Man page
FlatE_HDom	Man page
FlatE_NDom	Man page
Fleet-class	Man page
Fleet-class-objects	Man page
FleetDescription	Man page
Gen_Residuals	Source code
GenerateRandomWalk	Man page Source code
Generic_DecE	Man page
Generic_FlatE	Man page
Generic_Fleet	Man page
Generic_IncE	Man page
Generic_Obs	Man page
Gulf_blue_tilefish	Man page
Herm-int	Man page
Herring	Man page
Hist-class	Man page
HistDescription	Man page
HistMICE	Man page Source code
Imp-class	Man page
Imp-class-objects	Man page
ImpDescription	Man page
Imprecise_Biased	Man page
Imprecise_Unbiased	Man page
IncE_HDom	Man page
IncE_NDom	Man page
Input	Man page Source code
Kplot	Man page Source code
L2A	Man page Source code
LH2OM	Man page Source code
LHdatabase	Man page
LTY	Man page Source code
Lag_Data	Man page Source code
LinInterp	Man page Source code
LinInterp_cpp	Source code
Low_Effort_Non_Target	Man page
ML2D	Man page Source code
MMSE-class	Man page
MOM-class	Man page
MOM-class-objects	Man page
MOM_agg_fleets	Man page Source code
MPCalcsNAs	Man page Source code
MP_wrapper	Source code
MPtype	Man page Source code
MPurl	Man page Source code
MSC_rebuilding_zones	Source code
MSC_status_zones	Source code
MSC_status_zones_LTL	Source code
MSCplot	Source code
MSE-class	Man page
MSEDescription	Man page
MSEextra	Man page Source code
MSYCalcs	Man page Source code
Mackerel	Man page
NAor0	Man page Source code
NFref	Man page Source code
NIL	Man page Source code
NOAA_plot	Man page Source code
NOAA_plot2	Man page Source code
NPR_DD	Source code
Needed	Man page Source code
OM-class	Man page
OM-class-objects	Man page
OM2MOM	Source code
OMDescription	Man page
OMdoc	Man page Source code
OMexample	Man page Source code
OMinit	Man page Source code
Obs-class	Man page
Obs-class-objects	Man page
ObsDescription	Man page
OneRep	Man page Source code
Overages	Man page
P10	Man page Source code
P100	Man page
P50	Man page
PGK	Man page Source code
PMLimit	Man page Source code
PMObj	Man page Source code
PMobj-class	Man page
PNOF	Man page Source code
PWhisker	Man page
PackageFuns	Source code
Perfect_Imp	Man page
Perfect_Info	Man page
PerformanceMetric	Man page
Porgy	Man page
Pplot	Man page Source code
Pplot2	Man page Source code
Precise_Biased	Man page
Precise_Unbiased	Man page
Project	Man page
ProjectMOM	Man page
R0conv	Man page Source code
Range	Man page Source code
RealFease	Man page Source code
Rec-class	Man page
Red_snapper	Man page
Ref_int_cpp	Source code
Replace	Man page Source code
RepmissingVal	Source code
Report	Man page Source code
ReqData	Man page
Required	Man page Source code
ResFromRel	Man page Source code
Rockfish	Man page
SIL	Man page Source code
SRalphaconv	Man page Source code
SRbetaconv	Man page Source code
SRopt	Source code
SS2Data	Man page Source code
SS2DataMOM	Man page Source code
SS2Data_get_comps	Source code
SS2Data_get_index	Source code
SS2MOM	Man page Source code
SS2OM	Man page Source code
SSBrefplot	Man page
SSMOM2OM	Man page Source code
SS_fleet	Source code
SS_import	Source code
SS_seasonalyears_to_annual	Source code
SS_steepness	Source code
SS_stock	Source code
STY	Man page
SampleCpars	Man page Source code
SampleFleetPars	Man page Source code
SampleImpPars	Man page Source code
SampleObsPars	Man page Source code
SampleStockPars	Man page Source code
Sense	Man page Source code
Simulate	Man page Source code
SimulateMOM	Man page Source code
SimulatedData	Man page
Simulation_1	Man page
SketchFun	Man page Source code
SketchM	Source code
Snapper	Man page
Sole	Man page
Splot	Man page Source code
Stock-class	Man page
Stock-class-objects	Man page
StockDescription	Man page
Sub	Man page Source code
SubCpars	Man page
SubCpars,MOM-method	Man page
SubCpars,OM-method	Man page
SubCpars_proyears	Source code
SubCpars_sim	Source code
SubData_sim	Source code
SubOM	Man page Source code
TAC	Man page Source code
TACfilter	Man page Source code
TEG	Man page Source code
Target_All_Fish	Man page
Targeting_Small_Fish	Man page
Taxa_Table	Man page
Template	Source code
Thresh_tab	Man page Source code
Toothfish	Man page
Tplot	Man page Source code
Tplot2	Man page Source code
Tplot3	Man page Source code
TradePlot	Man page Source code
Turing	Man page Source code
TuringMOM	Man page Source code
UpdateObs	Source code
UpdateSlot	Source code
Uses	Man page Source code
VB	Source code
VOI	Man page
VOI2	Man page
VOIplot	Man page
VPA2OM	Man page
WHAM2OM	Man page Source code
XL2Data	Man page Source code
