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Package index
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.get_Nage_3_df()
- Extract Numbers at age 3
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.get_R_rel_df()
- Extract Recruits (R) from pollock run
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.get_ats_df()
- Extract Acoustic Trawl Survey Data
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.get_avo_df()
- Get avo data into frame
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.get_bts_df()
- Extract bottom trawl survey data from a list of models
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.get_cope_df()
- Extract copE data
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.get_cpue_df()
- Extract CPUE data
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.get_like_df()
- Extract Likelihood Data Frame
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.get_mnage_df()
- Extract mean age from pollock model run
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.get_recruitment_df()
- Get recruitment data
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.get_ser_df()
- Extract spawning exploitation rate
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.get_srr_df()
- Extract stock recruitment results
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.get_ssb_df()
- Extract spawning stock biomass (ssb)
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.get_ssb_rel_df()
- Extract spawning stock biomass (ssb)
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.run_mod()
- run pollock model
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.run_mod_windows()
- run pollock model on windows
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.run_proj()
- run projection model DOESN"T WORK...dunno why
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.run_proj_windows()
- run projection model for windows
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get_results()
- Fetch Model Results in Parallel
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get_tier3_res()
- Extract Tier 3 Results
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get_vars()
- Extract and Compute Several Metrics from Model Output
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plot_Nage_3()
- Plot predicted Numbers at age 3
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plot_R_rel()
- Plot predicted recruitment
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plot_agefit()
- Age Composition Data Plotter t(t() This function generates a series of plots visualizing the age composition data from fisheries assessment. It compares observed and predicted data across different years.
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plot_ats()
- Plot Acoustic Trawl Survey Biomass Data
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plot_avo()
- Plot avo data
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plot_bts()
- Plot bottom trawl survey data
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plot_cope()
- Plot copepod something
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plot_cpue()
- Plot predicted CPUE
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plot_likes()
- Plot Likelihood Values
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plot_mnage()
- Plot predicted mean age by gear type
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plot_recruitment()
- Plot predicted recruitment and approximate asymptotic error-bars
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plot_sel()
- Plot selectivity
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plot_ser()
- Plot predicted spawning stock biomass (SER)
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plot_srr()
- Plot Stock-Recruitment Relationship (SRR)
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plot_ssb()
- Plot predicted spawning stock biomass (ssb)
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plot_ssb_rel()
- Plot predicted spawning stock biomass (ssb)
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read_admb()
- Read ADMB output files
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read_ctl()
- Read ADMB .ctl file
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read_dat()
- Read ADMB Data File
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read_fit()
- Read ADMB .par, .std, and .cor file and return an R object of type 'list' of estimates and correlations
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read_psv()
- Read ADMB .psv file
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read_rep()
- Read ADMB .rep file
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rescale_cov()
- Rescale a Covariance Matrix
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run_model()
- Run Multiple ADMB Models in Parallel
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run_proj()
- Run Multiple projection models in Parallel
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tab_fit()
- Tabulate fits from models using extended metrics.
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tab_ref()
- Tabulate fits from models using extended metrics.
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upperCaseFirst()
- Helper function to convert the first character of a string to uppercase.
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write_dat()
- Write Data to Text File