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Rapid Conditioning Model (RCM)

Source: R/RCM_data.R, R/define_S4_generic_RCM.R
RCM.Rd

Intended for conditioning operating models for MSEtool. For data-limited stocks, this function can generate a range of potential depletion scenarios inferred from sparse data. From a historical time series of total catch or effort, and potentially age/length compositions and multiple indices of abundance, the RCM returns a range of values for depletion, selectivity, unfished recruitment (R0), historical fishing effort, and recruitment deviations for the operating model. This is done by sampling life history parameters provided by the user and fitting a statistical catch-at-age model (with the predicted catch equal to the observed catch). Alternatively one can do a single model fit and sample the covariance matrix to generate an operating model with uncertainty based on the model fit. Either a full catch (conditioned on catch) or effort (conditioned on effort) time series is needed but missing data (as NAs) are allowed for all other data types. check_RCMdata evaluates whether the inputs in the S4 RCMdata object are correctly formatted.

Usage

check_RCMdata(RCMdata, OM, condition = "catch", silent = FALSE)

RCM(OM, data, ...)

# S4 method for class 'OM,RCMdata'
RCM(
  OM,
  data,
  condition = "catch",
  selectivity = "logistic",
  s_selectivity = NULL,
  LWT = list(),
  comp_like = c("multinomial", "lognormal", "mvlogistic", "dirmult1", "dirmult2"),
  prior = list(),
  max_F = 3,
  cores = 1L,
  integrate = FALSE,
  mean_fit = FALSE,
  drop_nonconv = FALSE,
  drop_highF = FALSE,
  control = list(iter.max = 2e+05, eval.max = 4e+05),
  start = list(),
  map = list(),
  silent = FALSE,
  ...
)

# S4 method for class 'OM,list'
RCM(
  OM,
  data,
  condition = "catch",
  selectivity = "logistic",
  s_selectivity = NULL,
  LWT = list(),
  comp_like = c("multinomial", "lognormal", "mvlogistic", "dirmult1", "dirmult2"),
  ESS = c(30, 30),
  prior = list(),
  max_F = 3,
  cores = 1L,
  integrate = FALSE,
  mean_fit = FALSE,
  drop_nonconv = FALSE,
  drop_highF = FALSE,
  control = list(iter.max = 2e+05, eval.max = 4e+05),
  start = list(),
  map = list(),
  silent = FALSE,
  ...
)

# S4 method for class 'OM,Data'
RCM(
  OM,
  data,
  condition = "catch",
  selectivity = "logistic",
  s_selectivity = NULL,
  LWT = list(),
  comp_like = c("multinomial", "lognormal", "mvlogistic", "dirmult1", "dirmult2"),
  ESS = c(30, 30),
  prior = list(),
  max_F = 3,
  cores = 1L,
  integrate = FALSE,
  mean_fit = FALSE,
  drop_nonconv = FALSE,
  drop_highF = FALSE,
  control = list(iter.max = 2e+05, eval.max = 4e+05),
  start = list(),
  map = list(),
  silent = FALSE,
  ...
)

# S4 method for class 'list,RCMdata'
RCM(
  OM,
  data,
  condition = "catch",
  selectivity = "logistic",
  s_selectivity = NULL,
  LWT = list(),
  comp_like = c("multinomial", "lognormal", "mvlogistic", "dirmult1", "dirmult2"),
  prior = list(),
  max_F = 3,
  integrate = FALSE,
  control = list(iter.max = 2e+05, eval.max = 4e+05),
  start = list(),
  map = list(),
  silent = FALSE,
  ...
)

Arguments

RCMdata

An RCMdata object.

OM

An object of class MSEtool::OM that specifies natural mortality (M), growth (Linf, K, t0, a, b), stock-recruitment relationship, steepness, maturity parameters (L50 and L50_95), and standard deviation of recruitment variability (Perr). Alternatively, provide a named list of biological inputs, see "StockPars" section below.

condition

String to indicate whether the RCM is conditioned on "catch" (where F are estimated parameters), "catch2" (where F is solved internally using Newton's method), or "effort" (F is proportional to an index series in data@Ehist. Can be fleet specific, in which case some combination of "catch" and "effort" are permissible.

silent

Logical to indicate whether informative messages will be reported to console.

data

Data inputs formatted in a RCMdata (preferred) or MSEtool::Data object. Use of a list is deprecated. See Data section below.

