NEWS

Cyclops 3.7.1 (2026-05-27)

Changes:

  1. more robust unit-test for bootstrapping

Cyclops 3.7.0 (2026-02-28)

Changes:

  1. implement Schoenfeld residuals for Cox models with ties (Breslow) and strata
  2. implement score-test of Cox proportionality for models with ties (Breslow) and strata
  3. fix covariate type in confint() output
  4. remove use of Rf_error() that can cause memory leaks

Cyclops 3.6.0 (2025-07-18)

Changes:

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

Cyclops 3.5.2 (2025-06-24)

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

Cyclops 3.5.1 (2025-04-11)

Changes:

  1. check for negative curvature before computing CIs a. 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 3.5.0 (2024-12-02)

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 3.4.1 (2024-06-06)

Changes:

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

Cyclops 3.4.0 (2023-10-30)

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 a. breaking change in dbplyr v2.4.0

Cyclops 3.3.1 (2023-04-11)

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 3.3.0 (2023-04-05)

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

Cyclops 3.2.1 (2022-08-10)

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 3.2.0 (2022-06-30)

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 3.1.2 (2021-06-16)

Changes:

  1. adaptive likelihood profiling when objective function is concave.

Cyclops 3.1.1 (2021-03-23)

Changes:

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

Cyclops 3.1.0 (2020-11-05)

Changes:

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

Cyclops 3.0.0 (2020-06-05)

Changes:

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

Cyclops 2.0.4

Changes:

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

Cyclops 2.0.3 (2020-04-11)

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 2.0.2 (2019-03-17)

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 (2018-09-23)

Changes:

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

Cyclops 2.0.0 (2018-09-18)

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 (2018-06-15)

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 (2018-05-04)

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 (2017-08-23)

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 (2016-10-06)

Changes:

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

Cyclops 1.2.0 (2016-08-01)

Changes: initial submission to CRAN