change_em_binning: Change population and observed length composition bins in an...
In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description Usage Arguments Author(s) See Also Examples

View source: R/change_em_binning.r

change_em_binning alters the bin structure for the population and length composition data in an SS estimation model. It is done by taking the original length composition info from the EM ss3.dat then changing according to the user's specification. If the data file also contails conditional age-at-length data then these data will be re-binned as well.

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change_em_binning(dat_list, dat_file_out, bin_vector, lbin_method = NULL,
  pop_binwidth = NULL, pop_minimum_size = NULL, pop_maximum_size = NULL,
  write_file = TRUE)

`dat_list`	An SS data list object as read in from `SS_readdat` in the r4ss package. Make sure you select option `section=2`.
`dat_file_out`	A string providing the path to the output SS3 `.dat` file.
`bin_vector`	A numeric vector of new length bins to substitute into the `ss3.dat` file.
`lbin_method`	A numeric value of either `NULL, 1, 2, 3` to change the lbin_method for the population bin. Only supports either `NULL, 1, 2` at the moment. `NULL` means to keep it unchanged.
`pop_binwidth`	*Population length bin width. Only necessary for `lbin_method=2`. Note that this value must be smaller than the bin width specified in length composition data `len_bins` or SS3 will fail (see notes in the SS3 manual).
`pop_minimum_size`	*Population minimum length bin value. 'Only necessary for `lbin_method=2`
`pop_maximum_size`	*Population maximum length bin value. Only necessary for `lbin_method=2`
`write_file`	Should the `.dat` file be written? The new `.dat` file will always be returned invisibly by the function. Setting `write_file = FALSE` can be useful for testing. Note that you must supply a value to the argument `dat_file_out`, but this argument can be set to any arbitrary value (such as `NULL`) if `write_file = FALSE`.

Kotaro Ono (length-composition rebinning), Sean Anderson (conditional age-at-length rebinning)

Other change functions: change_data, change_e, change_f, change_maturity, change_retro, change_tv

d <- system.file("extdata", package = "ss3sim")
f_in <- paste0(d, "/example-om/data.ss_new")
dat_list <- r4ss::SS_readdat(file = f_in, verbose = FALSE)
l <- change_em_binning(dat_list, dat_file_out = NULL, lbin_method = 1,
  bin_vector = seq(8, 30, by = 1), write_file = FALSE)
print(l$lbin_vector)
print(head(l$lencomp))

# An small example with conditional age-at-length re-binning:
f <- system.file("extdata", "models", "cod-om", "codOM.dat", package = "ss3sim")
d <- r4ss::SS_readdat(f, verbose = FALSE)

# Add catch at length data (and simplify the bin structure for this example)
olddat <- change_data(d, outfile = NULL, write_file = FALSE,
  types = c("len", "age", "cal"), fleets = 1, years = seq(2000, 2002),
  age_bins = 1:3, len_bins = 4:8)
olddat$agecomp
newdat <- change_em_binning(olddat, dat_file_out = NULL, bin_vector = c(4, 6, 8),
  lbin_method = 1, write_file = FALSE)
newdat$agecomp

# A larger conditional age-at-length re-rebinning example:
olddat <- change_data(d, outfile = NULL, write_file = FALSE,
 types = c("len", "age", "cal"), fleets = 1, years = seq(2000, 2005),
 age_bins = seq(1, 5), len_bins = round(seq(20, 30, length.out = 13), 1))

olddat$lbin_vector
head(olddat$lencomp)
head(olddat$agecomp)
newdat <- change_em_binning(olddat, dat_file_out = NULL, bin_vector = seq(20, 30, 2),
 lbin_method = 1, write_file = FALSE)
newdat$lbin_vector
head(newdat$lencomp)
newdat$agecomp