The latest release of the SAMtool package is available on CRAN.

SAMtool 1.9.2

• Fix plot(RCM) when OM@nsim = 1
• Fix RCM2MOM when there is only one single fit (identical simulations).
• RCM reports recruitment of NA (rather than zero) in first projection year if spawn_time_frac > 0 (spawn timing in middle of time step).
• Add argument to allow Mohn’s rho calculation with na.rm = TRUE, e.g., summary(ret, na.rm = TRUE).
• Import simulate generic from stats package
• Update internal RCM_assess functions for better SPR search (avoid errors in selectivity and wider range of F)

SAMtool 1.9.1

• Minor update for RCM - uses IAL_n (multinomial sample size) to search for index length composition data to make predictions (cannot have NAs in IAL_n. Previously, NA’s in length composition IAL_hist caused issues introduced in 1.9.0.

SAMtool 1.9.0

• In RCM, adjust length-at-age probability by length selectivity function for prediction of length composition prediction.

SAMtool 1.8.2

• RCM check for identical simulations has more leeway, ensuring values of parameters don’t deviate by more than 0.01% of mean
• Fix RCM bug where the initial N-at-age only used the M value in simulation 1 when constructing values of OM@cpars$Perr_y

SAMtool 1.8.1

• Update markdown reporting and compare_RCM when fitting to StockPars list.
• RCM rescales selectivity to maximum of 1 when converting from length to age units
• diagnostic uses match() instead of grep() to find the correct MP. grep can return more than one match.

SAMtool 1.8.0

• Update error check for free selectivity parameters in RCM.
• Clean up RCM reporting of data fits (introduced in 1.6.5)
• Plot index SD in RCM
• Adjust rec devs for partial bias correction when converting RCM to OM (introduced in 1.7.0)
• Fix dimension of SLarray in RCM2MOM (introduced in 1.6.5)
• Move RCM reporting from slot @Misc to new slot @report. @Misc is now available for users to record information from OM building depending on the case study.
• RCM can fit to list of biological inputs StockPars instead of an operating model with RCM(StockPars, RCMdata). See StockPars section in help("RCM").
• Add partial bias correction to the initial abundance at age vector in RCM with argument pbc_earlyrecdev. The bias correction from logspace to normal space is exp(log_early_rec_dev[a] - 0.5 * pbc_earlyrecdev[a] * sigmaR^2) if the year-specific rec dev is estimated.
• RCMdata@I_delta (survey timing within time step) can now be a matrix by year and survey.
• Fix typo in Shortcut function

SAMtool 1.7.0

• Add argument to adjust annual recruitment deviation bias correction in RCM in argument pbc_recdev. The bias correction from logspace to normal space is exp(log_rec_dev[y] - 0.5 * pbc_recdev[y] * sigmaR^2) if the year-specific rec dev is estimated.
• Add RCMdata@I_delta slot to specify survey timing (0-1) within year. Default assumption is zero is used which is consistent with previous versions.

SAMtool 1.6.5

• Update RCM2MOM (report selectivity at length array, catch fractions).
• Update RCM report to identify non-converged simulations in figures and data predictions for which there is no likelihood.

SAMtool 1.6.4

• RCM passes maturity at length parameters to operating model. While RCM only uses the corresponding age ogive, the OM later will back-calculate to retrieve the length parameters, but may not recover the original values.
• RCM passes selectivity at length to operating model. This is needed to simulate length data in the projection.
• Plot maturity at length and length-weight relationship in RCM output if fitted to sized data.
• Histograms exclude extreme outliers (samples greater than the 95th percentile if the skewness > 3).

SAMtool 1.6.3 (2023-11-18)

• Under RCM_output tab in plot(RCModel), report simulations and convergence rate, and clean up comp plots.
• Fix issue with F calcs when RCM(condition = "catch2"), introduced in version 1.6.0.

SAMtool 1.6.2 (2023-10-26)

• Minor RCM updates to calculate fishery length comp when CAL_n > 0 and protect plot.RCM from empty index vectors.
• Update roxygen doc with markdown.

