Package index
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AFSCforeign_hauls - Example data for AFSCforeign_hauls
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CreateStrataDF.fn() - Create strata data frame using
StrataAreas.fn -
Format.AKSlope.fn() - Rename AFSC slope survey columns from data pulled before 2017
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GetSppDefault.fn() - Get Vector of Default Species Names for US West Coast
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GetStrata.fn() - Get Default Strata
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GetSurveyAbb.fn() - Get Survey Abbreviation
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PlotMap.fn() - Plot two figures showing catch-per-unit-effort data
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PlotSexRatio.fn() - Function to plot sex ratio
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PlotSexRatioStrata.fn() - Function to plot sex ratio by strata
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PlotVarLengthAtAge.fn() - Plot variability of length at age
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ReadInAges.fn() - Cleans triennial survey data by year and area
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ReadInLengths.fn() - Reads in the compositional survey data and filters the data into what is necessary It reads in catch and station data and makes sure only the species necessary are kept
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SA3 - A data set for determining strata areas (hectares)
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SA3_v2021.1 - A data set for determining strata areas (hectares)
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SexRatio.fn() - Assign sex to unsexed fish based on fish with similar traits
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StrataAreas.fn() - Calculate strata area
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StrataFactors.fn() - Creates a vector of strata factors by name
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availablecells - Available grid cell locations for the survey
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bio_nwfsc_combo - Example data for NWFSC bio data
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catch_nwfsc_combo - Example data for NWFSC catch data
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check_dir() - Directory check
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check_strata() - Calculate the number of observations by year and strata
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check_survey() - Check and create survey string
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codify_sex()codify_sex_ss3() - Code sexes into standardized strings
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combine_tows() - Combine data with multiple records for unique tows
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convert_to_hex_string() - Utility function used throughout the package
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createMatrix() - Survey name matching function used when pull from the data warehouse
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create_strata() - Create strata data frame using
get_strata_areas -
draw_USEEZ() - Bounds the figure with the limits of the U.S. EEZ
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draw_land() - Mapping function to draw land areas
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draw_projection() - Mapping projection
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draw_theme() - A ggplot2 theme for drawing maps
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est_growth() - Estimate length-at-age using the von Bertanlaffy parameterization
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est_vbgrowth() - Estimate length-at-age using the von Bertanlaffy parameterization
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estimate_weight_length() - Calculate weight-length relationship parameters
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filter_pull() - Filter data pulls
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fit_vbgrowth() - Estimate von Bertanlaffy growth parameters from lengths and ages
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get_design_based() - Calculates design based estimates from survey data for West Coast surveys.
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get_expanded_comps() - Calculate expanded composition data for lengths and marginal ages
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get_input_n() - Calculate input sample sizes
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get_json() - Get json content from a URL
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get_raw_caal() - Calculate unexpanded/raw length or marginal age compositions
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get_raw_comps() - Calculate unexpanded/raw length or marginal age compositions
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get_species_info() - Get Species Information
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get_spp_list() - Get Vector of Default Species Names for US West Coast
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get_strata_area_default() - Get Default Strata
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get_strata_areas() - Calculate strata area
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get_survey_names_abb() - Get Survey Abbreviation
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get_survey_names_long() - Survey name matching function used when pull from the data warehouse
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get_url() - Function to create url to pull data from the data warehouse
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label_axes() - Function to label axis for map plotting
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label_tow_expansion() - Label tow expanded compositions
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plot_age_length_sampling() - Plot the representativeness of age sampling based on lengths
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plot_bio_patterns() - This function plots length by latitude and depth
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plot_comps() - Plot frequency data as bubble plots
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plot_cpue() - This function plots cpue and length by latitude and depth
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plot_cpue_map() - Plot two figures showing catch-per-unit-effort data
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plot_index() - Plots the design based biomass estimates with confidence intervals
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plot_length_age() - Plots the length-at-age data and estimates
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plot_proportion() - Plot proportions of factor levels (y axis) by bins (x axis)
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plot_sex_ratio() - Function to plot sex ratio data in a barplot form
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plot_sex_ratio_strata() - Function to plot sex ratio by strata
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plot_varlenage() - Plot variability of length at age
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plot_weight_length() - Plots the weight-at-length data and estimates
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plot_westcoast() - Plot the United States west coast using ggplot2
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pull_bio() - Pull biological data (age, length, weight) from the NWFSC data warehouse
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pull_biological_samples() - Pull biological sample information from the NWFSC data warehouse for biological collections taken at sea. Generally these are samples that require lab processing. Generally, these types of biological sample are maturity, stomach, fin clips, and tissue samples. This function returns collection information for these samples include the sample numbers which allows the lab analysis to be linked back to the sampled fish.
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pull_catch() - Pull catch data for satisfactory tows from the NWFSC data warehouse
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pull_gemm() - Pull Groundfish Expanded Multiyear Mortality data
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pull_haul() - Pull haul data from the NWFSC data warehouse.
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pull_spppull_spp() - Sql pull of species names
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save_rdata() - Save an object in an
.rdatafile -
stopifnotcolumn() - Stop if column name is not present in the data
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strata_factors() - Creates a vector of strata factors by request column names
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wh_plot_proportion() - Save figures of proportions by depth and latitude using warehouse data