# Change population and observed length composition bins in an SS estimation model `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 contains conditional age-at-length data then these data will be re-binned as well. ```r change_em_binning(dat_list, outfile = NULL, bin_vector, lbin_method = NULL, pop_binwidth = NULL, pop_minimum_size = NULL, pop_maximum_size = NULL) ``` ## 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`. - `outfile`: 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. - `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` ## Examples ```r # Note that typically this function is used with estimation models in ss3sim, # but it is used with an operating model data file in the following examples. f <- system.file("extdata", "models", "cod-om", "codOM.dat", package = "ss3sim") d <- r4ss::SS_readdat(f, version = NULL, verbose = FALSE) # An example with lbin_method = 1 l1 <- change_em_binning(d, outfile = NULL, lbin_method = 1, bin_vector = seq(20, 152, by = 4)) l1$lbin_vector head(l1$lencomp) #An example with lbin_method = 2 new_bin_vec <- seq(min(d$lbin_vector), max(d$lbin_vector), by = 4) # add the max value if necessary. if(new_bin_vec[length(new_bin_vec)] != d$lbin_vector[length(d$lbin_vector)]){ new_bin_vec <- c(new_bin_vec, d$lbin_vector[length(d$lbin_vector)]) } pop_bin_input <- 5 pop_min_size_input <- min(d$lbin_vector_pop) - 1 pop_max_size_input <- max(d$lbin_vector_pop) + 5 lbin_vec_pop <-seq(pop_min_size_input, pop_max_size_input, length.out = (pop_max_size_input - pop_min_size_input)/ pop_bin_input + 1 ) l2 <- change_em_binning(dat_list = d, bin_vector = new_bin_vec, lbin_method = 2, #Note: need more inputs with lbin_method = 2 pop_binwidth = pop_bin_input, pop_minimum_size = pop_min_size_input, pop_maximum_size = pop_max_size_input) l2$lbin_method # note bin width is now the same as the input pop_bin_input l2$binwidth # note the minimum size has changed based on the input: pop_min_size_input l2$minimum_size # so has max l2$maximum_size l2$lbin_vector #other modified components: l2$lbin_vector_pop head(l2$lencomp) ``` ## See Also Other change functions: `change_data`, `change_e`, `change_f_par`, `change_f`, `change_o`, `change_retro`, `change_tv` ## Author(s) Kotaro Ono (length-composition rebinning), Sean Anderson (conditional age-at-length rebinning)

change_em_binning function