Man pages for nikolaifish/bamExtras
Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)
| add2rdat | Add elements to rdat |
| agelenprob | agelenprob |
| bam2r | BAM inputs to R object conversion function |
| bamdat2mat | Write BAM dat file values to a set of matrices and data... |
| bamStockMisc | A dataset containing miscellaneous information related to... |
| barplot_stacked | Stacked barplot developed for plotting landings data by fleet... |
| bic2lk | Convert Bayesian Information Criterion (BIC) to likelihood... |
| catch_curve | Fit catch curves to age composition data |
| check_bounds | Check to see if any estimated parameters are near bounds |
| color_trans | Make opaque color transparent |
| comp_combine | Complete and combine age or length comps |
| comp_complete | Complete each data frame in a list of comp data frames so... |
| comp_complete_bam | Complete a length or age composition data frame so that all... |
| comp_plot | Plot age or length composition data |
| cor2csv | Convert BAM cor file to csv |
| data_lim | Truncate variables in a numeric matrix to specified limits |
| data_polate | Linearly extrapolate/interpolate variables in a numeric... |
| dbllgs | dbllgs |
| exp_decay | Exponential decay |
| F_calc | F_calc |
| figs2tex | Loop through figure files (e.g. pdf) in a folder and generate... |
| find_replace | Find and replace single or multiple values in a vector. Usage... |
| geomean | Geometric mean: logarithm form |
| geomean2 | Geometric mean: product form |
| get_msy | get_msy |
| get_tpl_nm | Get the names of all objects named in the BAM tpl file, with... |
| get_weighted_current | get_weighted_current |
| inputData_RedPorgy | Raw input data: South Atlantic Red Porgy (SEDAR 60) |
| inputData_Tilefish | Raw input data: South Atlantic Tilefish (SEDAR 66) |
| L2F | L2F |
| L_calc | L_calc |
| lgs | lgs |
| lnorm_cv | Coefficient of variation (cv) of lognormal distribution |
| lnorm_cv2sd | Convert lognormal cv to lognormal sd |
| lnorm_sd | Standard deviation of lognormal distribution |
| lnorm_vector_boot | Generating bootstrap vectors of with lognormal error |
| logit | logit |
| M_calc | Compute constant natural mortality estimates from life... |
| M_Charnov | Compute age-varying natural mortality (M) based on Charnov et... |
| mean_noNA | Computes mean excluding NA values |
| M_Lorenzen | Compute age-varying natural mortality (M) based on Charnov et... |
| mse_calc | Compute mean squared errors (MSE) for indices |
| plot_bam | Plot results from Beaufort Assessment Model |
| plot_boot_density | Make density plots of bootstrapped parameters and add... |
| plot_boot_vec | Plot stochastic vectors |
| plot_data_timeline | plot_data_timeline |
| plot_MCBE | Plot results from MCBE uncertainty analysis |
| plot_profile | Plot results from MCBE parameter profile analysis |
| pmatage | Calculate proportion mature population from rdat. Either... |
| random_walk | Simulate a random walk |
| rdat_AtlanticMenhaden | BAM stock assessment results (rdat file): Atlantic Menhaden... |
| rdat_BlackSeaBass | BAM stock assessment results (rdat file): US Southeast... |
| rdat_BluelineTilefish | BAM stock assessment results (rdat file): Atlantic Blueline... |
| rdat_Cobia | BAM stock assessment results (rdat file): Atlantic Cobia... |
| rdat_GagGrouper | BAM stock assessment results (rdat file): South Atlantic Gag... |
| rdat_GrayTriggerfish | BAM stock assessment results (rdat file): South Atlantic Gray... |
| rdat_GreaterAmberjack | BAM stock assessment results (rdat file): South Atlantic... |
| rdat_RedGrouper | BAM stock assessment results (rdat file): South Atlantic Red... |
| rdat_RedPorgy | BAM stock assessment results (rdat file): South Atlantic Red... |
| rdat_RedSnapper | BAM stock assessment results (rdat file): South Atlantic Red... |
| rdat_SnowyGrouper | BAM stock assessment results (rdat file): South Atlantic... |
| rdat_SpanishMackerel | BAM stock assessment results (rdat file): South Atlantic... |
| rdat_Tilefish | BAM stock assessment results (rdat file): South Atlantic... |
| rdat_VermilionSnapper | BAM stock assessment results (rdat file): South Atlantic... |
| ROGBP | color function like rainbow() but without yellow (or indigo) |
| run_bam | Run bam model |
| run_MCBE | Run MCBE uncertainty analysis |
| run_proj | run_proj |
| run_proj_seq | Sequence of projection and estimation |
| run_retro | Simulate bam models for running retrospective analysis |
| sections | Identify sections of a vector of consecutive values whose... |
| sel_comp | sel_comp |
| sr_eq | sr_eq |
| standardize_bam | Standardize object names in bam files (dat, tpl, and cxx) |
| standardize_rdat | Change non-standard names of rdat objects to standard naming... |
| stepwise | stepwise |
| summarize_MCBE | Summarize results from MCBE uncertainty analysis |
| text_legend | Wrapper for legend function to quickly label a plot with text |
| tseries_plot | Time series plot |
| vb_age | Von Bertalanffy (VB) length to age function |
| vb_len | Von Bertalanffy (VB) age to length function |
| vector_combine | combine vectors using Conn 2010 hierarchical method |