...

Other arguments to pass in for starting values of parameters and fixing parameters. See details.

selectivity

A character vector of length nfleet to indicate "logistic_length", "dome_length", "logistic_age", "dome_age", or "free" selectivity for each fleet in Chist. If there is time-varying selectivity, this is a character vector of length nsel_block (see Data section below). "free" indicates independent selectivity parameters for each age, and additional modifications for fixing selectivity parameters will likely be needed. See Additional arguments section.

s_selectivity

A vector of length nsurvey to indicate the selectivity of the corresponding columns in data$Index. Use "B" for total biomass, or "SSB" for spawning biomass (by default, "B" is used). Use numbers if the survey selectivity follows a fleet (corresponding to the columns in data$Chist, e.g., 1 = first fleet/column and so on). If the survey selectivity is otherwise independent of anything else in the model, use "logistic_length", "dome_length", "logistic_age", "dome_age", or "free" to specify the functional form of selectivity, and see Additional arguments section for setup of survey selectivity parameters and Articles section for more information.

LWT

A named list of likelihood weights for the RCM. See below.

comp_like

A string indicating the statistical distribution for the composition data, either "multinomial" (default), "lognormal", "mvlogistic" (multivariate logistic), "dirmult1" (Dirichlet multinomial, linear version), or "dirmult2" (saturating version; see Thorson et al. 2017).

prior

A named list for the parameters of any priors to be added to the model. See below.

max_F

The maximum F for any fleet in the scoping model (higher F's in the model are penalized in the objective function). This argument will also update OM@maxF. See also drop_highF.

cores

Integer for the number of CPU cores (set greater than 1 for parallel processing).

integrate

Logical, whether to treat recruitment deviations as penalized parameters in the likelihood (FALSE) or random effects to be marginalized out of the likelihood (TRUE).

mean_fit

Logical, whether to run an additional with mean values of life history parameters from the OM.

drop_nonconv

Logical, whether to drop non-converged fits of the RCM, including fits where F = NA.

drop_highF

Logical, whether to drop fits of the RCM where F = max_F.

control

A named list of arguments (e.g, max. iterations, etc.) for optimization, to be passed to the control argument of stats::nlminb().

start

A list of starting values for the TMB model. See details.

map

A list of map argument to TMB models to override defaults. See MakeADFun and details.

ESS

A vector of length two. A shortcut method to setting the maximum multinomial sample size of the age and length compositions. Not used when data are provided in a RCMdata object.

Value

An object of class RCModel (see link for description of output).

check_RCMdata returns a list of updated RCMdata object, OM, and StockPars and FleetPars from the Hist object generated from the OM.

Details

Fleet selectivity is fixed to values sampled from OM if no age or length compositions are provided.

Survey selectivity is estimable only if IAA or IAL is provided. Otherwise, the selectivity should be mirrored to a fleet (vulnerable biomass selectivity) or indexed to total or spawning biomass (see s_selectivity).

Parameters that were used in the fitting model are placed in the RCM@OM@cpars list.

If the operating model OM uses time-varying growth or M, then those trends will be used in the RCM as well. Non-stationary productivity creates ambiguity in the calculation and interpretation of depletion and MSY reference points.

The easiest way to turn off time-varying growth/M is by setting: OM@Msd <- OM@Linfsd <- OM@Ksd <- c(0, 0).

To play with alternative fits by excluding indices, for example, or other optional data, set the corresponding likelihood weight to zero. The model will still generate the inferred index but the data won't enter the likelihood. See section on likelihood weights.

