Create marginal age composition data

Create marginal age composition data

Usage

SurveyAFs.fn(
  dir = NULL,
  datA,
  datTows,
  strat.vars = c("Depth_m", "Latitude_dd"),
  strat.df = NULL,
  ageBins = 1,
  SSout = TRUE,
  meanRatioMethod = TRUE,
  sex = 3,
  NAs2zero = T,
  sexRatioUnsexed = NA,
  maxSizeUnsexed = NA,
  sexRatioStage = 1,
  partition = 0,
  fleet = "Enter Fleet",
  agelow = "Enter",
  agehigh = "Enter",
  ageErr = "Enter",
  nSamps = "Enter Samps",
  month = "Enter Month",
  printfolder = "forSS3",
  remove999 = TRUE,
  outputStage1 = FALSE,
  verbose = TRUE
)

Arguments

dir

Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.

datA

the biological data frame exctrated from the data warehouse using the pull_bio()

datTows

the catch data frame extracted from the data warehouse using the pull_catch()

strat.vars

Variables in both data frame that are used to define the stratas. Default is bottom depth (m) and latitudes (decimal degrees), i.e., c("Depth_m", "Latitude_dd").

strat.df

A data frame that defines the strata and provides the calculated areas for each strata returned from createStrataDF.fn().

ageBins

Vector of age bins to create age compositions across. Values above or below the minimum or maximum values, respectively, are grouped into the first age or plus group age.

SSout

A logical with the default of TRUE. If TRUE, the output is returned in a format that can be directly pasted into an SS3 data file.

meanRatioMethod

A logical with the default of TRUE. If TRUE, then the mean ratio is implemented instead of the total ratio. Search the source code for the equations if more information is needed.

sex

Options of (0, 1, 2, 3). The integer will be used to define the sex column of the returned input for Stock Synthesis and specifies how the composition are treated with respect to sex. See the Stock Synthesis manual for more information. In short, 0 is for unsexed, 1 is females, 2 is males, and 3 is females and males. The default is 3.

NAs2zero

A logical specifying if NAs should be changed to zeros. The default is TRUE.

sexRatioUnsexed

sex ratio to apply to any length bins of a certain size or smaller as defined by the maxSizeUnsexed

maxSizeUnsexed

all sizes below this threshold will assign unsexed fish by sexRatio set equal to 0.50, fish larger than this size will have unsexed fish assigned by the calculated sex ratio in the data.

sexRatioStage

1/2 apply the sex ratio based on the tows (1) or the expanded numbers (2)

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.

agelow

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.

agehigh

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

ageErr

Single interget value of ageing error vector to apply to the age data based on Stock Synthesis. Default "Enter".

nSamps

Vector of integer sample sizes. A vector of sample sizes for all years in datA is required if a vector is provided. The input vector will be included in the output marginal age composition data. One option for calculating input sample size is the GetN.fn(). The default is "Enter Samps".

month

A single integer value between 1-12. A user input fleet number to assign to the month column based on the expected format for Stock Synthesis. See the Stock Synthesis manual for more information. 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".

remove999

The output object by the function will have the 999 column combined with the first age bin. Default TRUE.

outputStage1

return the first stage expanded data without compiling it for SS3

verbose

A logical that specifies if you want to print messages and warnings to the console. The default is TRUE.

Details

Create expanded marginal age composition data based on the pre-specified strata. This function is designed to be used with catch pulled using pull_catch() and biological data pulled using pull_bio(). The default output is formatted based on the formatting required by Stock Synthesis.

See also

SurveyLFs.fn

Author

Allan Hicks and Chantel Wetzel