Class-RCMdata — RCMdata-class • SAMtool

An S4 class for the data inputs into RCM.

Slots

Chist

Either a vector of historical catch, should be of length OM@nyears, or if there are multiple fleets, a matrix of OM@nyears rows and nfleet columns. Ideally, the first year of the catch series represents unfished conditions (see also slot C_eq).

C_sd

Same dimension as Chist. Lognormal distribution standard deviations (by year and fleet) for the catches in Chist. If not provided, the default is 0.01. Not used if RCM(condition = "catch2").

Ehist

A vector of historical effort, should be of length OM@nyears, or if there are multiple fleets: a matrix of OM@nyears rows and nfleet columns. See also slot E_eq).

C_wt

Optional weight at age for the catch Chist. Array with dimension [OM@nyears+1, OM@maxage+1, nfleet].

CAA

Fishery age composition matrix with nyears rows and OM@maxage+1 columns, or if multiple fleets: an array with dimension: nyears, OM@maxage+1, nfleet. Enter NA for years without any data. Raw numbers will be converted to annual proportions (see slot CAA_ESS for sample sizes).

CAA_ESS

Annual sample size (for the multinomial distribution) of the fishery age comps. A vector of length OM@nyears, or if there are multiple fleets: a matrix of OM@nyears rows and nfleet columns. Enter zero for years without observations. An annual cap to the ESS, e.g., 50, can be calculated with something like: pmin(apply(CAA, c(1, 3), sum, na.rm = TRUE), 50). By default,

CAL

Fishery length composition matrix with nyears rows and n_bin columns (indexing the length bin), or if multiple fleets: an array with dimension: nyears, n_bin, nfleets. Enter NA for years without any data. Raw numbers will be converted to annual proportions (see slot CAL_ESS for sample sizes).

CAL_ESS

Annual sample size (for the multinomial distribution) of the fishery length comps. Same dimension as CAA_ESS.

length_bin

A vector (length n_bin) for the midpoints of the length bins for CAL and IAL, as well as the population model, if all bin widths are equal in size. If length bins are unequal in width, then provide a vector of the boundaries of the length bins (vector of length n_bin + 1).

MS

Mean mean size (either mean length or mean weight) observations from the fishery. Same dimension as Chist. Generally, mean lengths should not be used alongside CAL, unless mean length and length comps are independently sampled.

MS_type

A character (either "length" (default) or "weight") to denote the type of mean size data.

MS_cv

The coefficient of variation of the observed mean size. If there are multiple fleets, a vector of length nfleet. Default is 0.2.

Index

Index of abundance. Enter NA for missing values. A vector length OM@nyears, or if there are multiple surveys: a matrix of OM@nyears rows and nsurvey columns.

I_sd

A vector or matrix of standard deviations (lognormal distribution) for the indices corresponding to the entries in Index. Same dimension as Index. If not provided, this function will use values from OM@Iobs.

I_wt

Optional weight at age for the index Index. Array with dimension [OM@nyears, OM@maxage+1, nsurvey].

IAA

Index age composition data, an array of dimension nyears, maxage+1, nsurvey. Raw numbers will be converted to annual proportions (see IAA_ESS for sample sizes).

IAA_ESS

Annual sample size (for the multinomial distribution) of the index age comps. A vector of length OM@nyears. If there are multiple indices: a matrix of OM@nyears rows and nsurvey columns.

IAL

Index length composition data, an array of dimension nyears, n_bin, nsurvey. Raw numbers will be converted to annual proportions (see slot IAL_ESS to enter sample sizes).

IAL_ESS

Annual sample size (for the multinomial distribution) of the index length comps. Same dimension as IAA_ESS.

C_eq

Vector of length nfleet for the equilibrium catch for each fleet in Chist prior to the first year of the operating model. Zero (default) implies unfished conditions in year one. Otherwise, this is used to estimate depletion in the first year of the data. Alternatively, if one has a full CAA matrix, one could instead estimate "artificial" rec devs to generate the initial numbers-at-age (and hence initial depletion) in the first year of the model (see additional arguments in RCM).

C_eq_sd

A vector of standard deviations (lognormal distribution) for the equilibrium catches in C_eq. Same dimension as C_eq. If not provided, the default is 0.01. Only used if RCM(condition = "catch").

E_eq

The equilibrium effort for each fleet in Ehist prior to the first year of the operating model. Zero (default) implies unfished conditions in year one. Otherwise, this is used to estimate depletion in the first year of the data.

abs_I

An integer vector length nsurvey to indicate which indices are in absolute magnitude. Use 1 to set q = 1, otherwise use 0 (default) to estimate q.

I_units

An integer vector of length nsurvey to indicate whether indices are biomass based (1) or abundance-based (0). By default, all are biomass-based.

I_delta

A vector of length nsurvey to indicate the timing of the indices within each time step (0-1, for example 0.5 is the midpoint of the year). By default, zero is used. Can also be a matrix by nyears, nsurvey. Use -1 if the survey operates continuously, the availability would be N * (1 - exp(-Z))/Z.

age_error

A square matrix of maxage + 1 rows and columns to specify ageing error. The aa-th column assigns a proportion of animals of true age aa to observed age a in the a-th row. Thus, all rows should sum to 1. Default is an identity matrix (no ageing error).

sel_block

For time-varying fleet selectivity (in time blocks), a integer matrix of nyears rows and nfleet columns to assign a selectivity function to a fleet for certain years. By default, constant selectivity for each individual fleet. See the selectivity article for more details.

Misc

A list of miscellaneous inputs. Used internally.

Author

Q. Huynh