Changes in version 0.99.1                        

2019-02-01

We are submitting to Bioconductor soon, so we are resolving as many of
the BiocCheck() ERRORs, WARNINGs, and NOTEs. See
https://github.com/gabrielodom/pathwayPCA/issues/64

                       Changes in version 0.98.0                        

2018-12-13

See the issues within the "Bioconductor Submission" and "Vignette Work"
milestones for detailed descriptions of these changes, their discussion,
and motivation: https://github.com/gabrielodom/pathwayPCA/issues

  - Standardized naming conventions to UpperCamelCase for consistency
  - Changed class name pathwaySet -> pathwayCollection
  - Added functions SubsetPathwayData, getPathPCLs, LoadOntoPCs,
    write_gmt, getSampleIDs, CheckSampleIDs, getTrimPathwayCollection,
    getPathwayCollection, CheckPwyColl, CheckAssay, and print and subset
    methods for pathwayCollection objects
  - Added sample ID requirements for input assays and phenotype data.
    Changed the phenotype required class from anything to a data frame.
  - Made the lars implementation a touch more robust. If the algorithm
    fails to converge, then we default back to regular SVD
  - The AESPCA function can also return pathway-specific vanilla PCA.
    Also, we inspected the parametric p-values compared to the
    permutation-based p-values. They congruence is nearly perfect for
    all of the data sets we tested. Thus, we changed the default p-value
    estimation method for AESPCA to be parametric.
  - Method functions (*_pVals()) now return a list with the p-values
    data frame, list of PC vectors (in a data frame), and list of
    loading vectors (in a data frame). The getPathPCLs function will
    subset this list to return the PCs, loadings, and administrivia of
    the method PCA output for a single pathway
  - added the June homo sapiens pathway collection from WikiPathways:
    wikipwsHS_Entrez_pathwayCollection
  - Lily wrote a vignette geared to show off the diverse functionality
    of the package, so this is the new main vignette. I broke off the
    plots from chapter 4 into their own chapter. The five vignettes I
    wrote are now supplemental chapters
  - updated vignettes and website

                     Changes in version 0.0.0.9000                      

2018-03-20

  - Added a NEWS.md file to track changes to the package.
  - Built website.