API for tcarruth/MSEtool
Management Strategy Evaluation Toolkit

Global functions
AAV Source code
Albacore_TwoFleet Man page
Assess_I_hist Source code
Assess_diagnostic Source code
Assessment Man page
Assessment-class Man page
Awatea2OM Man page Source code
AwateaRead Source code
CASAL2OM Man page Source code
CASALpars Man page Source code
CombineMMP Source code
DDSS_4010 Man page
DDSS_75MSY Man page
DDSS_MSY Man page
DD_ Source code
DD_SS Man page Source code
DD_TMB Man page Source code
Data-rich-MP Man page
Euler_Lotka_fn Source code
HCR40_10 Man page Source code
HCR60_20 Man page Source code
HCR_FB Man page Source code
HCR_MSY Man page Source code
HCR_ramp Man page Source code
HCRlin Man page Source code
HistMICE Man page Source code
LinInt Source code
MMSE-class Man page
MOM-class Man page
MP Man page
MPCalcsNAs Man page Source code
MSEtool Man page
MSEtool-package Man page
Model-based-MP Man page
Mohn_rho Source code
NIL Man page Source code
PRBcalc Man page Source code
PRBplot Source code
Probs Man page Source code
R_pred Source code
ResFromRel Man page Source code
SCA Man page Source code
SCA2 Man page Source code
SCA_4010 Man page
SCA_75MSY Man page
SCA_MSY Man page
SCA_MSY_calc Source code
SCA_Pope Man page Source code
SCA_Pope_MSY_calc Source code
SCA_catch_solver Source code
SCA_refpt_calc Source code
SIL Man page Source code
SOL Man page Source code
SP Man page Source code
SP_ Source code
SP_4010 Man page
SP_75MSY Man page
SP_Fox Man page Source code
SP_MSY Man page
SP_SS Man page Source code
SP_catch_solver Source code
SP_production Man page Source code
SRA Man page
SRA-class Man page
SRA_dynamic_SSB0 Source code
SRA_get_likelihoods Source code
SRA_posthoc_adjust Source code
SRA_retro Source code
SRA_retro_subset Source code
SRA_scope Man page
SRA_scope,OM,Data-method Man page
SRA_scope,OM,list-method Man page
SRA_scope_est Source code
SRA_scope_int Source code
SRA_tiny_comp Source code
SRopt Source code
SS2Data Man page Source code
SS2Data_get_comps Source code
SS2Data_get_index Source code
SS2MOM Man page Source code
SS2MOM_fleet Source code
SS2MOM_stock Source code
SS2OM Man page Source code
SSS Man page Source code
SSS_4010 Man page
SSS_75MSY Man page
SSS_MSY Man page
SS_import Source code
SS_steepness Source code
Sub_cpars Man page Source code
TAC_MSY Man page Source code
TEG Man page Source code
VPA Man page Source code
VPA2OM Man page Source code
applyMMP Source code
assign_Assessment_slots Source code
avail Man page Source code
cDD Man page Source code
cDD_ Source code
cDD_SS Man page Source code
cDD_catch_solver Source code
calc.mcmc Source code
calculate_Mohn_rho Source code
calculate_TAC Man page Source code
check_OM_for_sampling Source code
compare_SRA Man page Source code
compare_models Man page Source code
diagnostic_AM Man page Source code
expandHerm Man page Source code
expand_comp_matrix Source code
extract.area.sex.matrices Source code
extract.group.matrices Source code
extreme.outlier Source code
fetch.file.names Man page Source code
getDataList Source code
getGpars Source code
getGpars_r4ss_124 Source code
getGpars_r4ss_134 Source code
getSR Source code
get_MSY_DD Source code
get_MSY_cDD Source code
get_s_vul_len Source code
get_sdreport Source code
get_vul_len Source code
getclass Source code
getfirstlev Source code
getinds Man page Source code
getnIVs Man page Source code
getq_multi Man page Source code
getq_multi_MICE Man page Source code
getsegment 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
iVB Source code
ilogit Source code
ilogitm Source code
int_s_sel Source code
int_sel Source code
ldim Man page Source code
load.iscam.files Man page Source code
logit Source code
mahalanobis_contribution Source code
mahdensplot Source code
mahplot Man page Source code
make_LWT Source code
make_MP Man page Source code
makemov Man page Source code
match_R_years Source code
matrix_slot_fn Source code
mu Source code
multiData Man page Source code
multiDataS Man page Source code
multiMSE Man page Source code
multiMSE_int Source code
multidebug Man page Source code
negcorlogspace Source code
nlz Source code
optQ_multi Man page Source code
optSR Source code
optimize_TMB_model Source code
par_identical_sims_fn Source code
plot,Assessment,missing-method Man page
plot,Assessment,retro-method Man page
plot,MMSE,missing-method Man page
plot,MOM,missing-method Man page
plot,SRA,missing-method Man page
plot,prof,missing-method Man page
plot,retro,missing-method Man page
plot.Assessment Man page
plot.MMSE Man page
plot.MOM Man page
plot.SRA Man page
plot.prof Man page
plot.retro Man page
plotRel Man page Source code
plot_Kobe Source code
plot_SR Man page Source code
plot_betavar Man page Source code
plot_composition Man page Source code
plot_composition_SRA Source code
plot_crosscorr Man page Source code
plot_generic_at_age Source code
plot_hessian_convergence Source code
plot_iter Source code
plot_lognormalvar Man page Source code
plot_max_gr Source code
plot_mov Man page Source code
plot_msg Source code
plot_normalvar Source code
