News

============================= 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:

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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 [email protected]

Reference manual