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, then runs getcomps_long(), and finally returns the results of getcomps_long(), which calculates summaries by groupings. getcomps_long() was developed to make use of tidyverse but it still produces all of the old output. In the future, this function will be replaced by code that can summarize both survey data or commercial data. Until then, this is the best we can do and it mimics old output such that legacy code will not break. You can and should pass arguments to getcomps_long() using pass through arguments in your call to getComps(), i.e., ..., especially when calculating composition data related to age. See the input arguments for more details.

Usage

getComps(
  Pdata,
  strat = NULL,
  Comps = c("AAL", "LEN", "AGE"),
  defaults = c("fleet", "fishyr", "season"),
  verbose = lifecycle::deprecated(),
  ...
)

getcomps_long(
  data,
  towstrat,
  type,
  towid = "SAMPLE_NO",
  weightid = "Final_Sample_Size_L",
  dropmissing = TRUE
)

Arguments

Pdata	A data frame of biological samples originating from the Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014. Data are pulled using sql calls, see PullBDS.PacFIN().
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").
verbose	Is deprecated as of version 0.2.8. No information is printed to the screen from this function.
...	Pass additional arguments to getcomps_long(), such as dropmissing = FALSE where the default behavior is dropmissing = TRUE. The most important argument to consider modifying is getComps(weightid = "Final_Sample_Size_L"), which will only be applicable to length data. Instead of the default, you might want to weight each stratification by the final sample sizes found for age data, i.e., getComps(weightid = "Final_Sample_Size_A"). You can pass weightid any column that exists in Pdata. Legacy code required you to set Final_Sample_Size outside of a function call with something like Pdata$Final_Sample_Size = Pdata$Expansion_Factor_1 * Pdata$Expansion_Factor_2 and all weighting was done on the column called "Final_Sample_Size" but this is no longer the case.
data	A data frame. The data frame must have the column names that are specified for the next four input arguments, towstrat, type, towid, and weightid.
towstrat	A vector of character values providing the column names for which you want compositions for.
type	A character value specifying which category to summarize by, i.e., "length" or "Age".
towid	A vector of character values providing the column names that generate a unique id for each sample.
weightid	A character value giving the column name that holds the value to be summed for each type and strata.
dropmissing	A logical value supplied to the drop argument in stats::aggregate() that specifies whether or not to keep all levels in the data even if there are no values to report for summaries.

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., ...

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 (sometimes abbreviated with an m), females (sometimes abbreviated with an f), unsexed (sometimes abbreviated with a u), and sexed (noted as both or b) records. If no sex is provided then it is assumed all are unsexed and will be returned as such.

Functions

• getcomps_long(): The actual workhorse behind getComps().

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 March 19, 2024, 11:54 p.m.