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ChangeLog
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ChangeLog
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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.