Package index • PacFIN.Utilities

All functions
`EF1_Denominator()`	Calculate the denominator for the level-1 expansion factor.
`EF1_Numerator()`	Calculate the numerator for the first level expansion factor
`PacFIN.Utilities-package` `PacFIN.Utilities`	PacFIN.Utilities: Functions for working up PacFIN data
`PullBDS.PacFIN()`	Pull biological data
`PullCatch.PacFIN()`	Pull catch data from PacFIN
`PullNominal.PacFIN()`	Pull the species information table and return nominal code(s)
`age_representativeness_plot()`	Compare length histogram of aged samples to all lengthed samples
`ask_password()`	Get password from the user if `interactive()`
`capValues()`	Decrease all values greater than a maximum specified value.
`changecol_pacfin()`	Change Column Names of PacFIN Data To Match Survey
`checkGrade()`	Check Sample Numbers for Grade
`checkLenAge()`	Calculate von Bertalanffy Growth Parameters
`cleanColumns()`	Change Column Names to Vdrfd
`cleanColumns.bds()`	Clean columns of PacFIN biological data
`cleanColumns.catch()`	Clean columns of PacFIN catch data
`cleanPacFIN()`	Clean raw PacFIN data
`codify_age_method()`	Code ageing methods to standardized character strings
`combineCalCOM()`	Combine CalCOM and PacFIN data
`comps_bins()`	Bin a vector of data into groups
`comps_wide()`	Convert long data frame with composition data to wide data frame
`convertlength_skate()`	Convert Disc and Interspiracular Width to Length
`doSexRatio()`	Assign gender for unsexed fish
`find.matching.rows()`	Function find.matching.rows
`formatCatch()`	Format catches from long to wide
`getAge()`	Get age information for each fish
`getAgeMethod()`	Get the ageing method used for the age that is agreed to be the best age
`getArea()`	Get the general area that the information was taken from
`getComps()` `getcomps_long()`	Aggregate length, age, or age-at-length composition data by strata
`getDB()`	Get a connection to a database and return a query
`getExpansion_1()`	First-Stage Expansion for Composition Data
`getExpansion_2()`	Second-stage expansion of composition samples up to catch level
`getGearGroup()`	Create column for gear called `geargroup` according to PacFIN gears
`getLength()`	Get length for PacFIN commercial samples
`getSeason()`	Add a column to `Pdata` for season.
`getState()`	Create a state column based on input column specified in `source`
`getUserName()`	Get your username for the `database` of interest
`getWLpars()`	Calculate weight-length relationship parameters
`get_codelist()`	Get a list of available options, e.g., code_list, from PacFIN
`getweight()`	Calculate weight from length and the weight-length relationship
`grep_final_age()`	Find the column with the best age information
`plotCleaned()`	Plot cleaned fishery age- or length-composition data.
`plotRawData()`	Diagnostic plots and summaries for a raw PacFIN dataset pre-filtering.
`plotStrat()`	Plot Length Distributions with Aged and All Fish
`plotWL()`	Plot of the weight-length relationship by sex
`sql_area()` `sql_bds()` `sql_catch()` `sql_species()` `sql_check_FINAL_FISH_AGE_IN_YEARS()`	Write SQL text
`stopifnotcolumn()`	Stop if column name is not present in the data
`summaryAgeMethod()`	The number of samples per combination of ageing methods
`tableSample()`	Table of Sample Size By Fleet and Year
`writeComps()`	Write out composition data formatted for Stock Synthesis.

Reference

All functions