Man pages for quantifish/rlsd
LSD Package
| create_rules | Set MP rules |
| do_extract | Extract model fits and load into lsdOutput object class for... |
| do_extract_old | Extract model fits and load into lsdOutput object class for... |
| do_extract_ref | Extract model fits and load into lsdOutput object class for... |
| do_plot | Plot model fits |
| do_plot_compare | Plot model fits |
| dot-onAttach | Function to return version number |
| extract | Extract MCMC samples |
| extract-list-method | Extract thingy |
| initialize-lsdOutput-method | Set up the object class |
| looic | Table computing leave-one-out information criterion for... |
| lsdOutput-class | lsdOutput object class |
| lsdSave | Save lsdOutput object |
| parse_model_code | Parse model code |
| plot_aw_cpue_lm | Plot offset year CPUE linear model |
| plot_biomass | Plot biomass measures |
| plot_catch | Plot catch |
| plot_catch_rule | Plot catch |
| plot_catch_save | Save catch plots |
| plot_compare_cpue | Compare CPUE |
| plot_compare_lfs | Compare LFs from multiple models |
| plot_compare_q | Compare catchability coefficient q from multiple models |
| plot_compare_recruitment | Compare recruitment from multiple models |
| plot_compare_selectivity | Compare selectivity |
| plot_compare_ssb | Compare spawning biomass from multiple models |
| plot_compare_vb | Compare vulnerable biomass from multiple models |
| plot_cpue | Plot CPUE |
| plot_data_extent | Plot data extent |
| plot_dens | Plot dens |
| plot_F | Plot fishing mortality |
| plot_growth_increment | Plot growth increment |
| plot_growth_matrix | Plot growth matrix |
| plot_handling_mortality | Plot handling mortality by year |
| plot_initial_numbers | Plot initial nubers |
| plot_lfs | Length-frequency plots |
| plot_lfs_resid | Plot length frequency residuals |
| plot_lfs_resid2 | Plot length frequency residuals2 |
| plot_maturation | Plot maturation |
| plot_mls | Plot miminum legal size (mm) by sex and season |
| plot_money_biomass | Plot Money biomass |
| plot_money_vuln_biomass | Plot Money biomass and vulnerable biomass together |
| plot_movement | Plot movement |
| plot_mp_rules | Plot control rules |
| plot_numbers | Plot nubers |
| plot_offset_cpue | Plot Offset CPUE |
| plot_offset_cpue_lm | Plot offset year CPUE linear model |
| plot_proj_numbers | Plot projected numbers at length in the population |
| plot_puerulus | Plot puerulus |
| plot_q | Compare catchability coefficient q from multiple models |
| plot_recruitment | Plot recruitment |
| plot_recruitment_deviations | Plot recruitment deviations |
| plot_recruitment_size | Plot recruitment size |
| plot_refpoints | Calculate reference points and create relevant figures |
| plot_retro | Plot retrospective analysis |
| plot_rules | Plot rules |
| plot_selectivity | Plot selectivity |
| plot_sex_ratio | Plot sex-ratio |
| plot_snail | Plot snail trial |
| plot_ssb | Plot spawning stock biomass (SSB) |
| plot_ssb_AW_proj | Plot AW SSB with projections |
| plot_ssb_recruitment | Plot stock recruit relationship |
| plot_surplus_production | Plot surplus production |
| plot_tag_residuals | Plot tag residuals |
| plot_total_biomass | Plot total biomass |
| plot_vulnerable_biomass | Plot adjusted vulnerable biomass |
| plot_vulnerable_reference_biomass | Plot adjusted vulnerable biomass |
| plot_vulnref_AW | Plot AW adjusted vulnerable biomass |
| plot_vulnref_AW_proj | Plot AW adjusted vulnerable biomass with projections |
| plot_vulnref_rel | Plot relative adjusted vulnerable biomass |
| read_catch | Read Catch and CPUE info |
| read_SSB | Read SSB info |
| read_stan_map | Read CSV files created by CmdStan or RStan |
| read_stan_mcmc | Read Stan MCMC |
| read_stan_var | Read CSV files created by CmdStan or RStan |
| show-lsdOutput-method | Dunno what this does |
| table_compare_parameters | Table comparing estimated parameters across models |
| table_compare_residuals | Table comparing residuals for various data types across... |
| table_parameters | Create residuals table |
| table_residuals | Create residuals table |
| TACC | Calculate the TACC given a vector of CPUE |
| theme_lsd | LSD theme based on ggplot2 theme |
