Improved RStudio output, add plot_uncertainties, verbose option

• 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

Updates to RStudio console output and bugs for model names in OSX and Linux

There are two minor updates. First, users can now specify model='name' where 'name.tpl' is the model name, regardless of platform. Previously non-Windows users needed to use './name'. This makes the R code platform agnostic.

Second, is that when using RStudio in parallel mode nothing was printed to the console previously. Now, that output is captured and printed after completion of the chains so while it is not live updating, at least the user sees any important output.

Besides these there are some bug fixes and minor additions. Stock synthesis users may see an error when setting mceval=TRUE in previous versions. This is now fixed.

Use new ADMB 12.2 functionality, add S3 class, improve plotting

ADMB 12.2 was released in 8/2020 and includes some improvements to the algorithms. This adnuts release is designed to take advantage of those, but is backward compatible with ADMB 12.0 or 12.1. It also includes some major improvements:

• New sample_nuts and sample_rwm functions to replace sample_admb
• Deprecating the TMB functionality
• A new adfit class for fitted objects and methods for print, summary, and plot
• Improved plotting functionality
• Default to parallel sampling

This release is passing CRAN checks for Windows and Linux (via Travis CI) but is not expected to be officially pushed to CRAN in the near future.

Update package version 1.0.1 to CRAN

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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.

Initial package version on CRAN

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adnuts 1.0.0 (2018-02-04)

Initial release.