| autocorr_plot | An extended version of 'coda::autocorr.plot()' |
| batman | Call the Batman |
| calc_beta_mean_cv | Calculate the mean and CV for a Beta distribution given the... |
| calc_beta_params | Calculate the shape parameters (alpha and beta) for a Beta... |
| calc_logs | Calculate logs for several parameters using MCMC |
| calc_longer_quants | Calculate age fits / age residuals and selectivity estimates... |
| calc_mcmc | Perform some quantile calculations on the MCMC posteriors |
| calc_mpd_logs | Calculate logs for several parameters using MPD |
| calc_probs_biomass | Calculate the probabilities that biomasses are under or over... |
| calc_quantiles | Calculate and insert columns containing arbitrary quantiles... |
| calc_rho_vartheta | Calculation of rho and vartheta from sigma and tau |
| calc_sig_tau | Calculation of sigma and tau from rho and vartheta |
| c.model.list | Deprecated Extract the model class objects from the list of... |
| convert_prob_cols_language | Convert any columns in a data frame that appear as 22.5% (for... |
| create_rds_file | Create an rds file to hold the model's data and outputs. |
| delete_files_ext | Delete all files with a specific extension recursively. By... |
| dos.append.to.log | The DOS append to log operator string |
| dos.pipe.to.log | The DOS pipe to log operator string |
| extract_age_output | Extract an age structure MPD object from iSCAM output (.rep... |
| extract_area_sex_matrices | Extract the given data frame into a list of matrices by iscam... |
| extract_group_matrices | Extract the given data frame into a list of matrices by iscam... |
| fetch_file_names | Read the iscam starter file to get the iscam input file names |
| find_f_b40 | Find the Reference Removal Rate (RRR) 'bo_refpt' F_b0 which... |
| fix_m | Change the column name 'm1' to 'm' unless both 'm1' and 'm2'... |
| gear_lu_table | Create a gear lookup table showing which gear numbers are... |
| get_estimated_params | Fetch a data frame of the estimated MCMC parameters only |
| get_fancy_expr | Get a properly-typeset version of the parameter name |
| get_fancy_names | Get a version of iSCAM parameter names in latex math format... |
| get_group_parvals | Get a set of parameter values from the models within the... |
| get_num_params_est | Extract the number of parameters estimated in a model |
| get_parvals | Get a vector of values (median, CI interval, and end year)... |
| get_proj_biomass_raw | Extract the projection biomass or depletion columns of raw... |
| gfiscam_theme | ggplot theme for gfiscam |
| gfiscamutils | gfiscamutils package |
| iscam.exe.file | iscam executable filename |
| iscam_palette | The iSCAM model palette to use for plots by default |
| iscam.starter.file | iscam input data filename |
| is_iscam_model | Determine if a model is a valid iSCAM model |
| is_iscam_model_group | Determine if a list is a valid iSCAM model group |
| is_iscam_model_list | Determine if a list of models is a valid iSCAM model list |
| likelihood_table | Create a table of likelihood outputs |
| linux.append.to.log | The Linux (bash) append to log operator string |
| linux.pipe.to.log | The Linux (bash) pipe to log operator string |
| load_iscam_files | Construct an iscam model object from its input and output... |
| load_longer | Load CSV files in the 'longer' data format. These files will... |
| load_rds_file | Load RDS file which was generated by 'create_rds_file()' |
| load_selest | Load the specially-formatted selectivity estimates file.... |
| log.file | The name of the log file used when running scripts |
| make.likelihood.table | Make an xtable of likelihood values - Herring specific |
| mcmc.age.fits.file | iscam MCMC output age fits filename |
| mcmc.age.resids.file | iscam MCMC output age residuals filename |
| mcmc.biomass.file | iscam MCMC output biomass filename |
| mcmc.catch.file | The name of the ISCAM catch file (csv) |
| mcmc.file | iscam MCMC output filename |
| mcmc.fishing.mort.file | iscam MCMC output instantaneous fishing mortality filename |
| mcmc.fishing.mort.u.file | iscam MCMC output annual fishing mortality filename |
| mcmc.index.fits.file | iscam MCMC output index fits filename |
| mcmc.index.resids.file | iscam MCMC output index residuals filename |
| mcmc.index.standardized.resids.file | The name of the ISCAM residuals file (csv) |
| mcmc.natural.mort.file | iscam MCMC output natural mortality filename |
| mcmc.proj.file | iscam MCMC projection filename |
| mcmc.recr.devs.file | iscam MCMC output recruitment deviations filename |
| mcmc.recr.file | iscam MCMC output recruitment filename |
| mcmc.sel.female.file | The name of the ISCAM female selectivity file (csv) |
| mcmc.sel.file | iscam MCMC output selectivity fits filename |
| mcmc.sel.male.file | The name of the ISCAM male selectivity file (csv) |
| mcmc.sr.file | The name of the ISCAM stock recruitment file (csv) |
| mcmc_thin | Apply burnin and thinning to an MCMC posteriors data frame |
| mcmc.vuln.biomass.file | iscam MCMC output vulnerable biomass filename |
| mdl_cls | The iSCAM model class |
| mdl_grp_cls | The iSCAM model group class |
| mdl_lst_cls | The iSCAM model list class |
| model.class | The name of the ISCAM model class |
| model.lst.class | The name of the ISCAM model class |
| model_setup | Load models and set up lists and classes for the base model,... |
| modify_model_path | Read in model RDS files, modify the path attribute, and save |
| move_legend_to_empty_facet | Moves a ggplot legend to an empty facet if one exists |
| mpd.proj.file | iscam MPD projection filename |
| output.files | A vector of ADMB output files for ISCAM |
| par.file | iscam parameter estimate filename |
