API for SAMtool
Stock Assessment Methods Toolkit

Global functions
.onUnload Source code
AAV Source code
Assess_I_hist Source code
Assess_diagnostic Source code
Assessment Man page
Assessment-class Man page
Baranov 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
DD_dynamic_SSB0 Source code
Data-rich-MP Man page
Euler_Lotka_fn Source code
HCR40_10 Man page Source code
HCR60_20 Man page Source code
HCR80_40MSY Man page Source code
HCR_FB Man page Source code
HCR_MSY Man page Source code
HCR_escapement Man page Source code
HCR_ramp Man page Source code
HCR_segment Man page Source code
HCRlin Man page Source code
HCRlinesegment Source code
LinInterp Source code
MP Man page
Model-based-MP Man page
Mohn_rho Source code
PRBcalc Man page Source code
PRBplot Source code
Perfect Man page Source code
Probs Man page Source code
RCM Man page
RCM,OM,Data-method Man page
RCM,OM,RCMdata-method Man page
RCM,OM,list-method Man page
RCM_SPR Source code
RCM_dynamic_SSB0 Source code
RCM_est Source code
RCM_get_likelihoods Source code
RCM_int Source code
RCM_posthoc_adjust Source code
RCM_retro Source code
RCM_retro_subset Source code
RCMdata Man page
RCMdata-class Man page
RCModel Man page
RCModel-class Man page
R_pred Source code
SAMtool Man page
SAMtool-package Man page
SCA Man page Source code
SCA2 Man page Source code
SCA_ Source code
SCA_4010 Man page
SCA_75MSY Man page
SCA_CAL Man page Source code
SCA_DDM Man page Source code
SCA_MSY Man page
SCA_Pope Man page Source code
SCA_RWM Man page Source code
SCA_catch_solver Source code
SCA_dynamic_SSB0 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_dynamic_SSB0 Source code
SP_production Man page Source code
SSS Man page Source code
SSS_4010 Man page
SSS_75MSY Man page
SSS_MSY Man page
Shortcut Man page Source code
Shortcut2 Man page Source code
TAC_MSY Man page Source code
VPA Man page Source code
VPA_posthoc Source code
arrows Source code
assign_Assessment_slots Source code
cDD Man page Source code
cDD_ Source code
cDD_SS Man page Source code
cDD_catch_solver Source code
cDD_dynamic_SSB0 Source code
calc_NPR Source code
calculate_Mohn_rho Source code
calculate_TAC Man page Source code
catch_equation Source code
check_OM_for_sampling Source code
check_RCMdata Man page Source code
check_det Source code
compare_RCM Man page Source code
compare_models Man page Source code
dev_AC Source code
diagnostic Man page Source code
diagnostic_AM Man page Source code
dots_check Source code
expand_comp_matrix Source code
extreme.outlier Source code
find_na Source code
generate_PLA Source code
get_F01 Source code
get_FSPR Source code
get_Fmax Source code
get_SR Source code
get_ivul_len Source code
get_sdreport Source code
get_vul_len Source code
getinds Man page Source code
getsegment Source code
hist.numeric Source code
iVB Source code
ilogit Source code
ilogit2 Source code
ilogitm Source code
int_s_sel Source code
int_sel Source code
logit Source code
logit2 Source code
mahalanobis_contribution Source code
mahdensplot Source code
mahplot Man page Source code
make_LWT Source code
make_MP Man page Source code
make_interim_MP Man page Source code
make_prior Source code
make_unique_names Source code
match_R_years Source code
matrix_slot_fn Source code
max Source code
mu Source code
nll_depletion_profile Source code
optimize_TMB_model Source code
par_identical_sims_fn Source code
pcod Man page
plot,Assessment,missing-method Man page
plot,Assessment,retro-method Man page
plot,RCModel,missing-method Man page
plot,prof,missing-method Man page
plot,retro,missing-method Man page
plot.Assessment Man page
plot.RCModel Man page
plot.prof Man page
plot.retro Man page
plot_Kobe Source code
plot_SR Man page Source code
plot_betavar Man page Source code
plot_composition Man page Source code
plot_composition_RCM 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_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
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,RCModel-method Man page
profile_likelihood_DD_TMB Source code
profile_likelihood_RCM Source code
profile_likelihood_SCA 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
project_ASM Source code
projection Man page Source code
projection_DD_SS Source code
projection_SCA Source code
projection_SCA_internal Source code
projection_SP Source code
projection_VPA Source code
projection_cDD_SS Source code
pull_AddInd Source code
pull_Ind Source code
pull_Index Source code
r_prior_fn Source code
ref_pt_DD Source code
ref_pt_SCA Source code
ref_pt_VPA Source code
ref_pt_cDD Source code
report Source code
retro Man page
retro-class Man page
retrospective Man page
retrospective,Assessment-method Man page
retrospective,RCModel-method Man page
retrospective_AM Man page Source code
retrospective_DD_SS Source code
retrospective_DD_TMB Source code
retrospective_SCA 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_at_length Source code
rmd_C_mean_age Source code
rmd_C_mean_length 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_M_DD Source code
rmd_M_prior Source code
rmd_M_rw Source code
rmd_N Source code
rmd_N_at_age Source code
rmd_R Source code
rmd_R0 Source code
rmd_RCM_D Source code
rmd_RCM_Find Source code
rmd_RCM_Hist_compare Source code
rmd_RCM_Perr Source code
rmd_RCM_R0 Source code
rmd_RCM_R_output Source code
rmd_RCM_SPR Source code
rmd_RCM_SPR2 Source code
rmd_RCM_SR Source code
rmd_RCM_SSB_output Source code
rmd_RCM_fleet_output Source code
rmd_RCM_index_output Source code
rmd_RCM_initD Source code
rmd_RCM_likelihood_gradients Source code
rmd_RCM_retrospective Source code
rmd_RCM_sel Source code
rmd_SCA Source code
rmd_SP Source code
rmd_SPR Source code
rmd_SP_SS Source code
rmd_SR 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_YPR Source code
rmd_assess_fit Source code
rmd_assess_fit2 Source code
rmd_assess_fit_MW Source code
rmd_assess_fit_series Source code
rmd_assess_qq Source code
rmd_assess_resid Source code
rmd_assess_resid2 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_MW Source code
rmd_data_age_comps Source code
rmd_data_length_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_fit_length_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_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_steepness3 Source code
sdreport_int Source code
slp Source code
slp2 Source code
squeeze 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_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
tiny_comp Source code
ts_matplot Source code
userguide Man page Source code
vec_slot_fn Source code
yield_fn_DD Source code
yield_fn_SCA Source code
yield_fn_SCA_int Source code
yield_fn_cDD Source code
SAMtool documentation built on Jan. 12, 2022, 5:07 p.m.