getComps: Aggregate length, age, or age-at-length composition data by...

In nwfsc-assess/PacFIN.Utilities: Generate fishery composition data from PacFIN data for the NWFSC

Aggregate length, age, or age-at-length composition data by strata

Description

getComps() first sets up the local environment and returns summaries by groupings.

Usage

getComps(
  Pdata,
  strat = NULL,
  Comps = c("LEN", "AGE", "AAL"),
  defaults = c("fleet", "fishyr", "season"),
  towid = c("SAMPLE_NO"),
  weightid = "Final_Sample_Size_L",
  verbose = TRUE
)

Arguments

Pdata	A data frame returned from PullBDS.PacFIN() containing biological samples. These data are stored in the Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014 and are pulled using sql calls.
strat	A vector of column names to stratify the output over. For example, if you wish to summarize by ageing method, then the argument would look like strat = "agemethod" or, if you want to look at fleets and gear, strat = c("fleet", "usegear").
Comps	The type of composition data to create. See the function call for the available options. The first option listed is the default, which creates conditional age-at-length compositions by adding both lengthcm and Age to the grouping structure.
defaults	The default stratification columns which will typically be left at their default value of c("fleet", "fishyr", "season").
towid	A vector of character values providing the column names that generate a unique id for each sample. The default is "SAMPLE_NO" but you can pass a vector where all of the columns identified will be united to create a unique identifier for the tow/sample.
weightid	A character value giving the column name that holds the value to be summed for each type and strata, such as weightid = "Final_Sample_Size_L", if you are interested in length data. Instead of the default, you might want to weight each stratification by the final sample sizes found for age data, i.e., weightid = "Final_Sample_Size_A". You can pass weightid any column that exists in Pdata. Legacy code did not allow you to name the column and Final_Sample_Size was hard coded in the function.
verbose	A logical specifying if output should be written to the screen or not. Good for testing and exploring your data but can be turned off when output indicates information that you already know. The printing of output to the screen does not affect any of the returned objects. The default is to always print to the screen, i.e., verbose = TRUE.

Details

This function uses the expansions created in getExpansion_1() and getExpansion_2() using "weightid". Thus, whatever column name is passed to weightid will be used as the weight for each group. See the documentation for the pass-through arguments, i.e., .... If you are interested in generating unexpanded comps, then use the get_raw_comps() function from the nwfscSurvey package.

Value

A long data frame of weights for each grouping structure. Columns identifying the grouping structures will come first, followed by columns with sample sizes per group by sex category. The documentation for these sample size columns is sparse because this function is set to be deprecated next cycle and replaced with a simplified path to writing composition data. But, information is present for males (abbreviated with an M), females (abbreviated with an F), unsexed (abbreviated with a U). If no sex is provided then it is assumed all are unsexed and will be returned as such.

Author(s)

Andi Stephens, Kelli F. Johnson

See Also

• getExpansion_2() should be run before this function.

• writeComps() can be run on the output from this function.

nwfsc-assess/PacFIN.Utilities documentation built on July 4, 2025, 9:06 a.m.