R/change_lcomp_constant.R
change_lcomp_constant.RdThis function replaces the robustification value for length-composition data
in a .dat file that was read in using r4ss::SS_readdat()
with those specified in lcomp_constant.
It then writes a new file with name outfile into the working directory.
change_lcomp_constant(lcomp_constant, dat_list, outfile = NULL)The new value to be used. Must be a numeric value, as a proportion. For example 0.1 means 10 percent. See the Stock Synthesis manual for further information. A NULL value indicates no action resulting in using the current value, and a value of 0 will throw an error since that leads to an error when zeroes exist in the data. Instead use a very small value like 1e-07.
A Stock Synthesis data list object as read in from
SS_readdat.
Be sure to correctly specify which section of the data file you want
to work with when reading it in using the section argument.
Where, section = 1 reads in the input values used to run the model
and section = 2 reads in the expected values generated given all the
input to the OM. section = 3 is not used within ss3sim, but this
section provides bootstrapped data sets that have been sampled internally
within SS.
A character string specifying the file name to use
when writing the information to the disk. The string must include
the proper file extension. No file is written using the default value
of NULL, which leads to increased speed because writing the
file takes time and computing resources.
A modified Stock Synthesis .dat file, and that file returned invisibly
(for testing) as a vector of character lines.
The robustification constant is added to both the observed and expected proportions of length composition data, before being normalized internally. It is designed to help stabilize the model, but is unclear how and when to use it for optimal effect. The same value is used for all length data.