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

`data$I_type`

is now obsolete to remove redundancy with argument`s_selectivity`

. Use`s_selectivity`

to specify the selectivity of surveys. If`data$I_type`

is detected, the code will attempt to update`s_selectivity`

.`data$MS`

(mean size) is now used instead of`data$ML`

(fishery mean lengths).`data$MS`

can also be mean weights, specify with`data$MS_type`

to be either “length” or “weight”. The likelihood of`data$MS`

uses a normal distribution with constant CV specified in`data$MS_cv`

(default = 0.2).- The function is now a generic. The
`data`

argument can now be either a list (preferred) or a DLMtool Data S4 object.

- Update function to fill in new Data slots:
`CAL_mids`

and`Vmaxlen`

. - Both SS2Data and SS2OM imports all indices into
`Data@AddInd`

.

- Update calculation of Pearson residual of age/length comps in bubble residual plots.

- Allow for OM conditioning by resampling the Hessian matrix from a single model fit.
- Projection period rec devs are calculated with autocorrelation from the last estimated historical rec dev.
- More error checks if there are issues with the predicted catch in the model.
- Update
`AddInd`

calcs for DLMtool 5.4.4. - Constants, including fixed standard deviations, are removed from the normal and multinomial likelihoods.

- Rename model parameters that correspond with magnitude and estimated on the log-scale. By default, these estimated parameters are also rescaled internally to be within an order of magnitude of other parameters. As such, they are no longer the log of the corresponding population parameter, e.g., R0.
- Delay-difference and delay-differential models accommodate alternative initial depletion values in the first year of the model instead of the default unfished assumption. Along with the surplus production model, these models also accommodate multiple indices in the Data object.

- Time-varying fleet selectivity in
`SRA_scope`

can be set up with blocks. Unique blocks are defined and then assigned to fleet and year. New vignettes and updated help files for`SRA_scope`

describe the set up in the function call. - An implemention of Simple Stock Synthesis (function
`SSS`

, catch-only method with fixed depletion assumption) is now added to the package. - The retrospective function is now available for spict assessments.
- The delay-difference models (
`DD_TMB`

and`DD_SS`

) can now be conditioned on catch (previous versions only allowed conditioning on effort). The default is now to condition on catch, which is standard practice.

`SP`

and`SP_SS`

now support multiple indices in the model, using`Data@AddInd`

and`Data@CV_AddInd`

. These assessments still support`Data@Ind`

but a custom wrapper function is still needed to use either`Data@SpInd`

or`Data@VInd`

.

- Option to remove plusgroup in
`SRA_scope`

has been added. - When conditioned on catch,
`SRA_scope`

can now solve`F`

iteratively using Newton’s method (argument`condition = "catch2"`

). F as independently estimated parameters is still available with argument`condition = "catch"`

. - Added a
`retrospective`

generic function for`SRA`

objects. - An ageing error matrix can now be provided to the model.
- Improvements in the backend for reporting (plotting) and error messaging.
- Additional function arguments for adjusting control parameters for optimization (in function
`nlminb`

), generating replicates by resampling from the covariance matrix, and filtering non-converged simulation replicates.

- Bugs in (1) likelihood weights, and (2) indexing for initial biomass calcs have been fixed.
- Absolute indices, i.e., indices where q = 1, age-specific indices, and abundance/biomass-based indices can now be accommodated.
- The lognormal likelihood for composition data is now available as an alternative to the multinomial.
- When conditioned on catch, fishing mortality is estimated as deviations from the F in the middle of the time series (instead of all independent parameters) for more stability.
- Markdown reporting now includes likelihood weights. Slight changes in color schemes are included for consistency among plots.
`compare_SRA`

is a function that compares output and fits from multiple SRA objects with identical model structures in slot`SRA@mean_fit`

but different data weightings, omissions, multipliers, etc.

- Fixed error in Solaris build.

- Revised function arguments. Data inputs are in a single list in order to keep function calls tidy. The function should be backwards compatible for the most part.
- Mean weight-at-age is now used to calculate biomass and catch in order to match calculations in
`DLMtool::runMSE`

. Depletion calculations also match those in`DLMtool::runMSE`

. - Survey selectivity can now be estimated if age or length compositions for the survey are provided. See help file for setup.
- New plots have been added to the markdown report, include those that compare the outputs from the SRA and the updated operating model.
- A vignette for
`SRA_scope`

has now been added.

- Extensive revisions to
`SS2OM`

have been added. The function also generates a markdown report to compare operating model output to Stock Synthesis outputs, e.g., recruitment, catch, spawning biomass time series. - A log-Jacobian transform has been added for the r prior in
`SP`

and`SP_SS`

(surplus production models). This is needed because FMSY is estimated rate parameter rather than r. By default, the minimum CV on the r-prior is 0.1 to allow the model to update r. It is assumed n is fixed in the model. - Re-organize TMB files.

