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Changelog

Source: NEWS.md

adnuts 1.1.2.9000 (development)

  • Add sparse NUTS option for TMB & RTMB models, and shift focus of package back to TMB. Main function sample_snuts with defaults to automatically detect the metric and set the warmup samples to use.

  • Update pairs_admb function to be S3 method pairs and add ‘mismatch’ and ‘cor’ options for the order, and argument add.inits to plot initial values.

  • Add plot_Q function.

  • Cleaned up console output

  • Minor bug fixes and improvements

adnuts 1.1.2 (2021-03-02)

CRAN release: 2021-03-02

  • Improve console output for RStudio users. Was broken for NUTS chains and in serial.

  • Add new argument ‘verbose’ which suppresses almost all console output when set to FALSE

  • Update demo file, vignette and README in preparation for submission to CRAN

  • Add new function plot_uncertainties

  • Expand continuous testing

  • Add slot ‘par_names’ to objects of type adfit

adnuts 1.1.1 (2021-02-19)

  • Add slot for par_names to adfit objects

  • Add method as.data.frame for class adfit

  • Improved and expanded testing via continuous integration

  • Print the ADMB command to console when it fails to run properly to help user diagnose issues

  • Improve console output for RStudio users. It will now print at conclusion of parallel runs.

  • Fix bugs in model names for MacOS (use ./model instead of model internally)

  • Fix small bug with mceval=TRUE for newest version of stock synthesis

  • Fix sample_tmb to work again for short-term use

adnuts 1.1.0 (2020-07-13)

  • Change from sample_admb to sample_nuts and sample_rwm to run the NUTS and RWM algorithms, respectively.

  • Rework metric options to allow user to access ADMB 12.2’s new dense mass matrix adaptation scheme. Added new section demonstrating this in the vignette.

  • Add more control to via ‘skip_monitor’, ‘skip_unbounded’, and ‘skip_optimization’ arguments

  • Remove TMB references from documentation and vignette, instead pointing users to package ‘tmbstan’, and collate deprecated R code into a single file

  • Migrate to new github repo: github.com/Cole-Monnahan-NOAA per NOAA’s policy

  • Add testing via testthat package

  • Turn on calculation of ESS and Rhat manually, which get used in subsequent functions

  • Created S3 class ‘adfit’ and generic methods print, summary, and plot

  • Updated pairs_admb to have an ‘order’ argument for quickly plotting slow/fast parameters

  • Add new function plot_marginals for quickly plotting posterior histograms

  • Add new function plot_sampler_params to plot NUTS sampling

  • Make parallel the default and deprecate the ‘parallel’ argument.

  • Fix bug in parallel path which failed when it was absolute. Now can be relative or absolute.

  • Add check for valid version of ADMB

  • Minor bug fixes and documentation updates

  • Improve error handling and testing routines

adnuts 1.0.1 (2019-03-15)

CRAN release: 2019-04-04

  • Update ADMB algorithms to use “-maxfn 0 -phase 1000” instead of “-noest”. This helps with Stock Synthesis and likely other models where some initialization is skipped with -noest which can lead to unusual and undesirable behavior. Also changed behavior with inits=NULL to pull MLE values from the admodel.hes file instead of pulling from the .par file for inits. This fixes some models when negative phases are used.

  • Add function check_identifiable which examines a .hes file and reports which parameters are not well identified.

  • Add function sample_inits to generate inits from a previous fitted object.

  • Read in MLE values from the .hes file when inits=NULL, instead of from the .par file.

  • Add informative errors for common issues.

  • Minor bug fixes and updates.

adnuts 1.0.0 (2018-02-04)

CRAN release: 2018-02-08

Initial release.