Online Documentation

Several articles are available for RCM:

Priors

The following priors can be added as a named list, e.g., prior = list(M = c(0.25, 0.15), h = c(0.7, 0.1). For each parameter below, provide a vector of values as described:

R0

A vector of length 3. The first value indicates the distribution of the prior: 1 for lognormal, 2 for uniform on log(R0), 3 for uniform on R0. If lognormal, the second and third values are the prior mean (in normal space) and SD (in log space). Otherwise, the second and third values are the lower and upper bounds of the uniform distribution (values in normal space).

h

A vector of length 2 for the prior mean and SD, both in normal space. Beverton-Holt steepness uses a beta distribution, while Ricker steepness uses a normal distribution.

M

A vector of length 2 for the prior mean (in normal space) and SD (in log space). Lognormal prior.

q

A matrix for nsurvey rows and 2 columns. The first column is the prior mean (in normal space) and the second column for the SD (in log space). Use NA in rows corresponding to indices without priors.

See online documentation for more details.

Data

One of indices, age compositions, or length compositions should be provided in addition to the historical catch or effort. Not all arguments are needed to run the model (some have defaults, while others are ignored if not applicable depending on the data provided).

The data variable can be an object of class RCMdata. See help file for description of inputs.

Alternatively, the data input can be a MSEtool::Data S4 object which will retrieve data from the following slots:

Data@Cat

catch series (single fleet with the Data S4 object)

Data@Effort

effort series

Data@CAA

fishery age composition

Data@CAL, Data@CAL_mids

fishery length composition and corresponding length bins

Data@Ind, Data@SpInd, Data@VInd, Data@AddInd

indices of abundance

Data@CV_Ind, Data@CV_SpInd, Data@CV_VInd, Data@CV_AddInd

annual coefficients of variation for the corresponding indices of abundance. CVs will be converted to lognormal standard deviations.

Data@ML

fishery mean lengths

Data@AddIndV, Data@AddIndType, Data@AddIunits

Additional information for indices in Data@AddInd: selectivity and units (i.e., biomass or abundance).

There is no slot in the Data S4 object for the equilibrium catch/effort. These can be passed directly in the function call, i.e., RCM(OM, Data, C_eq = C_eq, ...).

Data list (deprecated)

Use of a list is deprecated. For backwards compatibility, here is the list of supported entries:

Chist

A vector of historical catch, should be of length OM@nyears. 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 C_eq).

C_sd

A vector or matrix of standard deviations (lognormal distribution) for the catches in Chist. If not provided, the default is 0.01. Only used if condition = "catch".

Ehist

A vector of historical effort, should be of length OM@nyears (see also E_eq).

Index

A vector of values of an index (of length OM@nyears). If there are multiple indices: a matrix of historical indices of abundances, with rows indexing years and columns indexing the index.

I_sd

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

I_type

Obsolete as of version 2.0. See s_selectivity argument.

CAA

Fishery age composition matrix with nyears rows and OM@maxage+1 columns. If multiple fleets: an array with dimension: nyears, OM@maxage, and nfleet.

CAL

Fishery length composition matrix with nyears rows and columns indexing the length bin. If multiple fleets: an array with dimension: nyears, length bins, and nfleet.

MS

A vector of fishery mean size (MS, either mean length or mean weight) observations (length OM@nyears), or if multiple fleets: matrix of dimension: nyears, nfleet. Generally, mean lengths should not be used if CAL is also provided, 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.

s_CAA

Survey age composition data, an array of dimension nyears, maxage+1, nsurvey.

s_CAL

Survey length composition data, an array of dimension nyears, length(length_bin), nsurvey.

length_bin

A vector for the midpoints of the length bins for CAL and s_CAL. All bin widths should be equal in size.

C_eq

A numeric 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).

C_eq_sd

A vector of standard deviations (lognormal distribution) for the equilibrium catches in C_eq. If not provided, the default is 0.01. Only used if 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

Optional, an integer vector to indicate which indices are in absolute magnitude. Use 1 to set q = 1, otherwise use 0 to estimate q.

I_units

Optional, an integer vector to indicate whether indices are biomass based (1) or abundance-based (0). By default, all are biomass-based.

age_error

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

sel_block

Optional, for time-varying fleet selectivity (in time blocks), a integer matrix of nyears rows and nfleet columns to assigns a selectivity function to a fleet for certain years.

