Calculates conditional age-at-length composition data

Calculates conditional age-at-length composition data using raw numbers at length, assuming that is a random sample conditioned on length and sex.

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 Age Error",
  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: A single integer value between 1-12. A user input fleet number to assign to the month column based on the expected format for Stock Synthesis. See the Stock Synthesis manual for more information. Default "Enter Month".
fleet: A single integer value. A user input fleet number to assign to the fleet column 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: Single interget value of ageing error vector to apply to the age data based on Stock Synthesis. Default "Enter".
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

Allan Hicks and Chantel Wetzel

Usage

Arguments

See also

Author