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Major development changes: SIAMCAT object structure, constructor function, pipeline versatility, vignettes, and several smaller bugfixes

Jakob Wirbel requested to merge dev into master

Major development changes:

  • The SIAMCAT object structure has changed: new slots for filtered and normalised data, also for association results
  • The constructor function takes named arguments now and runs by default
  • Pipeline versatility has been increased: by using feature.type, every function working with features can work on either the original, the filtered, or the normalised features
  • Updated data input vignette, included holdout testing vignette
  • Smaller bugfixes in almost every function in order to make it compatible with the new package structure and pipeline versatility
  • read.features and read.meta have been deprecated
  • Rscript flavour has been updated for the CI with the new package structure

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