plot_ogive Source code
plot_residuals Man page Source code
plot_steepness Man page Source code
plot_surplus_production Source code
plot_timeseries Man page Source code
plot_yield_DD Source code
plot_yield_SCA Source code
plot_yield_SCA_Pope Source code
plot_yield_SP Source code
plot_yield_VPA Source code
plot_yield_cDD Source code
plotmulti Man page Source code
plotquant Man page Source code
popdynMICE Man page Source code
popdynOneMICE Man page Source code
powdif Source code
prelim_AM Man page Source code
process_AddIndType Source code
process_AddIndV Source code
prof Man page
prof-class Man page
profile Man page
profile,Assessment-method Man page
profile_likelihood_DD_TMB Source code
profile_likelihood_SCA Source code
profile_likelihood_SCA2 Source code
profile_likelihood_SP Source code
profile_likelihood_SSS Source code
profile_likelihood_VPA Source code
profile_likelihood_cDD Source code
profile_likelihood_spict Source code
project Man page
project-class Man page
projection Man page Source code
projection_DD_SS Source code
projection_SCA2 Source code Source code
projection_SCA_Pope Source code
projection_SCA_internal Source code
projection_SP Source code
projection_VPA Source code
projection_VPA_internal Source code
projection_cDD_SS Source code
pull_AddInd Source code
pull_Ind Source code
pull_Index Source code
qestMICE Man page Source code
r_prior_fn 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
report Source code
rescale_report Source code
retro Man page
retro-class Man page
retrospective Man page
retrospective,Assessment-method Man page
retrospective,SRA-method Man page
retrospective_AM Man page Source code
retrospective_DD_SS Source code
retrospective_DD_TMB Source code
retrospective_SCA Source code
retrospective_SCA2 Source code
retrospective_SCA_Pope Source code
retrospective_SP Source code
retrospective_SP_SS Source code
retrospective_SSS Source code
retrospective_VPA Source code
retrospective_cDD Source code
retrospective_cDD_SS Source code
retrospective_spict Source code
rmd_B Source code
rmd_B_B0 Source code
rmd_B_B0_terminal Source code
rmd_B_BMSY Source code
rmd_B_BMSY_terminal Source code
rmd_C_at_age Source code
rmd_C_mean_age Source code
rmd_DD_SS Source code
rmd_DD_TMB Source code
rmd_F Source code
rmd_FMSY Source code
rmd_F_FMSY Source code
rmd_F_FMSY_terminal Source code
rmd_Kobe Source code
rmd_LAA Source code
rmd_LW Source code
rmd_MSY Source code
rmd_N Source code
rmd_N_at_age Source code
rmd_R Source code
rmd_R0 Source code
rmd_SCA Source code
rmd_SCA2 Source code
rmd_SCA_Pope Source code
rmd_SP Source code
rmd_SP_SS Source code
rmd_SR Source code
rmd_SRA_D Source code
rmd_SRA_Find Source code
rmd_SRA_Perr Source code
rmd_SRA_R0 Source code
rmd_SRA_R_output Source code
rmd_SRA_SR Source code
rmd_SRA_SSB_output Source code
rmd_SRA_fleet_output Source code
rmd_SRA_initD Source code
rmd_SRA_retrospective Source code
rmd_SRA_sel Source code
rmd_SRA_survey_output Source code
rmd_SSB Source code
rmd_SSB_SSB0 Source code
rmd_SSB_SSBMSY Source code
rmd_SSS Source code
rmd_U Source code
rmd_U_UMSY Source code
rmd_VPA Source code
rmd_WAA Source code
rmd_assess_fit Source code
rmd_assess_fit2 Source code
rmd_assess_fit_series Source code
rmd_assess_qq Source code
rmd_assess_resid Source code
rmd_assess_timeseries Source code
rmd_at_age Source code
rmd_bubble Source code
rmd_cDD Source code
rmd_cDD_SS Source code
rmd_data_age_comps Source code
rmd_data_timeseries Source code
rmd_dynamic_SSB0 Source code
rmd_fit_age_comps Source code
rmd_fit_comps Source code
rmd_footer Source code
rmd_h Source code
rmd_head Source code
rmd_log_rec_dev Source code
rmd_mat Source code
rmd_matplot Source code
rmd_meanR Source code
rmd_persp_plot Source code
rmd_residual Source code
rmd_retrospective Source code
rmd_sel Source code
rmd_sel_annual Source code
rmd_sel_persp Source code
rmd_sp Source code
rmd_spict Source code
rmd_spict_FMSY Source code
rmd_spict_yield_header Source code
rmd_summary Source code
rmd_yield_F Source code
rmd_yield_U Source code
rmd_yield_depletion Source code
sample_recruitment Source code
sample_steepness3 Source code
sdreport_int Source code
simmov Man page Source code
slp Source code
slp2 Source code
squeeze Source code
strip.areas.groups Source code
strip.static.params Source code
summary,Assessment-method Man page
summary,retro-method Man page
summary.Assessment Man page
summary.retro Man page
summary_DD_SS Source code
summary_DD_TMB Source code
summary_SCA Source code
summary_SCA2 Source code
summary_SCA_Pope Source code
summary_SP Source code
summary_SP_SS Source code
summary_SSS Source code
summary_VPA Source code
summary_cDD Source code
summary_cDD_SS Source code
summary_spict Source code
swordfish Man page
tinyErr Man page
tinyErr,MOM-method Man page
tinyErr_MOM Source code
ts_matplot Source code
update_SRA_data Source code
userguide Man page Source code
validateTMB Source code
vec_slot_fn Source code
vector2char Source code
vul_fn Source code
tcarruth/MSEtool documentation built on Sept. 16, 2020, 5:59 a.m.