NEWS.md

In adnuts: No-U-Turn MCMC Sampling for 'ADMB' Models

adnuts 1.1.2 (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)

• 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)

Initial release.

adnuts documentation built on March 3, 2021, 1:07 a.m.