writeComps: Write out composition data formatted for Stock Synthesis

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

Write out composition data formatted for Stock Synthesis

Description

Write out composition data to a file, binning the data as specified to work in a Stock Synthesis model. Note, that this function does not work for conditional age-at-length data because it is assumed that one would not want to estimate growth in that way from fishery-dependent data.

Usage

writeComps(
  inComps,
  comp_bins,
  fname = NULL,
  abins = lifecycle::deprecated(),
  lbins = lifecycle::deprecated(),
  column_with_input_n = c("n_tows", "n_stewart", "n_fish"),
  maxAge = lifecycle::deprecated(),
  month = 7,
  partition = 2,
  ageErr = 0,
  dummybins = lifecycle::deprecated(),
  sum1 = lifecycle::deprecated(),
  digits = 4,
  overwrite = lifecycle::deprecated(),
  verbose = FALSE
)

Arguments

inComps	A dataframe returned from getComps().
comp_bins	The binning structure to use for ages and lengths.
fname	A filename with the appropriate extension, used to save the function output to the disk. For example, LenComps.csv or file.path(getwd(), "LenComps.csv"). Full, relative, or simple paths are allowed because the argument is used as is, i.e., not redirected to a directory different than getwd(). Note that various functions within pacfintools have different default values for this input argument. If NULL in writeComps, then no csv file will be written to disk.
abins, lbins	Deprecated as of 0.2.10 to reduce complication in the code and make it more intuitive for the user when running this function. The binning structure to use for ages and lengths. For both arguments, the default is NULL which leads to the natural bins of the data being used, i.e., no additional binning is performed.
column_with_input_n	A string providing the column name with the appropriate value for the input sample size that will be given to Stock Synthesis as input_n (what we and nwfscSurvey provide as a column name) or NSamp (what Stock Synthesis wants as a name). The default is "n_tows", which is the number of tows that were performed for the given stratifications passed to getComps() that created inComps. One might want to use "n_fish" or some column that you created yourself.
maxAge	Deprecated as of 0.2.10 to reduce complication in the code and make it more intuitive for the user when running this function. All fish present in inComps will be binned according to the bins provided or the bins present.
month	Month for all observations. Defaults to 7. If input has multiple seasons, this must be a vector of equal length to the maximum seasons where the order of months in the vector will be assigned to season in ascending order. For example, if there are two seasons and the month = c(1, 7) season 1 will be assigned to month 1 and season 2 to month 7.
partition	Used by Stock Synthesis for length- or age-composition data where 0 = retained + discarded, 1 = discarded, and 2 = retained fish. The default is to assume that these fish are retained only. The default was changed in 2020 from a value of 0, and code should be updated accordingly if you really want 0.
ageErr	Defaults to 1 to use the first ageing error matrix specified in your Stock Synthesis model.
dummybins	Deprecated as of version 0.2.10 because you can just run the function with different abins or lbins rather than this function changing the first and end bin for you. The original default, years ago was TRUE, then it was changed to FALSE. Now, without this argument, it is essentially FALSE.
sum1	Deprecated as of version 0.2.10 because SS3 will normalize the composition data for you and thus it does not need to be done here. The previous default was FALSE so the removal of this argument does not change the default behavior of this function.
digits	Integer indicating the number of decimal places to round value to (value is passed to round()). The default is 4, which will lead to rounding to four digits. If you do not want to round the results, then use Inf, which will lead to the use of R's default precision.
overwrite	Deprecated as of version 0.2.10. The file will be automatically overwritten if present.
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

The structure of the input dataframe determines whether the results produce age- or length-composition data. As of version 0.2.10, conditional age-at-length compositions are no longer available within this function.

Composition data are raw weights rather than proportions. Stock Synthesis internally converts these to proportions. The raw weights should be examined for anomalies. To create proportions use prop.table() on the columns containing composition data.

The columns in the output preceding 'lengthcm' or 'Age' are those that were used in stratifying the data.

Value

A data frame is returned and a .csv is created and written to the disk with the same data frame.

Author(s)

Andi Stephens, Chantel R. Wetzel, Kelli F. Johnson, Ian G. Taylor

See Also

• getComps()

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