SurveyAgeAtLen.fn: Calculates conditional age-at-length composition data

In nwfsc-assess/nwfscSurvey: Northwest Fisheries Science Center Survey

Calculates conditional age-at-length composition data

Description

This function has been deprecated as of version 2.6. Please use get_raw_caal().

Usage

SurveyAgeAtLen.fn(
  dir = NULL,
  datAL,
  datTows,
  strat.vars = c("Depth_m", "Latitude_dd"),
  strat.df = NULL,
  lgthBins = 1,
  ageBins = 1,
  sex = 3,
  SSout = TRUE,
  meanRatioMethod = TRUE,
  raw = TRUE,
  NAs2zero = TRUE,
  month = "Enter Month",
  fleet = "Enter Fleet",
  partition = 0,
  ageerr = "Enter Numeric",
  ageErr = lifecycle::deprecated(),
  returnSamps = FALSE,
  printfolder = "forSS3",
  verbose = TRUE
)

Arguments

dir	Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.
datAL	the biological data frame exctrated from the data warehouse using pull_bio()
datTows	the catch data frame extracted from the data warehouse using pull_catch()
strat.vars	Variables in both data frame that are used to define the stratas. Default is bottom depth (m) and latitudes (decimal degrees), i.e., c("Depth_m", "Latitude_dd").
strat.df	A data frame that defines the strata and provides the calculated areas for each strata returned from createStrataDF.fn().
lgthBins	Vector of length bins to create length compositions across. Values above or below the minimum or maximum values, respectively, are grouped into the first size or plus group size.
ageBins	Vector of age bins to create age compositions across. Values above or below the minimum or maximum values, respectively, are grouped into the first age or plus group age.
sex	Options of (0, 1, 2, 3). The integer will be used to define the sex column of the returned input for Stock Synthesis and specifies how the composition are treated with respect to sex. See the Stock Synthesis manual for more information. In short, 0 is for unsexed, 1 is females, 2 is males, and 3 is females and males. The default is 3.
SSout	A logical with the default of TRUE. If TRUE, the output is returned in a format that can be directly pasted into an SS3 data file.
meanRatioMethod	A logical with the default of TRUE. If TRUE, then the mean ratio is implemented instead of the total ratio. Search the source code for the equations if more information is needed.
raw	Logical input to define whether or not to expand numbers in the csv file with a default unexpanded sample numbers.
NAs2zero	A logical specifying if NAs should be changed to zeros. The default is TRUE.
month	Month the samples were collected based on the expected format for Stock Synthesis to determine the length/age estimate to compare to. Default "Enter Month".
fleet	A fleet number to assign the composition data to based on the expected format for Stock Synthesis. Default "Enter Fleet".
partition	Partition to assign the composition data based on the expected format for Stock Synthesis. Partition of 0 indicates that the composition data include all composition data, 1 for discarded composition data, and 2 for retained fish only. Default of 0.
ageerr	Number of ageing error vector to apply to the age data based on Stock Synthesis. Default "Enter Numeric".
returnSamps	A logical with the default of FALSE. A value of TRUE stops the function after the sample size is calculated.
printfolder	A string that will be appended to dir, creating a folder where the output will be saved. If specified as "", the output will just be saved directly in dir. The default is "forSS3".
verbose	A logical that specifies if you want to print messages and warnings to the console. The default is TRUE.

Author(s)

Allan Hicks and Chantel Wetzel

See Also

StrataFactors.fn

nwfsc-assess/nwfscSurvey documentation built on Feb. 16, 2025, 5:06 p.m.