SAMtool 1.6.1 (2023-08-23)

• Patch updates to tidy up RCM report to prevent empty length selectivity figures.
• Perfect uses spawn_timing to calculate spawning biomass (exp(-spawn_time * M)) in the middle of projection year. Note that perfect HCR implementation needs to iteratively re-calculate the projection year biomass, B/BMSY, B/B0 (exp(-spawn_time * [Ftarget + M])) when applying the HCR. Recommend spawn_time = 0 to implement HCR perfectly.
• Update URLs to describe how to map index q in RCM.
• RCM no longer uses ObsPars$Isd.
• Update yield curve calcs for RCM with fecundity and spawn timing.
• Update retrospective function for RCM (map dimensions changed in TMB).

SAMtool 1.6.0 (2023-07-19)

RCM updates

• Add spawn_time_frac argument to RCM.
• Add fleet-specific option for catch/effort conditioning to RCM.
• Allow map argument for index q RCM(map = list(q = c(1, 1))). This example allows sharing q between 2 indices. Currently, q can only be an explicit estimated parameter (map argument is an integer), solved analytically (map argument is NA), or fixed to 1 (map argument is NA and additional specification in RCMdata@abs_I).
• Add explicit selectivity for length (“logistic_length”, “dome_length”) or age-based (“logistic_age”, “dome_age”) functions. For backwards compatibility, “logistic” and “dome” map to their length-based equivalents.
• Update prior for the length or age of full selectivity to be x^0.01 * (1 - x)^0.01 where x is the ratio of the length of full selectivity to Linf or age of full selectivity to maxage.
• Update figures for RCM markdown reports.

Other additions

• Add heat (red/blue) residuals for age comps in plot_composition(plot_type = "heat_residuals"). Also re-adjust default bubble residual size.
• Switch back to TMB compilation with CppAD. TMBad appears to cause “file too big” errors with codecov.
• Import abind (already done by MSEtool)

SAMtool 1.5.3 (2023-05-23)

• Fix indexing issue when estimating steepness post-hoc in SCA2 and VPA.
• Return warning when arguments to make_MP don’t match formal arguments in .Assess and .HCR

SAMtool 1.5.2 (2023-04-04)

• Custom internal hist function will report NA rate (percent of NA’s) in a vector. Seen in markdown reports.
• Internal max function excludes infinite values. Primarily used when generating axes limits in markdown reports.
• Fix bugs when Data object is passed to RCM.
• Allow resample = TRUE with stochastic fits to RCM.

SAMtool 1.5.1 (2023-02-08)

• Add gridlines to markdown plots for easier viewing. Update some plots and re-organize tabs in RCM markdown report.
• Add a Gaussian penalty of dnorm(log(Shinge/min(SSB)), 0, 2) for hockey-stick SRR when the hinge point is less than the smallest SSB.
• Convert zeros to 1e-8 when found in RCMdata@Chist. The trivially small catch still allows predictions of fishery age composition from Baranov equation.
• Turn various RCM messages to warnings, e.g., for non-convergence, high F, etc.
• Fix bug in diagnostic introduced in 1.5.0.

SAMtool 1.5.0 (2023-01-29)

• Add simulate method for RCM and assessment models.
• New map and start arguments for RCM.
• Add progress bar with timers for RCM and various diagnostic functions using pbapply.
• Add hockey-stick stock-recruit relationship in RCM using the Mesnil and Rochet (2010) parameterization.
• Users can now add lognormal priors for r and MSY for surplus production models.
• Update reporting of assessment output inside MSE. Use of data frames instead of lists should save space in the MSE object.

SAMtool 1.4.1 (2022-11-16)

• Fix Data@CAL check when using RCM.
• Use Gmisc::fastDoCall when fitting models, e.g., SP_Fox. Gmisc is a Suggests package.

SAMtool 1.4.0 (2022-06-07)

• RCM can now use multivariate logistic and Dirichlet multinomial distributions for fitting to age/length comps.
• Compile with TMBAD library.
• Import individual functions in NAMESPACE to avoid package conflicts.

SAMtool 1.3.1 (2022-05-06)

• Patch in RCM markdown report for plotting fishery length composition.

SAMtool 1.3.0 (2022-04-08)

• Require TMB 1.8 (need TMB package consistency between compilation and model fitting)

SAMtool 1.2.6 (2022-03-31)

New features

• RCM2MOM converts the output of RCM to a multi-fleet operating model.
• Vignette is now hosted online.
• Added a beta version of RCM_assess for using the RCM model as an assessment in closed-loop projections. More arguments will be added in the future for flexibility with model configuration.
• make_project_MP creates management procedures that update TAC annually from stock assessment projections.
• posterior wrapper function added to run MCMC of RCM models. RCMstan updates OMs with MCMC output.