XL2Fleet	Man page Source code
XL2OM	Man page Source code
XL2Stock	Man page Source code
Yield	Man page Source code
addMPs	Man page
add_zones	Source code
add_zones_A	Source code
add_zones_bar	Source code
add_zones_bar_D	Source code
add_zones_bar_horiz	Source code
add_zones_bar_horiz_D	Source code
agg_data	Source code
alphaconv	Man page Source code
applyAC	Source code
applyMMP	Man page Source code
applyMP	Man page Source code
avail	Man page Source code
betaconv	Man page Source code
biology_plots	Source code
boxplot.Data	Man page Source code
caa_plot	Source code
cal_plot	Source code
calc.mcmc	Source code
calcF	Source code
calcMean	Man page Source code
calcProb	Man page Source code
calcRecruitment	Source code
calcRecruitment_int	Source code
calcRefYield	Man page Source code
calcV	Source code
calcVatAge	Source code
calc_recs	Source code
calc_survival	Source code
calc_survival_yr	Source code
calc_weightedmean_c	Source code
calculate_single_fleet_dynamics	Source code
char.log-class	Man page
checkDefault	Source code
checkHerm	Man page Source code
checkMSE	Man page Source code
checkSlot	Source code
check_Index_Fit	Source code
combine	Source code
compareAmulti	Source code
compareBmulti	Source code
compareC_overallmulti	Source code
compareCmulti	Source code
compareNmulti	Source code
compareRecmulti	Source code
compareSB_depmulti	Source code
compareSBmulti	Source code
convert_units	Source code
cpars_season	Source code
cpars_season_Find	Source code
cpars_season_Perr	Source code
cpars_season_mov	Source code
cparscheck	Man page Source code
curEref	Man page Source code
cv	Man page Source code
defaultplotPars	Source code
derive_beta_par	Man page Source code
dnormal	Man page Source code
doHCR	Man page Source code
doIfreq	Man page Source code
doRec	Man page Source code
encircle	Source code
expandHerm	Man page Source code
extract.area.sex.matrices	Source code
extract.group.matrices	Source code
fetch.file.names	Man page Source code
findIntRuns	Source code
fitVB	Source code
genSizeComp	Source code
genSizeComp2	Source code
genSizeCompWrap	Man page Source code
getAFC	Man page Source code
getBlow	Man page Source code
getDataList	Man page Source code
getEffhist	Man page Source code
getFleetPars	Source code
getGpars	Source code
getGpars_r4ss_124	Source code
getGpars_r4ss_134	Source code
getLHpars	Source code
getMP	Man page Source code
getSR	Source code
getStockPars	Source code
get_Dlag	Source code
get_Dnam	Source code
get_Dp	Source code
get_Ninit_DD	Source code
get_V_from_Asel2	Source code
get_freq	Source code
get_freq2	Source code
get_funcs	Source code
getbeta	Source code
getclass	Man page Source code
getfifth	Man page Source code
getfirstlev	Man page Source code
getmov2	Man page Source code
getnIVs	Man page Source code
getq_multi_MICE	Man page Source code
getsel	Man page Source code
gettaxa	Source code
grav	Source code
growth_plots	Source code
hconv	Man page Source code
hist2	Man page Source code
hrate	Man page Source code
iSCAM	Man page
iSCAM2Data	Man page Source code
iSCAM2OM	Man page Source code
iSCAMcomps	Man page Source code
iSCAMinds	Man page Source code
identifyPch	Source code
ilogit	Source code
ilogitm	Source code
importslot	Source code
indfit	Source code
initialize	Man page
initialize,DLM_general-method	Man page
initialize,Data-method	Man page
initialize,Fease-method	Man page
initialize,Fleet-method	Man page
initialize,MSE-method	Man page
initialize,OM-method	Man page
initialize,Obs-method	Man page
initialize,Stock-method	Man page
initialize-methods	Man page
int_tune	Source code
joinData	Man page Source code
joinHist	Man page
joinMSE	Man page
join_HistRef	Source code
join_HistSampPars	Source code
join_HistTSdata	Source code
join_MSERefPoint	Source code
join_PPD	Source code
join_arrays	Source code
join_list_of_arrays	Source code
join_list_of_vectors	Source code
join_plots	Man page Source code
join_rows	Source code
join_vectors	Source code
label.class-class	Man page
lag_slot	Source code
lcs	Source code
ldim	Man page Source code
load.iscam.files	Man page Source code
logit	Source code
makeDF	Source code
makeData	Source code
makeMOM	Man page Source code
makeRel	Man page Source code
makeTransparent	Man page
makemov	Man page Source code
makemov2	Man page Source code
markov_frac	Source code
match_slots	Source code
mconv	Man page Source code
meanLen_plot	Source code
mean_array	Source code
mean_array2	Source code
