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