Minor updates

• Fix FSPR reporting Shortcut and Perfect assessment functions.
• Fix F calculation in HCR_segment with yield per recruit (F01 and Fmax).
• Updates to interim_MP include adding NULL catch for catch advice and adding missing feature to report assessment output when diagnostic = 'full'.
• Create ability to specify output F in absolute magnitude (independent of model output) in HCR_segment and HCR_ramp.
• Uniform prior available for R0 and log(R0) for RCM models and assessment models.
• Shared recruitment deviation parameters in RCM only enter the objective function once.
• New correlation plots of estimated productivity parameters (steepness, M, R0, as well as depletion) in RCM reporting.
• Clean up TMB code to fix clang-14 compiler warnings.

SAMtool 1.2.5 (2022-01-12)

• SCA_RWM can accept multiple years to the refyear argument, e.g., expression(1:Data@Year). The model will calculate reference points (MSY, unfished values, and steepness) using the mean M during the specified years.
• Fix bug in interim MPs to return NA in Rec@TAC when multiple assessments do not converge.

SAMtool 1.2.4 (2021-12-15)

• Update Shortcut indexing to align year of assessment with projection. An MP using the Perfect assessment and HCR_MSY annually will produce F = FMSY in the OM.
• Stabilize VPA when the catch-at-age in the plusgroup and plusgroup-1 is very small.

SAMtool 1.2.3 (2021-11-28)

• RCM will check age and length comp data for NA’s and replaces with zero
• RCM reports annual equilibrium unfished reference points using constant stock recruit alpha and beta
• Unlink TMB executable when unloading package
• Fix punctuation issue in markdown reports that use knitr v1.36.
• Other minor fixes

SAMtool 1.2.2 (2021-09-16)

• The make_interim_MP function is added to generate MPs that adjust the TAC between periodic assessments using the index.
• An additional posfun to SP is added to avoid negative biomass situations.
• Fix sampling of recruitment deviations for projections in RCM so that the mean is one in normal space. This error was apparent when autocorrelation was very large.
• Assessment and RCModel objects now save the package version as attributes.
• Shortcut function now reports year-specific reference points for the harvest control rule.
• HCR returns TAC = NA when a control point or target point is negative.

SAMtool 1.2.1 (2021-08-12)

• HCR_segment allows for creating control rules with any number of linear segments.
• Assign index beta = 1 for OMs conditioned by RCM.
• The ESS argument is re-instated for RCM to maintain backwards compatibility.
• Fix assignment of length bins in OM by RCM.

SAMtool 1.2.0 (2021-07-06)

RCM

• A new S4 object, RCMdata, is used to send data to the RCM model, i.e., RCM(OM, RCMdata). For now, backwards compatibility should still be maintained when feeding a data list (used prior to v1.2) to fit the model.
• Internal R and TMB code for RCM has been revised, e.g., reducing interchangeability between the terms ‘survey’ and ‘index’ to focus on ‘index’ as much as possible when maintaining backwards compatibility.
• The profile generic is now available for RCM models. Steepness, R0, and final depletion can be profiled.
• Fixed plotting bug in compare_RCM.
• Priors for index q in RCM are now lognormal instead of normal.
• Annual equilibrium and transitional SPR are now calculated and reported.
• Uneven length bin widths are now supported.
• An example is added to the help documentation and online article, using Pacific cod (courtesy of R. Forrest).

Assessment models

• Priors on M, steepness, R0, and index q (lognormal, see RCM) can be created SCA, DD, and cDD assessment models.
• Likelihood weights to SCA assessments can now be provided for Catch, CAA, and CAL in addition to Index in a named list LWT. Backwards compatibility remains to provide LWT as a vector for index likelihood weights only.
• A new SCA assessment model that incorporates density-dependent natural mortality (SCA_DDM) is added.
• A new SCA assessment model that fits to length composition (SCA_CAL) is added.
• Delay-difference assessments (DD_TMB, DD_SS, cDD, cDD_SS) can now fit to mean weight with argument MW = TRUE. The functions will look for mean weight data series in Data@Misc[[x]]$MW, otherwise will convert length composition Data@CAL to weights and calculate annual means.
• Delay-difference assessments (DD_TMB and DD_SS) now use an instantaneous F formulation for the catch equation instead of Pope’s approximation. The models should now be more robust for high F situations.
• Dynamic SSB0 is calculated for all assessment models.
• A variant of the shortcut assessment emulator for closed-loop simulation is available (Shortcut2). This function fits an SCA assessment and then characterizes the assessment error relative to the operating model using a vector autoregressive (VAR) model. The functions samples the operating model with error predicted from the VAR model for the projection period. This is a useful function to guide the level of error in the shortcut method.

