============================= 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 2.0-11, 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