StockPars

When an operating model is provided, the RCM function will generally fit to each simulation of biological parameters.

Alternatively for a single fit to data independent of any operating model, provide a named list containing the following (naming conventions follow internal operating model variables):

  • SRrel Integer, stock-recruit function (1 = Beverton-Holt, 2 = Ricker, 3 = Mesnil-Rochet hockey stick)

  • R0 Numeric, starting value for unfished recruitment parameter

  • M_ageArray Matrix [maxage+1, nyears] for natural mortality

  • Len_age Matrix [maxage+1, nyears + 1] for length at age

  • Linf Numeric. Asymptotic length. Only used for the upper bound for the size of full selectivity (if selectivity functions are length-based)

  • LatASD Matrix [maxage+1, nyears + 1] for the standard deviation in length at age

  • Wt_age Matrix [maxage+1, nyears + 1] for stock weight at age

  • Mat_age Matrix [maxage+1, nyears + 1] for maturity at age

  • Fec_Age Matrix [maxage+1, nyears + 1] for fecundity at age. Frequently the product of maturity and weight at age

  • ageMarray Numeric, age of 50 percent maturity. Used to average the initial years for the unfished replacement line of the stock recruit relationship and steepness/R0. Irrelevant if fecundity and natural mortality are not time-varying (set to 1).

  • spawn_time_frac Numeric, fraction of the year when spawning occurs

  • hs Numeric, steepness of the stock recruit relationship

  • procsd Numeric, lognormal recruitment deviation standard deviation

Additional arguments

For RCM, additional arguments can be passed to the model via ...:

plusgroup

Logical for whether the maximum age is a plusgroup or not. By default, TRUE.

fix_dome

Logical for whether the dome selectivity parameter for fleets is fixed. Used primarily for backwards compatibility, this is overridden by the map argument.

resample

Logical, whether the OM conditioning parameters (recruitment, fishing mortality, SSB, selectivity, etc.) are obtained by sampling the Hessian matrix from a single model fit. By default FALSE. This feature requires identical biological parameters among simulations.

pbc_recdev

Vector of length nyears. Proportion of the bias correction to apply annually to the recruitment deviations (if estimated). The bias correction from logspace to normal space is exp(log_rec_dev[y] - 0.5 * pbc_recdev[y] * sigmaR^2). Default proportion is 1.

pbc_earlyrecdev

Vector of length maxage. Proportion of the bias correction to apply to the abundance deviations in the first year of the model (if estimated). The bias correction from logspace to normal space is exp(log_early_rec_dev[a] - 0.5 * pbc_recdev[a] * sigmaR^2). Default proportion is 1.

start

Starting values can be specified in a named list for the following:

vul_par

A matrix of 3 rows and nfleet columns for starting values for fleet selectivity. The three rows correspond to LFS (length of full selectivity), L5 (length of 5 percent selectivity), and Vmaxlen (selectivity at length Linf). By default, the starting values are values from the OM object. If any selectivity = "free", then this matrix needs to be of maxage+1 rows where the row specifies the selectivity at age. See Articles section.

ivul_par

A matrix of 3 rows and nsurvey columns for starting values for fleet selectivity. Same setup as vul_par. Values in the column are ignored if s_selectivity is mapped to a fishing fleet (add NA placeholders in that case). If any s_selectivity = "free", then this matrix needs to be of maxage+1 rows where the row specifies the selectivity at age.

log_rec_dev

A numeric vector of length nyears for the starting values of the log-recruitment deviations.

log_early_rec_dev

A numeric vector of length OM@maxage for the starting values of the recruitment deviations controlling the abundance-at-age in the first year of the model.

q

A numeric vector of length nsurvey for index catchability. See online article for more information.

map

Parameters can be fixed with the map argument (also a named list, corresponding to the start list). Each vector or matrix in the map argument will be the same dimension as in the start entry. If an entry is NA, the corresponding parameter is fixed in the model to the starting value. Otherwise, an integer for each independent parameter, i.e., shared or mirrored parameters get the same integer entry.

