=============================
PROJECTED DEVELOPMENT:
- Better handling of environments
- Better formula parsing (hopefully to remove dependence on lme4::lFormula)
- Write automated tests
- Improvements to GUI in shiny_clme(), particularly:
  - Allow for custom constraints to be specified.
- Implement unconstrained model testing all pairwise comparisons.
- Add argument to not bootstrap the random effect residuals. See Morris (2002) doi:10.1016/S0167-7152(02)00041-X
  - How does lme4 handle this, just use the observed random effects?
- Enable parallel processing for the bootstrap samples (foreach, dopar).
- Generalized LME models
=============================
VERSION HISTORY:


<<<<<<< HEAD

Version 2.0-13, 02026-04-05
- Removed dependency on prettyR from summary_clme


Version 2.0-11, 2019-02-07
- Removed a default value for seed in summary.clme
- Fixed error from setting names to NULL


Version 2.0-10, 2018-05-18
- Fixed out-of-sync metadata.
- Model now assumes ordred factor for constrained effect. If not, issues warning and attempts to force ordered=TRUE .


Version 2.0-9, 2018-02-01
- Fixed error in naming to prevent error with R 3.4.3


Version 2.0-8, 2017-11-16
- Streamlined of formula parsing (less messy).
- Fixes to plot.clme() for tree orders.
- Fixed error in removing duplicate patterns from auto-generated contraints.
- Added option to specify node in shiny_clme.
- shiny_clme will produce code used to run the specified model.


Version 2.0-5, 2016-11-07
- Added reference to JSS manuscript: Jelsema and Peddada (2016)


Version 2.0-4, 2015-07-01
- Fixed error in logLik.clme.
- Changed maintainer email.
- Added explicit BIC.clme method (instead of forcing custom use of AIC.clme)
- Removed the bootstrap computations from clme() and put them into summary.clme(). 
- summary.clme() now returns a list of values (largely equivalent to output of 
  clme()) but does not automatically print output to console.
- print.summary.clme() prints the output of summary.clme to the console.
- Improvements to the shiny_clme() application:
  - Added "model running" indicator
  - Enabled tab-delimited and xlsx formatted data input
  - Multiple tabs for output.


Version 2.0-3, 2015-05-14
- Noted nsim is in the fitted object of clme().
- Fixed error with method VarCorr() (failed unless "lme4" or "nlme" was loaded, 
  redefined method VarCorr)
- Replaced vignette with static document.
- Implemented work-around to prevent error (stemming from package isotone) when 
  there was only 1 constraint.


Version 2.0-2, 2015-01-20
- Fixed typo in printing of log-likelihood, AIC, BIC
- Added ellipses to MINQUE function to prevent errors from arguments em.eps and em.iter
- Improvements to shiny_clme() application


Version 2.0-1, 2014-12-05
- Minor updates to several functions


Version 2.0-0, 2014-12-01
- Major changes to arguments, particularly:
  - Formula interface implemented
  - Removed necessity for custom PAVA algorithms (implemented function 'activeSet'
    from package isotone)
  - Nks replaced with group vector input
  - Qs removed, each random term now gets individual variance
- Provided more common methods for fitted objects

Version 1.0-0, 2014-09-09
- Initial release of package

===========================
Author / Maintainer:
Casey M. Jelsema
Assistant Professor
Department of Biostatistics
West Virginia University
<jelsema.casey@gmail.com>