| plot_age_fits_mcmc | Plot MCMC age fits for an iSCAM model |
| plot_age_fits_mpd | Plot MPD age fits for an iSCAM model |
| plot_age_resids_boxes_mcmc | Plot MCMC age residuals for an iSCAM model |
| plot_age_resids_mcmc | Plot MCMC age residuals bubbles for an iSCAM model |
| plot_age_resids_mpd | Plot the age fits for an MPD model |
| plot_autocorr_mcmc | Plot MCMC autocorrelations for iSCAM models |
| plot_biomass_grid_mcmc | Plot a grid of MCMC biomass plots for iSCAM models |
| plot_biomass_mcmc | Plot MCMC biomass for iSCAM models |
| plot_biomass_mpd | Plot the MCMC time series trajectories for iscam models,... |
| plot_biomass_proj_mcmc | Plot a model's time series (either spawning biomass or... |
| plot_catch_fit_mcmc | Plot catch fit against catch data |
| plot_catch_fleet | Plot catch by fleet |
| plot_distribution | Plot a distribution function. Mostly for use with making... |
| plot_f_mcmc | Plot MCMC fishing mortalities for iSCAM models |
| plot_index_mcmc | Plot MCMC index fits or residuals for iSCAM models |
| plot_index_mpd | Plot MPD index fits or residuals for iSCAM models |
| plot_pairs_mcmc | Plot MCMC pairs for iSCAM models |
| plot_param_stats_mcmc | Plot Autocorrelation, Effective sample size, Geweke... |
| plot_priors_posts_mcmc | Plot MCMC priors and posteriors for iSCAM models |
| plot_q_mcmc | Plot MCMC catchabilities for iSCAM models |
| plot_rdevs_mcmc | Plot MCMC recruitment deviations for iSCAM models |
| plot_recr_grid_mcmc | Plot a grid of MCMC recruitment plots for iSCAM models |
| plot_recr_mcmc | Plot MCMC recruitments for iSCAM models |
| plot_recr_mpd | Plot MPD recruitments for iSCAM models |
| plot_ref_points | Plot reference point boxplots |
| plot_ref_points_dist_mcmc | Plot DFO-style reference point figure with horizontal... |
| plot_selex_gear_mcmc | Plot MCMC selectivities by single gear for iSCAM models |
| plot_selex_mcmc | Plot MCMC selectivities for iSCAM models |
| plot_selex_mpd | Plot MPD selectivities for iSCAM models |
| plot_sr_mcmc | Plot the stock-recruitment relationship for an MCMC ISCAM... |
| plot_traces_mcmc | Plot MCMC traces for iSCAM models |
| plot_ts_mcmc | Plot MCMC time series plots for iSCAM models |
| plot_tv_selex_mpd | Plor MCMC selectivities for iSCAM models |
| plot_vuln_mcmc | Plot MCMC vulnerable biomass for iSCAM models |
| rdata.file | Name of the model rdata file |
| read_control_file | Read in the iscam control file |
| read_data_file | Read in the iscam data file |
| read.list | Read the data from the file into a list and return the list |
| read_mcmc | Read in the MCMC results from an iscam model, reformat them,... |
| read_par_file | Read in the contents of the iscam par file |
| read_projection_file | Read in the contents of the iscam projection file |
| read_psv | Read ADMB-generated psv file |
| read_report_file | Read in the iscam report (.rep) file |
| rename_gear_iscam | Read in an ISCAM data file, replace all instances of the old... |
| rep.file | iscam report filename |
| replace_gear_name_and_save | Replace gear names in objects in an iSCAM output list, from... |
| replace_gear_names | Change the gear names in already-loaded models |
| retro.dir | Name of the retrospectives directory |
| run_iscam | Run an iscam model through the 'base::shell()' command |
| run_multiple_iscam | Run multiple iscam models in parallel |
| run_retro | Run retrospectives for the given iscam model directory |
| sel_param_est_mpd_table | Make a table of selectivity parameter estimate comparisons... |
| set_dirs | Set and return all model directories for the project |
| set_gear_language | Translate the gear names and abbreviations in the models list... |
| simplify_names | Simplify MCMC parameter names for this package code |
| standardize_comps | Update an iSCAM 'dat' file by standardizing all the age comps |
| strip_static_params | Strip static parameters from MCMC output data |
| table_bio_depl | Create a table containing biomass and depletion estimates |
| table_catch | Create a table of catch, by Landings and Discards |
| table_catch_area | Return a table by area, where the areas are defined by the... |
| table_catch_fleet | Return a table by fleet, where the fleets are determined by... |
| table_catch_fleets | Return a table by fleet, where the fleets are determined by... |
| table_decision | Create a decision table with a single reference point or... |
| table_decisions | Create a wide decision table for iSCAM models, with all... |
| table_growth_params | Create table of the growth parameters which were input into... |
| table_index_values | Create a table of index data values |
| table_iscam_param_desc | Create the ISCAM model parameter description table as found... |
| table_param_est_mcmc | Create a table of parameter estimates for iSCAM models |
| table_param_est_mpd | Create a table of MPD parameter comparisons |
| table_param_phi_mpd | Create a table comparing phi parameter |
| table_param_settings | Create a table summarizing parameterization of an iSCAM model |
| table_ref_points_mcmc | Make a table of reference points for MCMC iSCAM models |
| table_ref_rate | Make a table containing the reference rate and values... |
| table_sens_param_changes | Create a table summarizing changes for sensitivity models |
| table_sens_q | Create a table comparing estimates of q across models |
| table_ts_values_mcmc | Create a table of time series estimates for MCMC iSCAM models |
| tex | Create an expression from a string that may have a latex... |
| tr | Translate from English to French |
| vec2df | Create a one-row tibble from a vector of values |
| write_projection_file | Write an ISCAM projection file (pfc file) |
