2021-11-06: Ver 0.1-4 * Update to autoconf version 2.71. * Add e-mails. 2021-07-26: Ver 0.1-4 * Add a check for data.frame() in plotaddmodel(). * Fix URLs in man Rd files. 2016-01-24: Ver 0.1-2 * Fix tons of warnings and notes from R CMD check. 2014-07-24: Ver 0.1-2 * Incorporate Cedric's codes for restarting and multiple chains. * Add man pages for Cedric's functions. * Add Cedric's codes to rename b.Mat. 2014-06-26: Ver 0.1-2 * New work flows. 2014-06-24: Ver 0.1-1 * Include Cedric's code. 2014-05-30: Ver 0.1-1 * Add bias.Phi to simulation. 2014-05-19: Ver 0.1-1 * Add bias random walk, adjust prior data structures, and modify logL. ======================= Log Before Release ===================================== 2014-05-16: Ver 0.1-1 * Add bias adjustment. 2014-05-15: Ver 0.1-0 * Add random walk back... 2014-05-05: * Change random walk to M-H algorithm with restriction to hyper-parameters. 2014-04-30: * Add log mixture normal to Phi distribution. 2014-04-28: * Add random walk with restriction to hyper-parameters. 2014-04-22: * Add ROC + NSEf work flows. 2014-04-17: * Implement RW_Norm to get rid of independent chain via VGAM. 2014-04-14: * Add NSEf work flows. 2014-03-11: * Clean and reformat all work flows. 2014-02-26: * Add MG's methods lognormal_MG and lognormal_MG0 back, but it still not work. * Add trace of logL to work flows. 2014-02-21: * Add two component mixture normal to fit Yassour 2009 using constrOptim(). * Add simulating expression from two component mixture fits. * Add above to simulation work flows. 2014-02-20: * Add Yassour 2009 dataset and man page. * Add ASL related functions and man page. 2014-02-19: * Remove MG's method since it did not work. * Add a misc code to extract parameters in work flows. 2014-02-07: * Add MG's proposal method for expected expression. 2014-01-16: * Finish conversion and debugging. * Add negative selection conversion to work flows. 2014-01-09: * Rename variables and functions (everything) to be consistent with papers. 2014-01-03: * Add vignettes. 2013-12-30: * Add with and without phi work flows. * Modify shell scripts. * Incorporate all work flows into cubfits. * Drop dependence of seqinr and VGAM. 2013-12-27: * Add man pages. 2013-12-24: * Test all other 24 genomes. 2013-12-14: * Add simulation work flow. 2013-12-13: * Add examples. * Merge back 'cubds' code to simplify dependency. 2013-11-15: * Add simulation code. 2013-11-14: * Copy input/output to "cubds". 2013-11-07: * Add SCUO code. 2013-10-30: * Add MLE and posterior mean for initial values of testing data. 2013-10-17: * Rename to 'cubfits'. * Rewrite several nasty functions. * Add ROC, NSEf, and ROC+NSEf models. 2013-09-xx: * Start a 'cub' package.