Calculate unexpanded/raw length or marginal age compositions

Usage

get_raw_comps(
  data,
  comp_bins,
  comp_column_name = "Length_cm",
  input_n_method = c("stewart_hamel", "tows", "total_samples"),
  two_sex_comps = TRUE,
  month = "Enter Month",
  fleet = "Enter Fleet",
  partition = 0,
  ageerr = "Enter Numeric",
  Lbin_lo = -1,
  Lbin_hi = -1,
  age_low = lifecycle::deprecated(),
  age_high = lifecycle::deprecated(),
  age_error = lifecycle::deprecated(),
  dir = NULL,
  printfolder = "forSS3",
  verbose = TRUE
)

Arguments

data: A data frame that includes columns of year, sex, and length/ages. The data frame can be survey data pulled using pull_bio from the data warehouse or any data frame that includes column names of sex, year, and the comp_column_name. The sex column is expected to have sexes denoted by F, M, and U.
comp_bins: Vector of intergers to bin length or age data by create expanded composition data.Values above or below the minimum or maximum values in the vector are grouped into the first size or plus group size, respectively. For example, creating length compositions that uses a vector bin of seq(10, 50, 2) would create 2 cm bins where fish length between [0, 11.99) would be included in the 10 cm bin, fish of length [12, 13.99) would be included in the 12 cm bin, and all fish [50- Inf) would be included in the 50 cm plus bin.
comp_column_name: The column name to create composition data for. This column can be is used to determine whether to format the composition data for length or age compositions by looking for either age (e.g., age_years, Age, best_age) or length (e.g., Length, length, Length_cm) in the comp_column_name. The default is Length_cm.
input_n_method: Determines the default input sample size to add to the composition data for SS3. There are three options: c("stewart_hamel", "tows", "total_samples") where the default is "stewart_hamel".
two_sex_comps: Default TRUE. If TRUE composition data will be formatted for a Stock Synthesis two-sex model and if FALSE composition data will be formatted for a single-sex model.
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".
Lbin_lo: Lower age bin for all age composition data based on the expected format for Stock Synthesis. Default value of -1 which translates to the lowest age bin.
Lbin_hi: Upper age bin for all age composition data based on the expected format for Stock Synthesis. Default value of -1 which translates to the highest
age_low: Deprecated with nwfscSurvey 2.2. Use Lbin_lo instead.
age_high: Deprecated with nwfscSurvey 2.2. Use Lbin_hi instead.
age_error: Deprecated with nwfscSurvey 2.2. Use Lbin_hi instead.
dir: Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.
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.

Value

A list of length or marginal age compositions for sexed and unsexed fish formatted for Stock Synthesis.

Details

Creates a matrix of unexpanded (or raw) marginal length or age composition data formatted for Stock Synthesis. The code will return composition data for all sexes present in the data frame and no sex assignment is done for unsexed fish. The function will create composition data for either lengths or ages based on the comp_column_name. The function will return a list of composition data based upon the sexes present in the data for a two-sex model or all length/ages for single-sex model.

Author

Chantel Wetzel

Examples

if (FALSE) { # \dontrun{
bio <- pull_bio(
  common_name = "lingcod",
  survey = "NWFSC.Combo"
)

length_comps <- get_raw_comps(
  data = bio,
  comp_bins = seq(20, 70, 4)
)

age_comps <- get_raw_comps(
  data = bio,
  comp_bins = 1:20,
  comp_column_name = "Age"
)
} # }