change_em_binning: Change population and observed length composition bins in an...

In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description

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.

Usage

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)

Arguments

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.

Author(s)

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

See Also

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

Examples

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

ss3sim documentation built on May 30, 2017, 6:41 a.m.