vul_par

An integer matrix of the same dimension as start$vul_par. By default, selectivity is fixed if there are no age or length composition for that fleet or survey, otherwise estimated. Unused cells in the start$vul_par matrix should be given NA in the map matrix.

ivul_par

The map argument for the survey selectivity parameters (same dimension as start$ivul_par). Placeholder parameters should have a map value of NA.

log_early_rec_dev

A vector of length OM@maxage that indexes which recruitment deviates for the cohorts in the first year of the model are fixed (using NA) or estimated (a separate integer). By default, no deviates are estimated (all are NA).

log_rec_dev

A vector of length OM@nyears that indexes which recruitment deviates are fixed (using NA) or estimated (a separate integer). By default, all these deviates are estimated.

q

A vector of length nsurvey for index catchability. q should be an estimated parameter when sharing across surveys (perhaps with differing selectivity). Otherwise, it is solved analytically where individual parameters are independent of other indices. Use RCMdata@abs_I for fixing the catchability to 1. See online article for more information.

Likelihood weights

LWT is an optional named list containing the likelihood weights (values >= 0) with the possible options:

  • Chist, CAA, CAL, MS, C_eq: A vector of length nfleet for each.

  • Index, IAA, IAL: A vector of length nsurvey for each.

By default, all likelihood weights are equal to one if not specified by the user.

Annual multinomial sample sizes for the age and length comps can now be provided directly in the RCMdata object. For a list or MSEtool::Data object, use the ESS argument.

References

Thorson et al. 2017. Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution. Fish. Res. 192:84-93. doi:10.1016/j.fishres.2016.06.005

See also

plot.RCModel RCModel compare_RCM pcod RCM2MOM posterior

Author

Q. Huynh

Examples

# \donttest{ 
# An example that conditions a Pacific cod operating model. There are 48 simulations, 
# where values of natural mortality and steepness are sampled from distributions. 
# The model is fitted with priors on the index catchability. Maturity and selectivity 
# are knife-edge at the age of 2 years. See online tutorial for more information.

data(pcod) 
mat_ogive <- pcod$OM@cpars$Mat_age[1, , 1]
out <- RCM(OM = pcod$OM, data = pcod$data, 
           condition = "catch", mean_fit = TRUE,
           selectivity = "free", s_selectivity = rep("SSB", ncol(pcod$data@Index)),
           start = list(vul_par = matrix(mat_ogive, length(mat_ogive), 1)),
           map = list(vul_par = matrix(NA, length(mat_ogive), 1),
                      log_early_rec_dev = rep(1, pcod$OM@maxage)),
           prior = pcod$prior)
#> ℹ Checking data...
#> ✔ 1 fleet(s) detected.
#> ✔ RCM is conditioned on:
#> ✔ Fleet 1: catch
#> ✔ 65 years of data detected.
#> ✔ First year in model: 1956
#> ✔ Last year in model: 2020
#> ✔ 5 survey(s) detected.
#> ✔ Checking OM and getting biological parameters...
#> ✔ Mean weight data found.
#> ✔ Passing user arguments (LWT, map, start, prior, etc.) to RCMdata@Misc..
#> ✔ Maximum F in RCM will be 3. OM@maxF is also updated.
#>   
#> ℹ No fishery length or age compositions were provided. Selectivity is fixed to values from OM.
#>   
#> ℹ Fishery selectivity setup:
#> ℹ Fleet 1: individual parameters at age (free)
#>   
#> ℹ Index selectivity setup:
#> ℹ Index 1: spawning biomass
#> ℹ Index 2: spawning biomass
#> ℹ Index 3: spawning biomass
#> ℹ Index 4: spawning biomass
#> ℹ Index 5: spawning biomass
#>   
#> ✔ Beverton-Holt stock-recruitment relationship used.
#> ✔ Prior for q found.
#> ℹ Fitting model (48 simulations) ...
#> ℹ Generating additional model fit from mean values of parameters in the operating model...
#> ✔ Updating operating model:
#>   
#> ✔ Range of unfished age-0 recruitment (OM@cpars$R0): 6383.46 - 13782.9
#> ✔ Range of initial spawning depletion: 0.44 - 1.45
#> ✔ Range of spawning depletion (OM@cpars$D): 0.14 - 0.45
#> ✔ Historical F set with OM@cpars$Find and OM@cpars$qs.
#> ✔ Annual selectivity at age set in OM@cpars$V. Projection period uses selectivity of last historical year.
#> ✔ RCMdata length bins will be added to OM.
#> ✔ Recruitment standard deviation set in OM@cpars$Perr: 0.8 - 0.8
#> ✔ Historical recruitment deviations set in OM@cpars$Perr_y.
#> ✔ Range of recruitment autocorrelation OM@AC: 0.21 - 0.31
#> ✔ Future recruitment deviations in OM@cpars$Perr_y sampled with autocorrelation.
#> ✔ Growth, maturity, natural mortality, and stock recruit parameters from RCM are set in OM@cpars.
#>   
#> ℹ Adding some RCMdata inputs into OM@cpars$Data:
#>   
#> ✔ Historical catch data added to OM@cpars$Data@Cat.
#> ✔ Historical indices added to OM@cpars$Data@AddInd.
#> ✔ Complete.
plot(out, s_name = colnames(pcod$data@Index))
#> ℹ Rendering markdown file: /tmp/RtmpHMgW4v/RCM.Rmd
#> ℹ See help(plot.RCModel) to adjust report and file directory.
#> ✔ Rendered file: /tmp/RtmpHMgW4v/RCM.html

