API for MSEtool
Management Strategy Evaluation Toolkit

Global functions
AAVE Man page Source code
AAVY Man page Source code
AddRealData Source code
Add_predictive Source code
Albacore Man page
Albacore_TwoFleet Man page
Atlantic_mackerel Man page
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
CalcDistribution Source code
CalcMPDynamics Man page Source code
CalcMSYRefs Source code
CalcSPRdyn Source code
CalcSPReq Source code
CalcUnfishedRefs 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
CheckSelect 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
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
FlatE_Dom Man page
FlatE_HDom Man page
FlatE_NDom Man page
Fleet-class Man page
Fleet-class-objects Man page
FleetDescription Man page
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
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
LinInt 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
MPCalcsNAs Man page 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
Needed Man page Source code
OM-class Man page
OM-class-objects Man page
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
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
Range Man page Source code
RealFease Man page Source code
Rec-class Man page
Red_snapper Man page
Ref_int Source code
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
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
Stock-class Man page
Stock-class-objects Man page
StockDescription Man page
Sub Man page Source code
SubCpars Man page 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
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 Source code
XL2Data Man page Source code
XL2Fleet Man page Source code
XL2OM Man page Source code Source code
XL2Stock Man page Source code
Yield Man page Source code
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
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
calcRefYield Man page Source code
calcV Source code
calcVatAge Source code
calculate_single_fleet_dynamics Source code
char.log-class Man page
checkMSE Man page 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
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
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
generateRes 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
getSR Source code
getStockPars 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
getq_multi_MICE Man page Source code
getsel Man page Source code
gettaxa Source code
grav Source code
growth_plots Source code
hist2 Man page Source code
hrate Man page Source code
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
joinData Man page Source code
joinHist Man page
joinMSE Man page
join_plots Man page Source code
label.class-class Man page
lcs Source code
ldim Man page Source code
load.iscam.files Man page Source code
logit Source code
makeDF Source code
makeData Source code
makeTransparent Man page
makemov Man page Source code
match_slots Source code
mconv Man page Source code
meanLen_plot Source code
mean_array Source code
mean_vector Source code
message 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
ourReefFish Man page
per_recruit_F_calc Source code
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.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
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
predictLH Man page Source code
prob.class-class Man page
projectEq Source code
qestMICE 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
sample_lnorm Source code
sample_recruitment Source code
sample_steepness2 Man page Source code
sample_unif Source code
sdconv Man page Source code
select_plots Source code
set_parallel Source code
setup Man page Source code
show Source code
show,PMobj-method Man page
show,Rec-method Man page
simCAA Man page Source code
simCAL Man page Source code
simmov Man page Source code
split.along.dim Source code
strip.areas.groups Source code
strip.static.params Source code
summary,Data-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
unpackList Source code
updateData 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
MSEtool documentation built on July 8, 2021, 5:09 p.m.