NEWS.md
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
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
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
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.