sample_comp: Sample composition data from expected values
In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description Usage Arguments Details Value Author(s)

Apply the multinomial or Dirichlet distribution to sample composition data, creating a data frame that mimics observed composition data.

1	sample_comp(data, Nsamp, fleets, years, ESS = NULL, cpar = 1)

`data`	A data frame with informational columns followed by columns of compositional data. The informational columns must include columns labeled 'Yr' and 'FltSvy' and end with a column labeled 'Nsamp'. Columns of compositional data should follow 'Nsamp'. Rows of compositional data do not need to sum to one.
`Nsamp`	*A numeric list of the same length as `fleets`. Either single values or vectors of the same length as the number of years can be passed through. Single values are repeated for all years. If no fleet collected samples, keep the value to `Nsamp=NULL`.
`fleets`	*A vector of integers specifying which fleets to include. The order of the fleets pertains to the input order of other arguments. An entry of `fleets=NULL` leads to zero samples for any fleet.
`years`	*A list the same length as `fleets` giving the years as numeric vectors. If no fleet collected samples, keep the value to `years=NULL`.
`ESS`	The final effective sample size (ESS) associated with the simulated data. The ESS is not used to generate the simulated data but can be used as an input sample size in subsequent models that estimate population parameters or status. The default, `NULL`, leads to the true (internally calculated) #' ESS being used, which is `Nsamp` for the multinomial case or given by the formula under `cpar` for the Dirichlet case. At least one value must be provided for each fleet or a vector of year-specific values can be used for any given fleet. The argument accepts a list with entries, either a single integer or a vector of integers, for each fleet.
`cpar`	A numeric value or vector the same length as `fleets` controlling the variance of the Dirichlet distribution used for sampling. A value of `1` leads to the same standard deviation as a multinomial of the given `Nsamp`, `2` indicates twice, etc. Values greater than one indicate overdispersion, and less underdispersion. `NULL` or `NA` for a given fleet will lead to no dispersion.

Sample size, i.e., 'Nsamp', is used as a measure of precision, where higher sample sizes lead to simulated samples that more accurately represent the truth provided in data.

A data frame of observed composition data.

Kelli Faye Johnson

ss3sim documentation built on Nov. 9, 2019, 1:06 a.m.