get_expanded_comps: Calculate expanded composition data for lengths and marginal...

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

Calculate expanded composition data for lengths and marginal ages

Description

Conduct a two-stage expansion of length and age composition data. The first stage expands data up to the tow level and the second stage expands the data up the user-defined strata areas. This function is designed to be used with catch pulled using pull_catch() and biological data pulled using pull_bio().

Usage

get_expanded_comps(
  bio_data,
  catch_data,
  comp_bins,
  strata,
  dir = NULL,
  comp_column_name = "length_cm",
  output = c("full_expansion_ss3_format", "tow_expansion_only",
    "full_expansion_unformatted"),
  two_sex_comps = TRUE,
  input_n_method = c("stewart_hamel", "tows", "total_samples"),
  partition = 0,
  fleet = "Enter Fleet",
  age_low = -1,
  age_high = -1,
  age_error = "Enter Numeric",
  month = "Enter Month",
  printfolder = "forSS3",
  verbose = TRUE
)

Arguments

bio_data	A data frame of length-composition data returned from pull_bio().
catch_data	A data frame of catch data returned from pull_catch().
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.
strata	A data frame that defines the strata and provides the calculated areas for each strata returned from createStrataDF.fn().
dir	Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.
comp_column_name	The name of the column to create composition data for that must be a string. 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, age, best_age) or length (e.g., length, length_cm, Length, Length_cm) in the comp_column_name. The comp_column_name is not case sensitive.The default is length_cm.
output	Switch to specify how to return the composition data where the options are c("full_expansion_ss3_format", "tow_expansion_only", "full_expansion_unformatted"). The default is output = "full_expansion_ss3_format" where a list is returned with formatted composition data for SS3. The tow_expansion_only retuns a dataframe of composition data only expanded up to the tow level (first-stage) and full_expansion_unformatted returns a dataframe with compositon data expanded up to the tow and strata level but not formatted for SS3.
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.
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".
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.
fleet	A fleet number to assign the composition data to based on the expected format for Stock Synthesis. Default "Enter Fleet".
age_low	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.
age_high	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_error	Number of ageing error vector to apply to the age data based on Stock Synthesis. Default "Enter Age Error Vector".
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".
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 or dataframe is returned depending upon output. The default output = "full_expansion_ss3_format" returns a list of expanded composition data by sex grouping (e.g., sexed and unsexed fish) formatted for Stock Synthesis v.3.30+. If output = "full_expansion_unformatted" a dataframe is returned of unformatted expanded composition data and if output = "tow_expansion_only" a dataframe is returned with the composition data only expanded to the tow level (first stage expansion only).

Author(s)

Chantel Wetzel and Allan Hicks

See Also

See get_input_n for information on input sample size calculations.

Examples

## Not run: 
bio <- pull_bio(
  common_name = "lingcod",
  survey = "NWFSC.Combo"
)

catch <- pull_catch(
  common_name = "lingcod",
  survey = "NWFSC.Combo"
)

strata <- CreateStrataDF.fn(
  names = c("shallow_wa", "shallow_or", "shallow_nca", "shelf_wa", "shelf_or", "shelf_nca"),
  depths.shallow = c(55, 55, 55, 183, 183, 183),
  depths.deep = c(183, 183, 183, 350, 350, 350),
  lats.south = c(46.0, 42.0, 40.10, 46.0, 42.0, 40.10),
  lats.north = c(49.0, 46.0, 42.0, 49.0, 46.0, 42.0)
)

length_comps <- get_expanded_comps(
  bio_data = bio,
  catch_data = catch,
  strata = strata,
  comp_bins = seq(20, 70, 4),
  comp_column_name = "length_cm"
)

## End(Not run)

nwfsc-assess/nwfscSurvey documentation built on Oct. 23, 2024, 10:59 a.m.