1.0 not updated. Fixed now
Changed analyze.r to lm.r
Fixed the default data error
All warnings from R CMD check have been addressed and removed. Package is clear to ship.
Modularized the collapsing and burden tests. New collapsing methods can now be added as modules.
Partially through adding sliding window analysis module. I'm having to make some quick and dirty if/else type changes to other code though. Could be done better with more time
Revert "Partially through adding sliding window analysis module. I'm having to make some quick and dirty if/else type changes to other code though. Could be done better with more time"

This reverts commit 889014f0b0550da1a64f230f2366619ca5fea81c.
Beginning restructing to better facilitate soft clustering methods. CLUSTERID will be removed from the variants data frame, and all cluster operations will work from the clusters data frame
Removed the generic format for all functions. Functions now take an rvclustobject as a parameter, but do not require the S3 format.
Added new parameters to clustering algorithms that I'd like to implement. Functionality not yet implemented.
Removed operations including CLUSTERID and substituted syntax using the clusters list. Testing for errors now.
Many changes to update RVCLUST so that all cluster operations are now performed on the rvobject list. Pamk is now compatible, but rvcluster will require a rewrite.
Cleaning up debugging and code snippets
Added support for logistic regression using logreg, a wrapper for rms::lrm, a logistic regression with stats support developed by the BioStats department at Vanderbilt
RVCLUST now allows for covariate files and alternative phenotype files. All included covariates will be used. The phenotype will default to that in the PED file, but can be specified as any of the available phenotypes in the call to the statistics interfaces.
Started refactoring rvclustobject.r
Updated rvclustobject.r to take generic input, but enabled PEDMAP recognition for automated handling of genetic data
Updated the other files with the new naming conventions
Updated the roxygen documentation for rvclust-package.r and rvclustobject.r
Removed the outdated load_data method from rvclustobject.r