- Defaults for
`SRA_scope`

are now more robust (set maximum F in model, higher std. dev. for likelihood of mean lengths). - Users can choose to use
`SRA_scope`

conditioned on either observed catch or observed effort. `SRA_scope`

returns an S4 object of class`SRA`

with a`plot()`

method that generates a markdown report of model fits.

- A prior for r is now possible with
`SP`

and`SP_SS`

using life history information (priors in natural mortality and steepness, as well as maturity/weight at age). To use this feature, set argument`use_r_prior = TRUE`

. - Default process error standard deviation for
`SP_SS`

is reduced to 0.1. `cDD`

and`cDD_SS`

are more robust when catch is very, very small (F is set to 0). This is important for management procedures that shut down fishing.- Minor updates to simplify TMB code.
- Minor revision to
`make_MP`

.

- Vignette links are now available through the MSEtool help page. Type
`?MSEtool`

into the console. - Minor fixes to
`multiMSE`

. `SS2OM`

now has an option for selecting male or female life history parameters.

- Fixed error in Solaris build.

For the new features described below, DLMtool version 5.3.1 is recommended.

- The initial release for multi-fleet and multi-stock operating models and MSEs are released in this version, with
`multiMSE`

being the core function. The multiMSE vignette will be quite useful and can be accessed at`browseVignettes("MSEtool")`

.

Quite a few additions and changes have been made to the Assessment models. See the help manual and vignettes for descriptions of these new Assessment functions.

- The continuous delay-differential model with deterministic and stochastic recruitment (
`cDD`

and`cDD_SS`

, respectively) have been added as new Assessment models to the package. The continuous formulation should be more stable in high F situations. - A virtual population analysis
`VPA`

model has also been added to the package. - The surplus production model
`SP`

assumes continuous production and estimates continuous F’s, similar to ASPIC. This formulation will be more stable in high F situations. The Fox model can be implemented by setting the production function exponent`n = 1`

. - A wrapper function for
`spict`

(state-space surplus production model) has been written and is available in the`DLMextra`

package (located on Github). While reporting functions are available in MSEtool, the output of the wrapper function can still be used with the diagnostic functions in the spict package. `SCA`

and`SCA2`

estimate annual F’s and include a likelihood function for the catch. In previous versions,`SCA`

matched the predicted catch to observed catch. This feature has been transfered over to the`SCA_Pope`

function.- Summary of assessment results can be obtained by the
`plot`

function which now generates a markdown report. This will be useful for diagnosing model fits and evaluating parameter estimates.

- A scoping function
`SRA_scope`

fits an assessment model to catch, indices, and age/length comps to inform historical effort, recruitment deviations, and depletion for data-moderate operating models. Multiple fits are done based on the different life history parameters assumed in the operating model. This function is intended to be an alternative to`DLMtool::StochasticSRA`

. `profile`

and`retrospective`

functions for profiling the likelihood and retrospective analyses, respectively, of assessment models are now improved.- The
`compare_models`

function has been added to compare time series estimates, e.g. B/BMSY and F/FMSY, among different assessment models. - Manual starting values (the
`start`

argument) for parameters of assessment models can be expressions and subsequently evaluated in the assessment function. This can be very helpful when passing starting values in the`make_MP`

function. - The
`CASAL2OM`

function can be used to generate an operating model from CASAL assessments. - The
`SS2OM`

and`SS2Data`

functions are updated for the latest versions of r4ss on Github. - More options are provided to increase flexibility for ramped harvest control rules (
`HCR_ramp`

).

- Re-parameterization of dome selectivity in SCA so that estimated parameters are age-based after transformation.
- Additional argument in SCA for lognormal distribution for age comps.
- A more efficient method is used to report convergence diagnostics of assessment models when running in closed-loop simulation.

- By default, steepness is now fixed in the SCA and SCA2 assessment functions.
- By default, nine data-rich MPs are now included in the package. See the help documentation: ?
`Data-rich-MP`

- A generic function for ramped harvest control rules (
`HCR_ramp`

) is now included. Users can input the desired limit and target reference points. `make_MP`

adds dependencies to the MP so that`DLMtool::Required`

returns the appropriate dependencies. Dependencies are dynamic based on the configuration of the assessment model. For example,`Data@steep`

is a dependency for a SCA-based model only if steepness is fixed.

- Initial CRAN release.
- Assessment models: Delay-Difference (DD_TMB, DD_SS); Surplus Production (SP, SP_SS); Statistical Catch-at-Age (SCA, SCA2)
- Harvest control rules: HCR_MSY, HCR40_10, HCR60_20
`simmov`

function for multiple-area movement models (age-independent)- Functions for converting Stock Synthesis and iSCAM assessments to OM and Data objects (classes inherited from DLMtool)