# Alternative OM with age-3 maturity and selectivity instead.
out_age3 <- local({
  pcod$OM@cpars$Mat_age[, 2, ] <- 0
  mat_ogive_age3 <- pcod$OM@cpars$Mat_age[1, , 1]
  RCM(OM = pcod$OM, data = pcod$data, 
      condition = "catch", mean_fit = TRUE,
      selectivity = "free", s_selectivity = rep("SSB", ncol(pcod$data@Index)),
      start = list(vul_par = matrix(mat_ogive_age3, length(mat_ogive_age3), 1)),
      map = list(vul_par = matrix(NA, length(mat_ogive_age3), 1),   
                 log_early_rec_dev = rep(1, pcod$OM@maxage)),
      prior = pcod$prior)
})
#> ℹ Checking data...
#> ✔ 1 fleet(s) detected.
#> ✔ RCM is conditioned on:
#> ✔ Fleet 1: catch
#> ✔ 65 years of data detected.
#> ✔ First year in model: 1956
#> ✔ Last year in model: 2020
#> ✔ 5 survey(s) detected.
#> ✔ Checking OM and getting biological parameters...
#> ✔ Mean weight data found.
#> ✔ Passing user arguments (LWT, map, start, prior, etc.) to RCMdata@Misc..
#> ✔ Maximum F in RCM will be 3. OM@maxF is also updated.
#>   
#> ℹ No fishery length or age compositions were provided. Selectivity is fixed to values from OM.
#>   
#> ℹ Fishery selectivity setup:
#> ℹ Fleet 1: individual parameters at age (free)
#>   
#> ℹ Index selectivity setup:
#> ℹ Index 1: spawning biomass
#> ℹ Index 2: spawning biomass
#> ℹ Index 3: spawning biomass
#> ℹ Index 4: spawning biomass
#> ℹ Index 5: spawning biomass
#>   
#> ✔ Beverton-Holt stock-recruitment relationship used.
#> ✔ Prior for q found.
#> ℹ Fitting model (48 simulations) ...
#> ℹ Generating additional model fit from mean values of parameters in the operating model...
#> ✔ Updating operating model:
#>   
#> ✔ Range of unfished age-0 recruitment (OM@cpars$R0): 6383.46 - 13782.9
#> ✔ Range of initial spawning depletion: 0.44 - 1.45
#> ✔ Range of spawning depletion (OM@cpars$D): 0.14 - 0.45
#> ✔ Historical F set with OM@cpars$Find and OM@cpars$qs.
#> ✔ Annual selectivity at age set in OM@cpars$V. Projection period uses selectivity of last historical year.
#> ✔ RCMdata length bins will be added to OM.
#> ✔ Recruitment standard deviation set in OM@cpars$Perr: 0.8 - 0.8
#> ✔ Historical recruitment deviations set in OM@cpars$Perr_y.
#> ✔ Range of recruitment autocorrelation OM@AC: 0.21 - 0.31
#> ✔ Future recruitment deviations in OM@cpars$Perr_y sampled with autocorrelation.
#> ✔ Growth, maturity, natural mortality, and stock recruit parameters from RCM are set in OM@cpars.
#>   
#> ℹ Adding some RCMdata inputs into OM@cpars$Data:
#>   
#> ✔ Historical catch data added to OM@cpars$Data@Cat.
#> ✔ Historical indices added to OM@cpars$Data@AddInd.
#> ✔ Complete.
  
