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NEWS.md

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DMRnet 0.4.0.9000

  • Starting a new development version

DMRnet 0.4.0

  • Variable selection algorithm var_sel added
  • GLAMER implemented as a net version respective to its $\tau$ parameter (issue #57)
  • Features package load message with citation info
  • Fixing a problem with zero-length arrow in CV plots resulting from sd=0 (problem still remaining in issue #39 after the 0.3.2.9002 fix)
  • Citation update
  • Hierarchical clustering based on segmentation of 1D points with hclust1d package for PDMR and GLAMER

DMRnet 0.3.4

  • PDMR added

DMRnet 0.3.3

  • Updating documentation to reflect that for inference the matrix must be provided without the intercept column
  • Fixing incorrect inference for columns not in first-factors-then-numerics sequence
  • Candidate fix for warnings related to issue #33
  • Setting a default nlambda value to 100 in cv.DMRnet() (issue #41)
  • Fixing problems when few or no models are available in cross validation
  • Fixing problems when few or no models are available after grpreg (issue #39)
  • Refactoring the code to distribute the no-model fixes from gaussian DMRnet into binomial family DMRnet and both SOSnets and GLAMERs
  • Fixing a few other minor long-standing issues in GIC-indexed cross validation
  • Fixing df.1se in GIC-indexed cross validation for binomial GLAMER
  • Fixing incorrect loglik calculation for the first (largest) model in binomial family, for both GLAMER (-Inf) and DMRnet (incorrect)

DMRnet 0.3.2

  • Improved readability of a getting-started vignette
  • Fixed a bug in model-indexed cross validation related to folds with different model sizes
  • Added df.1se to GIC-indexed cross validation
  • Improved CV plots with df.1se model
  • Improved readability of README on CRAN (issue #32)
  • Welcome message on package load added

DMRnet 0.3.1

Major changes

  • GLAMER (Group LAsso MERger) algorithm added
  • Rebuild of the existing cross validation routine (models indexed by model dimension)
  • New cross validation routine added (models indexed by GIC) and made a new default
  • Handling of mismatched factor levels restructured

Stability improvements

  • Adding pivots in SOSnet for gaussian families
  • Adding a try-catch clause to recalculate QR decomposition for pivoted columns within rank in case of failure
  • Adding the regularization in gaussian family in DMR direct calls and calls via DMRnet
  • fixing NA values resulting in attempting non-penalized regression in case of non-full rank design matrices

Other improvements

  • Fixing how the parameters get passed in plot family of functions
  • Returning only non-zero coefficients in coef
  • Fixing DRMnet and cross validation in handling data with a single two-factor column
  • Fixing negative Wald statistics in binomial case
  • Workaround in GLAMER for cases of grpreg not observing a group constraint