Harvest control rules

• Additional OCP types in HCR_ramp are available to create harvest control rules based on dynamic B0, and F-based rules (F/FMSY, F/F01, F/F-SPR).
• Added a shortcut function for a fixed escapement harvest control rule (HCR_escapement).

SAMtool 1.1.2 (2021-03-09)

• Minor fix to vignette to fix MSEtool reverse dependency issue.

SAMtool 1.1.1 (2021-02-17)

• Fix year range for depletion calculation from time-varying SSB0 in RCM.

SAMtool 1.1.0 (2021-02-02)

• Edits to fix valgrind and sanitizer issues in TMB code.
• Likelihood gradients, the derivatives of the likelihood of each annual data point with respect to model parameters, are plotted in the RCM markdown report. For this purpose, the annual age or length composition is considered to be a single piece of data. This diagnostic could be informative on how informative the data are to model parameters, with more influential data points having larger gradients.
• When conditioned on effort, the RCM will now incorporate catches into the likelihood as a default. This allows the model to estimate F and R0 when conditioned on effort and there is patchy catch data.

SAMtool 1.0.0 (2021-01-22)

• Development of the assessment models and OM conditioning model in SAMtool 1.0.0 continues from MSEtool 2.0.1. multiMSE remains in MSEtool.
• The age structure of the SCA models (SCA, SCA_Pope, SSS) start at age 0 following the change in the MSEtool OM.
• An additional SCA model (SCA_RWM) can be used to estimate time-varying M (constant with age) as a random walk. Fix the random walk SD to a low value to effectively estimate a time-constant M (see help page).
• Warnings during the fit of the assessment models (through nlminb) are turned off. Convergence status and issues can be checked in the conv slot of the output Assessment object. In closed-loop simulation, the diagnostic function can be used to track the behavior of model-based MPs. By default, pre-packaged model-based MPs and MPs made from the make_MP function are designed to report convergence info (stored in MSE@PPD).
• Assessment functions now calculate and report spawning potential ratio and yield per recruit in the forecast slot of the S4 object. Also in this slot is a catch equation function calculates the TAC for a given F.
• HCR nomenclature has changed. Operational control points (OCPs) are used instead of reference points (to help distinguish between reference points in the estimation model vs. the operating model. Various types of F can now be used in the HCR, including F0.1, Fmax, and FSPR, in addition to FMSY for the TAC calculation.
• A Shortcut assess function samples the OM with error and autocorrelation for HCRs as an emulator of a stock assessment in closed-loop simulation. The Perfect function samples the OM without error.
• All assessment models now accommodate multiple indices in model fitting, specify in the AddInd argument of functions which index slots in the Data object will be used among Data@Ind, Data@SpInd, Data@VInd, and Data@AddInd. Within series weighting is applied by using the corresponding CV slot, i.e., Data@CV_Ind for Data@Ind, etc. Among series weighting can also be tuned using likelihood weights with LWT argument. For SCA and VPA models, the selectivity is fixed in the model using Data@AddIndV for indices in Data@AddInd.

RCM

• The function for the OM conditioning model is now re-named to RCM (Rapid Conditioning Model).
• The age structure of the model now starts at age 0, following the change in the MSEtool OM. The dimension associated with age in matrices and arrays need to be of length maxage + 1 which corresponds to ages 0 to maxage.
• When estimating fleet F in the model (condition = "catch"), the likelihood for the catch can now have a user-defined standard deviation indicated in data$C_sd (year and fleet specific, the previous default was 0.01 was built-in for all catches).
• For generating length comps, variability in length-at-age can now be age-specific. Specify the length-at-age standard deviation in OM@cpars$LatASD.
• Priors for log_R0 (normal distribution), steepness (beta distribution for Beverton-Holt, normal for Ricker), log_M (age and time constant, normal), and survey q (normal) can now be specified.