v0.10.0

• Updated JARs to TASSEL 5.2.96
• Updated formula parsing:
  • Drop and keep traits by using - and +, respectively
  • Added keywords to drop/keep all covariate or factor traits:
    • I(cov)
    • I(fct)
• Added stepwiseModelFitter() function:
  • Runs stepwise regression via TASSEL 5's "Stepwise" plugin
  • Returns AssociationResults object
• Added new function readNumericGenotypeFromRMatrix() (#15):
  • Converts formatted R matrix to TASSEL 5 numeric genotype
• Added experimental function readGenotype():
  • Reads data into new TasselGenotype class (future update)
  • Dynamically read genotype data based on data type
• Added experimental function readPhenotype():
  • Reads data into new TasselPhenotype class (future update)
  • Dynamically read phenotype data based on data type
• Added deprecation warnings to the following methods:
  • getPhenotypeDF()
  • getSumExpFromGenotypeTable()
  • readGenotypeTableFromPath()
  • readGenotypeTableFromGigwa()
  • readGenotypePhenotype()
  • readPhenotypeFromDataFrame()
  • readPhenotypeFromPath()
  • ldJavaApp()
  • treeJavaApp()
  • NOTE: these will be removed in future updates
• Updated vignettes:
  • Visualization section updates
  • Formula parsing
  • AssociationResults and PCAResults object handling
  • Memory allocation guide (#16)
  • Numeric genotype handling
• Updated website CSS