Cyclops v3.6.0

Changes:

  1. resurrect boot-strapping
  2. add JNI interface for manipulating Cyclops objects in an across-language persistent cache
  3. add cyclopsGetLogLikelihoodGradient()

Cyclops v3.5.2

  1. fix cyclic dependency with SelfControlledCaseSeries in a test-unit

Cyclops v3.5.1

Changes:

  1. check for negative curvature before computing CIs
    1. change to “lange”-convergence when needed
  2. fix vcov when model has an offset
  3. fix profiling when in bad initial state
  4. sort output of predict for compatibility with Andromeda:duckbd

Cyclops v3.5.0

Changes:

  1. provide optional (optimalWarmStart = FALSE) more parallelization when profiling likelihood
  2. make maxResets a function parameter
  3. ensure compatibility with R v4.4

Cyclops v3.4.1

Changes:

  1. fix some NaN/-Inf inconsistencies with likelihood profiling

Cyclops v3.4.0

Changes:

  1. remove dependence on BH
  2. improvements on adaptive likelihood profiling
  3. add auto option to cvRepetitions
  4. bumped explicit C++11 requirement up to R v4.1
  5. removed deprecated use of dbplyr:::$.tbl_lazy
    1. breaking change in dbplyr v2.4.0

Cyclops v3.3.1

Changes:

  1. fix uninitialized value in detected in computeAsymptoticPrecisionMatrix(); value was priorType
  2. fix memory leak caused by call to ::Rf_error()
  3. fix line-endings on Makevar on windows

Cyclops v3.3.0

  1. bump for R 4.2
  2. fix CRAN warnings
    1. used minValues
  3. fix CRAN notes
    1. remove explicit dependence on C++11 (except for R <= 4.0)

Cyclops v3.2.1

Changes:

  1. fix small memory leak caused by direct call to ‘::Rf_error()’
  2. disable JVM calls on CRAN due to uninitialized memory in Java JVM

Cyclops v3.2.0

Changes:

  1. fixed likelihood profiling when non-convex due to numerical instability
  2. fixed parsing of 64-bit covariate IDs
  3. fix BLR convergence criterion when there are 0 (survival) events
  4. add Jeffrey’s prior for single regression coefficient

Cyclops v3.1.2

Changes:

  1. adaptive likelihood profiling when objective function is concave.

Cyclops v3.1.1

Changes:

  1. specify new option nocenter in survival package when testing predicted hazard function

Cyclops v3.1.0

Changes:

  1. implement Fine-Gray competing risks regression
  2. fixed getCyclopsProfileLogLikelihood when starting with extreme coefficients

Cyclops v3.0.0

Changes:

  1. switch to Andromeda from ff to hold large datasets. This change breaks API

Cyclops v2.0.4

Changes:

  1. removed, unused variable imputation functions that contained a std::exit

Cyclops v2.0.3

Changes:

  1. fix computation under conditional Poisson models by reverting to v1.3.4-style loop
  2. fix several unit-tests for compatibility with R 4.0 factors
  3. add ability to profile likelihood function in parallel
  4. add initial infrastructure for competing risks models

Cyclops v2.0.2

Changes:

  1. use RNGversion("3.5.0") in unit-tests to reproduce old RNG behavior
  2. fix prior-type checks when specifying multiple types

Cyclops 2.0.1

Changes:

  1. patch two memory leaks in ModelData.cpp and ModelSpecifics.hpp

Cyclops 2.0.0

Changes:

  1. simplify internal transformation-reductions loops
  2. implemented non-negative weights
  3. allow for run-time selection of 32-/64-bit reals
  4. remove dependence on GNUmake
  5. temporarily remove dependence on RcppParallel (until TBB is again R-compliant)

Cyclops 1.3.4

Changes:

  1. fix undeclared dependencies in unit-tests: MASS and microbenchmarks
  2. fix issues with ATLAS compilation
  3. add contexts to testthat files
  4. fix ASAN errors in AbstractModelSpecifics

Cyclops 1.3.3

Changes:

  1. fix testthat expected error message

Cyclops 1.3.2

Changes:

  1. explicitly includes <complex> header, needed for R 3.5 builds
  2. remove pragma statements used to quiet RcppEigen and RcppParallel

Cyclops 1.3.1

Changes:

  1. fixes covariate indices returned from .checkCovariates when excluding covariates from regularization

Cyclops 1.3.0

Changes:

  1. implements specialized priors through callbacks for use, for example, in the BrokenAdaptiveRidge package to provide L0-based model selection
  2. implements specialized control through callbacks for use, for example, auto-and-grid-based cross-validation hyperparameter searches
  3. removes src/boost that clashes with BH 1.65.0

Cyclops 1.2.3

Changes:

  1. fixed predict error with ff.data.frame with size == 0

Cyclops 1.2.2

Changes:

  1. fixed solaris build errors
  2. added compatibility for C++14 (make_unique)
  3. fixed multiple ASan warnings

Cyclops 1.2.0

Changes: initial submission to CRAN