compare_RCM(out, out_age3, scenario = list(names = c("Age-2 maturity", "Age-3 maturity")),
            s_name = colnames(pcod$data@Index))
#> ℹ Rendering markdown file: /tmp/RtmpHMgW4v/compare_RCM.Rmd
#> ✔ Rendered file: /tmp/RtmpHMgW4v/compare_RCM.html
             
Hist <- runMSE(out@OM, Hist = TRUE)            
#> ℹ Checking OM for completeness
#> ✔ Loading operating model
#> ✖ Invalid names found in custom parameters:
#> ✖ not_used_cpars
#>   1       L50array
#>   2       L95array
#> ℹ Valid custom parameters found: 
#>    M 
#>   h 
#>   V 
#>   Mat_age 
#>   R0 
#>   D 
#>   Find 
#>   qs 
#>   CAL_bins 
#>   CAL_binsmid 
#>   Perr 
#>   AC 
#>   Perr_y 
#>   Len_age 
#>   Linf 
#>   K 
#>   t0 
#>   LenCV 
#>   LatASD 
#>   Wt_age 
#>   ageMarray 
#>   age95array 
#>   hs 
#>   M_ageArray 
#>   AddIbeta 
#>   Data 
#> ✔ Note: Maximum age (10) is lower than assuming 1% of cohort survives to maximum age (24)
#> ✔ Optimizing for user-specified movement
#> ✔ Calculating MSY reference points for each year
#> ℹ Skipping optimization for depletion - using catchability (q) from OM@cpars.
#> ✔ Calculating historical stock and fishing dynamics
#> ✔ Calculating per-recruit reference points
#> ✔ Calculating B-low reference points
#> ✔ Calculating reference yield - best fixed F strategy
#> ✔ Simulating observed data
#> ✔ Updating Simulated Data with Real Data from `OM@cpars$Data`
#> ℹ Using `OM@cpars$Data@LenCV` (0.1)
#> ✔ Updating Simulated Catch from `OM@cpars$Data@Cat`
#> ℹ Updating Catch bias from `OM@cpars$Data@Cat`
#> ℹ Updating Catch variability from `OM@cpars$Data@Cat`
#> ℹ Updating catch observation error from `OM@cpars$Data@Cat`
#> ✔ Adding Additional Indices to Simulated Data from `OM@cpars$Data@AddInd`
#> ℹ cpars$AddIbeta detected. Not updating beta for additional indices
#> ℹ Updating observation variability (AddIerr) for additional indices from real data
#> ℹ Additional index 1 - spawning stock (biomass)
#> ℹ Additional index 2 - spawning stock (biomass)
#> ℹ Additional index 3 - spawning stock (biomass)
#> Warning: An error occurred in calculating statistical properties of fit to Additional Index 3 (possibly because there was only one observed data point). 
#> Using the index observation error for slot `Ind` from `Obs` object (or possibly conditioned if `cpars$Data@Ind` was provided).
#> Use `cpars$AddIerr` to manually set the observation error.
#> ℹ Additional index 4 - spawning stock (biomass)
#> ℹ Additional index 5 - spawning stock (biomass)
#> ✔ Returning historical simulations
# }