Description Usage Arguments Value Author(s)
format_input
Formats data, parameters, random effects, and mapped parameters for TMB input
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | format_input(
input,
data_avail,
Fpen,
SigRpen,
SigRprior,
LFdist,
C_type,
est_more,
fix_more,
est_F_ft,
f_startval_ft,
rdev_startval_t,
est_selex_f,
vals_selex_ft,
est_rdev_t,
mirror,
est_totalF,
prop_f
)
|
input |
tagged list of LIME inputs. Output from create_inputs. |
data_avail |
types of data included, must at least include LCX where X is the number of years of length composition data. May also include "Catch" or "Index" separated by underscore. For example, "LC10", "Catch_LC1", "Index_Catch_LC20". |
Fpen |
penalty on fishing mortality 0= off, 1=on |
SigRpen |
penalty on sigmaR, 0=off, 1=on |
SigRprior |
vector with prior info for sigmaR penalty, first term is the mean and second term is the standard deviation |
LFdist |
likelihood distribution for length composition data, default=0 for multinomial, alternate=1 for dirichlet-multinomial |
C_type |
default=0, NO catch data available. Copt=1 means the catch is in numbers, Copt2 means the catch is in weight. |
est_more |
list of variance parameters to estimate, must match parameter names: log_sigma_R, log_sigma_C, log_sigma_I, log_CV_L, log_sigma_F |
fix_more |
default=FALSE - parameters are fixed depending on the data available. Can also list vector of parameter names to fix at their starting values (use param_adjust and val_adjust to set these adjustments) |
est_F_ft |
default=TRUE, otherwise 0 for off and 1 for on |
f_startval_ft |
default=NULL and F starting values are at 0 for all years. Can also specify vector of F starting values for all years to be modeled (can start at truth for debugging). |
rdev_startval_t |
default=NULL and Recruitment deviation starting values are at 0 for all years. Can also specify vector of recruitment deviation starting values for all years to be modeled (can start at truth for debugging) |
est_selex_f |
default=TRUE to estimate selectivity parameters, can set to FALSE for all or multiple fleets |
vals_selex_ft |
input selectivity-at-length (columns) by fleet (rows) - negative values in the first column indicate to estimate selectivity |
est_rdev_t |
default=TRUE to estimate recruitment deviations, or specify vector with 0 to turn off deviations in a specific year and 1 to keep them on |
mirror |
vector of parameter names to mirror between fleets |
est_totalF |
TRUE estimate total F instead of by fleet |
prop_f |
proportion of catch from each fleet |
List, a tagged list of Data, Parameters, Random, Map
M.B. Rudd
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