SS_write_comps: Function to write age and length composition data from...

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Function to write age and length composition data from atlantisom to Stock Synthesis 3.30. Note: every time this function is called, it overwrites the age and length composition data currently in the ss_data_list object.

Description

Function to write age and length composition data from atlantisom to Stock Synthesis 3.30. Note: every time this function is called, it overwrites the age and length composition data currently in the ss_data_list object.

Usage

SS_write_comps(
  ss_data_list,
  comp_matrix,
  data_rows,
  sampling_month,
  data_type,
  fleet_number,
  bins,
  caal_bool
)

Arguments

ss_data_list	the list object containing SS data
comp_matrix	a list, where each list item is the matrix of composition data (age or length)
data_rows	a list, where each entry is a vector corresponding to the year column of the composition data. For length and age composition data, this is the 1:nyears repped each row for the number of length or age bins. For conditional age-at-length composition data, this is nyears:lengthbins .
sampling_month	a list where each list item is a vector of the sampling month for each composition data type
data_type	a vector of strings, each entry needs to be either "agecomp" or "lengthcomp"
fleet_number	a vector of numbers, each entry corresponds to which fleet the comp data are from
bins	a list item, each item is a vector specifying either the age or length bins
caal_bool	a vector of length ss_data_list with boolean values for whether the data is conditional age-at-length

Value

modified ss_data_list that includes added composition data

r4atlantis/atlantisom documentation built on Nov. 12, 2023, 2:59 a.m.