Package index

All functions

AFSCforeign_hauls: Example data for AFSCforeign_hauls

Biomass.fn(): Calculates design based estimates from survey data for West Coast surveys.

CheckStrata.fn(): Calculate the number of observations by year and strata

CreateStrataDF.fn(): Create strata data frame using StrataAreas.fn

Format.AKSlope.fn(): Rename AFSC slope survey columns from data pulled before 2017

GetN.fn(): Calculate input sample sizes

GetSppDefault.fn(): Get Vector of Default Species Names for US West Coast

GetStrata.fn(): Get Default Strata

GetSurveyAbb.fn(): Get Survey Abbreviation

PlotBio.fn(): Plots the designed based biomass estimates with confidence intervals

PlotBioStrata.fn(): Plots the design-based biomass estimates by strata with confidence intervals

PlotFreqData.fn(): Plot length or age compositions by year in bubble plots

PlotMap.fn(): Plot two figures showing catch-per-unit-effort data

PlotPresenceAbsence.fn(): Plot showing presence and absence per haul by depth, latitude, or sex bin

PlotSexRatio.fn(): Function to plot sex ratio

PlotSexRatioStrata.fn(): Function to plot sex ratio by strata

PlotVarLengthAtAge.fn(): Plot variability of length at age

PullBio.fn(): Pull biological data (age, length, weight) from the NWFSC data warehouse The website is: https://www.webapps.nwfsc.noaa.gov/data This function can be used to pull a single species or all observed species In order to pull all species leave Name = NULL and SciName = NULL

PullCatch.fn(): Pull catch data from the NWFSC data warehouse

PullHaul.fn(): Pull haul data from the NWFSC data warehouse The website is: https://www.webapps.nwfsc.noaa.gov/data This function can be used to pull haul data and associated covariates

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 into what is necessary It reads in catch and station data and makes sure only the species necessary are kept

may want to keep NA (blank in Excel) to select the zero tows

removeCAN is a flag if you want tows in Canadian waters removed need the file called foreign_hauls.csv

SA3: A data set for determining strata areas (hectares)

SA3_v2021.1: A data set for determining strata areas (hectares)

SexRatio.fn(): Assign sex to unsexed fish based on fish with similar traits

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 over strata for each year

UnexpandedAFs.fn(): Creates a matrix of unexpanded age compositions

UnexpandedLFs.fn(): Creates a matrix of unexpanded length composition data

availablecells: Available grid cell locations for the survey

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

check_survey(): Check and create survey string

codify_sex() codify_sex_SS3(): 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 warehouse The website is: https://www.webapp.nwfsc.noaa.gov/data

draw_USEEZ(): Bounds the figure with the limits of the U.S. EEZ

draw_theme(): A ggplot2 theme for drawing maps

est_growth(): Estimate length-at-age using the von Bertanlaffy parametization

est_vbgrowth(): Estimate length-at-age using the von Bertanlaffy parametization

estimate_weight_length(): Calculate weight-length relationship parameters

filter_pull(): Filter data pulls

fit_vbgrowth(): Estimate von Bertanlaffy growth parameters from lengths and ages

get_design_based(): Calculates design based estimates from survey data for West Coast surveys.

get_expanded_comps(): Calculate expanded composition data for lengths and marginal ages

get_input_n(): Calculate input sample sizes

get_json(): Get json content from a URL

get_raw_comps(): Calculate unexpanded/raw length or marginal age compositions

get_species_info(): Get Species Information

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

plot_bio_patterns(): This function plots length by latitude and depth

plot_comps(): Plot frequency data as bubble plots

plot_cpue(): This function plots cpue and length by latitude and depth

plot_index(): Plots the design based biomass estimates with confidence intervals

plot_length_age(): Plots the length-at-age data and estimates

plot_proportion(): Plot proportions of factor levels (y axis) by bins (x axis)

plot_varlenage(): 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 data warehouse

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. The website is: https://www.webapps.nwfsc.noaa.gov/data.

pull_catch(): Pull catch data for satisfactory tows 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.

pull_spp(): Pull species names from the warehouse

save_rdata(): Save an object in an .rdata file

stopifnotcolumn(): Stop if column name is not present in the data

wh_plot_proportion(): Save figures of proportions by depth and latitude using warehouse data

All functions

may want to keep NA (blank in Excel) to select the zero tows