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Expands the lengths up to the total stratum area then sums over strata for each year

SurveyLFs.fn.Rd

Create expanded length 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.

Usage

SurveyLFs.fn(
  dir = NULL,
  datL,
  datTows,
  strat.vars = c("Depth_m", "Latitude_dd"),
  strat.df = NULL,
  lgthBins = 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,
  sum100 = TRUE,
  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.

datL

A data frame of length-composition data returned from pull_bio().

datTows

A data frame of catch data returned from 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().

lgthBins

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

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

A numerical value within [0.0, 1.0] that will be used as the sex ratio for measured individuals less than maxSizeUnsexed. If NA_real_, then the sex ratio for stage-1 expansion will not be conducted.

maxSizeUnsexed

A numerical value specifying the right side of the following bin [0, maxSizeUnsexed], where all fish measured in this bin are assigned a sex based on sexRatioUnsexed. Fish with a measurement larger than this value will be assigned a sex based on the calculated sex ratio in the data.

sexRatioStage

(1, 2). The stage of the expansion to apply the sex ratio. The default is 1.

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 single integer value. A user input fleet number to assign to the fleet column based on the expected format for Stock Synthesis. Default "Enter Fleet".

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 datL 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 length bin. Default TRUE.

outputStage1

A logical specifying if you would like the function to stop after the end of the first stage of the expansion process and return output that is not ready for Stock Synthesis. This can be helpful when wanting output that can be used as input for VAST.

sum100

A logical value specifying whether to rescale the compositions to sum to 100. The default is TRUE.

verbose

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

See also

Author

Allan Hicks (16 March 2009) and Chantel Wetzel (maintainer)