Man pages for nwfsc-assess/nwfscSurvey
Northwest Fisheries Science Center Survey
| AFSCforeign_hauls | Example data for AFSCforeign_hauls |
| availablecells | Available grid cell locations for the survey |
| Biomass.fn | Calculates design based estimates from survey data for West... |
| bio_nwfsc_combo | Example data for NWFSC bio data |
| catch_nwfsc_combo | Example data for NWFSC catch data |
| check_dir | Directory check |
| check_strata | Calculate the number of observations by year and strata |
| CheckStrata.fn | Calculate the number of observations by year and strata |
| check_survey | Check and create survey string |
| codify_sex | Code sexes into standardized strings |
| combine_tows | Combine data with multiple records for unique tows |
| convert_to_hex_string | Utility function used throughout the package |
| createMatrix | Survey name matching function used when pull from the data... |
| CreateStrataDF.fn | Create strata data frame using 'StrataAreas.fn' |
| draw_theme | A ggplot2 theme for drawing maps |
| draw_USEEZ | Bounds the figure with the limits of the U.S. EEZ |
| est_growth | Estimate length-at-age using the von Bertanlaffy... |
| estimate_weight_length | Calculate weight-length relationship parameters |
| est_vbgrowth | Estimate length-at-age using the von Bertanlaffy... |
| filter_pull | Filter data pulls |
| fit_vbgrowth | Estimate von Bertanlaffy growth parameters from lengths and... |
| Format.AKSlope.fn | Rename AFSC slope survey columns from data pulled before 2017 |
| get_design_based | Calculates design based estimates from survey data for West... |
| get_expanded_comps | Calculate expanded composition data for lengths and marginal... |
| get_input_n | Calculate input sample sizes |
| get_json | Get json content from a URL |
| GetN.fn | Calculate input sample sizes |
| get_raw_comps | Calculate unexpanded/raw length or marginal age compositions |
| get_species_info | Get Species Information |
| GetSppDefault.fn | Get Vector of Default Species Names for US West Coast |
| GetStrata.fn | Get Default Strata |
| GetSurveyAbb.fn | Get Survey Abbreviation |
| get_url | Function to create url to pull data from the data warehouse |
| label_tow_expansion | Label tow expanded compositions |
| plot_age_length_sampling | Plot the represntativeness of age sampling based on lengths |
| PlotBio.fn | Plots the designed based biomass estimates with confidence... |
| plot_bio_patterns | This function plots length by latitude and depth |
| PlotBioStrata.fn | Plots the design-based biomass estimates by strata with... |
| plot_comps | Plot frequency data as bubble plots |
| plot_cpue | This function plots cpue and length by latitude and depth |
| PlotFreqData.fn | Plot length or age compositions by year in bubble plots |
| plot_index | Plots the design based biomass estimates with confidence... |
| plot_length_age | Plots the length-at-age data and estimates |
| PlotMap.fn | Plot two figures showing catch-per-unit-effort data |
| PlotPresenceAbsence.fn | Plot showing presence and absence per haul by depth,... |
| plot_proportion | Plot proportions of factor levels (y axis) by bins (x axis) |
| PlotSexRatio.fn | Function to plot sex ratio |
| PlotSexRatioStrata.fn | Function to plot sex ratio by strata |
| plot_varlenage | Plot variability of length at age |
| PlotVarLengthAtAge.fn | Plot variability of length at age |
| plot_weight_length | Plots the weight-at-length data and estimates |
| plot_westcoast | Plot the United States west coast using ggplot2 |
| pull_bio | Pull biological data (age, length, weight) from the NWFSC... |
| PullBio.fn | Pull biological data (age, length, weight) from the NWFSC... |
| pull_biological_samples | Pull biological sample information from the NWFSC data... |
| pull_catch | Pull catch data for satisfactory tows from the NWFSC data... |
| PullCatch.fn | Pull catch data from the NWFSC data warehouse |
| pull_gemm | Pull gemm data from the NWFSC data warehouse |
| pull_haul | Pull haul data from the NWFSC data warehouse. |
| PullHaul.fn | Pull haul data from the NWFSC data warehouse The website is:... |
| pull_spp | Pull species names from the warehouse |
| PullSpp | Sql pull of species names |
| PullSpp.fn | Pull species names from the warehouse |
| ReadInAges.fn | Cleans triennial survey data by year and area |
| ReadInLengths.fn | Reads in the compositional survey data and filters the data... |
| SA3 | A data set for determining strata areas (hectares) |
| SA3_v2021.1 | A data set for determining strata areas (hectares) |
| save_rdata | Save an object in an '.rdata' file |
| SexRatio.fn | Assign sex to unsexed fish based on fish with similar traits |
| stopifnotcolumn | Stop if column name is not present in the data |
| StrataAreas.fn | Calculate strata area |
| StrataFactors.fn | Creates a vector of strata factors by name |
| SurveyAFs.fn | Create marginal age composition data |
| SurveyAgeAtLen.fn | Calculates conditional age-at-length composition data |
| SurveyLFs.fn | Expands the lengths up to the total stratum area then sums... |
| UnexpandedAFs.fn | Creates a matrix of unexpanded age compositions |
| UnexpandedLFs.fn | Creates a matrix of unexpanded length composition data |
| wh_plot_proportion | Save figures of proportions by depth and latitude using... |
