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Improve console output for RStudio users. Was broken for NUTS chains and in serial.
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Add new argument 'verbose' which suppresses almost all console output when set to FALSE
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Update demo file, vignette and README in preparation for submission to CRAN
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Add new function plot_uncertainties
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Expand continuous testing
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Add slot 'par_names' to objects of type adfit
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Add slot for par_names to adfit objects
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Add method
as.data.frame
for classadfit
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Improved and expanded testing via continuous integration
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Print the ADMB command to console when it fails to run properly to help user diagnose issues
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Improve console output for RStudio users. It will now print at conclusion of parallel runs.
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Fix bugs in model names for MacOS (use ./model instead of model internally)
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Fix small bug with mceval=TRUE for newest version of stock synthesis
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Fix
sample_tmb
to work again for short-term use
-
Change from
sample_admb
tosample_nuts
andsample_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
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Remove TMB references from documentation and vignette, instead pointing users to package 'tmbstan', and collate deprecated R code into a single file
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Migrate to new github repo: github.com/Cole-Monnahan-NOAA per NOAA's policy
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Add testing via testthat package
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Turn on calculation of ESS and Rhat manually, which get used in subsequent functions
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Created S3 class 'adfit' and generic methods print, summary, and plot
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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.
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Add check for valid version of ADMB
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Minor bug fixes and documentation updates
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Improve error handling and testing routines
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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.
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Add function check_identifiable which examines a .hes file and reports which parameters are not well identified.
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Add function sample_inits to generate inits from a previous fitted object.
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Read in MLE values from the .hes file when inits=NULL, instead of from the .par file.
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Add informative errors for common issues.
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Minor bug fixes and updates.
Initial release.