mean_vector	Source code
message	Source code
message_info	Source code
message_oops	Source code
message_warn	Source code
metadatatable	Source code
movestockCPP	Man page Source code
movfit_Rcpp	Man page Source code
multiData	Man page Source code
multiDataS	Man page Source code
multiMSE	Man page Source code
multidebug	Man page Source code
myrunif	Source code
needed	Source code
nlz	Source code
optCPU	Man page Source code
optDfun	Source code
optDfunwrap	Source code
optESS	Source code
optMSY_eq	Man page Source code
optQ	Man page Source code
optSR	Source code
optYield	Man page Source code
opt_mov	Source code
opt_mov2	Source code
ourReefFish	Man page
per_recruit_F_calc	Source code
plot,MOM,missing-method	Man page
plot.Catchability	Source code
plot.Data	Man page Source code
plot.Depletion	Source code
plot.Effort	Source code
plot.Fleet	Man page Source code
plot.Growth	Source code
plot.Hist	Man page Source code
plot.Imp	Man page Source code
plot.MMSE	Man page Source code
plot.MOM	Man page
plot.MPA	Source code
plot.MSE	Man page Source code
plot.Maturity	Source code
plot.NaturalMortality	Source code
plot.OM	Man page Source code
plot.Obs	Man page Source code
plot.Recruitment	Source code
plot.Selectivity	Source code
plot.Spatial	Source code
plot.Stock	Man page Source code
plot.character	Source code
plot.pars	Man page Source code
plotCAAdata	Source code
plotDep	Source code
plotEff	Source code
plotFun	Man page Source code
plotGrowth	Source code
plotM2	Source code
plotMat	Source code
plotOFL	Man page Source code
plotQcv	Source code
plotRec	Source code
plotRel	Man page Source code
plotSelHists	Source code
plotSelect	Source code
plotSlot	Source code
plotTSdata	Source code
plotText	Source code
plot_SS2MOM	Man page Source code
plot_SS2OM	Man page Source code
plot_mov	Man page Source code
plot_sample_hist	Source code
plot_sample_ts	Source code
plotmulti	Man page Source code
plotquant	Man page Source code Source code
plotquant2	Source code
popdynCPP	Man page Source code
popdynMICE	Man page Source code
popdynOneMICE	Man page Source code
popdynOneTScpp	Man page Source code
predict.Rel	Man page Source code
predictLH	Man page Source code
print.Rel	Man page Source code
prob.class-class	Man page
projectEq	Source code
qestMICE	Man page Source code
quantile_plot	Man page Source code
range01	Source code
read.control.file	Man page Source code
read.data.file	Man page Source code
read.mcmc	Man page Source code
read.par.file	Man page Source code
read.projection.file	Man page Source code
read.report.file	Man page Source code
ref_plots	Source code
render_plot	Source code
replic8	Man page Source code
rnormSelect2	Source code
runCOSEWIC	Man page Source code
runInMP	Man page Source code
runMP	Man page Source code
runMSE	Man page Source code
runMSE_sac	Source code
sample_lnorm	Source code
sample_norm	Source code
sample_recruitment	Source code
sample_steepness2	Man page Source code
sample_unif	Source code
sdconv	Man page Source code
select_MP	Man page Source code
select_plots	Source code
set_parallel	Source code
setup	Man page Source code
show	Man page Source code
show,Data-method	Man page
show,Hist-method	Man page
show,MMSE-method	Man page
show,MSE-method	Man page
show,OM-method	Man page
show,PMobj-method	Man page
show,Rec-method	Man page
show-MSEtool	Man page
show_int	Source code
simCAA	Man page Source code
simCAL	Man page Source code
simmov	Man page Source code
simmov2	Man page Source code
simulate.Rel	Man page Source code
single_fleet_F_at_age	Source code
single_fleet_Fdisc	Source code
single_fleet_Fret_at_age	Source code
single_fleet_V	Source code
single_fleet_retA	Source code
smoothy	Man page Source code
solve_spat_targ	Source code
split_along_dim	Source code
strip.areas.groups	Source code
strip.static.params	Source code
subsetHerm	Man page Source code
summary,Data-method	Man page
summary,MMSE-method	Man page
summary,MSE-method	Man page
tdlnorm	Man page Source code
tdnorm	Source code
testOM	Man page
tinyErr	Man page
tinyErr,OM-method	Man page
trlnorm	Man page Source code
ts_plots	Source code
tune_MP	Man page Source code
updateData	Source code
updateData_MS	Source code
updateMSE	Man page Source code
update_plot_num	Source code
vB	Source code
validateTMB	Source code
validcpars	Man page Source code
vecminInd	Source code
vuln_addInd_plot	Source code
wormplot	Man page
writeCSV	Man page Source code
writeCSV2	Source code Source code
writeSection	Source code