# SLOPE 0.5.1

## Minor Changes

- Website updated to bootstrap 5-based pkgdown theme.
- Updated e-mail of maintainer.
- Dependencies on checkmate and mice were dropped.
- Update sparse matrix coercion to avoid deprecated functionality in the Matrix
  package.

# SLOPE 0.5.0

## Major changes

- `plot.SLOPE()`, `plot.trainSLOPE()` and `plotDiagnostics()` have been
  reimplemented in ggplot2.

## Deprecated Functions

- `caretSLOPE()` has been deprecated and will be made defunct in version 0.6.0.

# SLOPE 0.4.1

## Bug Fixes

- The C++ standard library _memory_ was added to a source file to fix
  compilation errors on some systems.

# SLOPE 0.4.0

## New Functions

- `sortedL1Prox()` is a new function that computes the proximal operator for the
  sorted L1 norm (the penalty term in SLOPE).
- `regularizationWeights()` is a new function that returns the penalty weights
  (lambda sequence) for SLOPE or OSCAR.

## Major changes

- The parametrization for OSCAR models have been corrected and changed. As a
  result, `SLOPE()` gains two arguments: `theta1` and `theta2` to control the
  behavior using the parametrization from L. W. Zhong and J. T. Kwok, “Efficient
  sparse modeling with automatic feature grouping,” IEEE Transactions on Neural
  Networks and Learning Systems, vol. 23, no. 9, pp. 1436–1447, Sep. 2012, doi:
  10.1109/TNNLS.2012.2200262. `q` is no longer used with OSCAR models. Thanks,
  Nuno Eusebio.
- `SLOPE()` has gained a new argument, `prox_method`, which allows the user to
  select prox algorithm to use. There is no an additional algorithm in the
  package, based on the PAVA algorithm used in isotonic regression, that can be
  used. Note that this addition is mostly of academic interest and does not need
  to be changed by the user.

## Minor Changes

- The `q` parameter is no longer allowed to be smaller than `1e-6` to avoid
  constructions of regularization paths with infinite `lambda` values.
- The `lambda` argument in `SLOPE()` now also allowed the input `"lasso"` to
  obtain the standard lasso.
- The performance of `trainSLOPE()`

## Vignettes

- A new vignette has been added to compare algorithms for the proximal operator.

## Bug Fixes

- For very small numbers of observations (10 or so), the regularization weights
  for `lambda = "gaussian"` were incorrectly computed, increasing and then
  decreasing. This is now fixed and regularization weights in this case are now
  always non-increasing.
- Misclassification error was previously computed incorrectly in `trainSLOPE()`
  for multinomial models (thanks @jakubkala and @KrystynaGrzesiak)
- Performance of `trainSLOPE()` was previously hampered by erroneous refitting
  of the models, which has been fixed now (thanks @jakubkala and
  @KrystynaGrzesiak)

## Deprecated and Defunct

- `yvar` argument in `plotDiagnostics()` that was previously deprecated is now
  defunct.
- Using `missclass` for the `measure` argument in `trainSLOPE()` has been
  deprecated in favor of `misclass`.

# SLOPE 0.3.3

## Bug fixes

- Fixed first coefficient missing from plot if no intercept was used in the call
  to `SLOPE()`.
- Fixed incorrect results when `intercept = FALSE` and `family = "gaussian"`
  (#13, thanks, Patrick Tardivel).

# SLOPE 0.3.2

## Minor changes

- Added `tol_rel_coef_change` argument to `SLOPE()` as a convergence criterion
  for the FISTA solver that sets a tolerance for the relative change in
  coefficients across iterations.

## Bug fixes

- Fixed premature stopping of the solver for the first step of the
  regularization path (the null model).
- Actually fix UBSAN/ASAN sanitizer warnings by modifying code for FISTA solver.

# SLOPE 0.3.1

## Bug fixes

- Fixed package build breaking on solaris because of missing STL namespace
  specifier for `std::sqrt()` in `src/SLOPE.cpp`.
- Fixed erroneous scaling of absolute tolerance in stopping criteria for the
  ADMM solvers. Thanks, @straw-boy.
- Fixed sanitizer warning from CRAN checks.

# SLOPE 0.3.0

## Major changes

- Scaling of `alpha` (previously `sigma`) is now invariant to the number of
  observations, which is achieved by scaling the penalty part of the objective
  by the square root of the number of observations if `scale = "l2"` and the
  number of observations if `scale = "sd"` or `"none"`. No scaling is applied
  when `scale = "l1"`.
- The `sigma` argument is deprecated in favor of `alpha` in `SLOPE()`,
  `coef.SLOPE()`, and `predict.SLOPE()`.
- The `n_sigma` argument is deprecated in favor of `path_length` in `SLOPE()`
- The `lambda_min_ratio` argument is deprecated in favor of `alpha_min_ratio` in
  `SLOPE()`
- The default for argument `lambda` in `SLOPE()` has changed from `"gaussian"`
  to `"bh"`.
- Functions and arguments deprecated in 0.2.0 are now defunct and have been
  removed from the package.
- `scale = "sd"` now scales with the population standard deviation rather than
  the sample standard deviation, i.e. the scaling factor now used is the number
  of observations (and not the number of observations minus one as before).

## Minor changes

- Default `path_length` has changed from 100 to 20.
- `plot.SLOPE()` has gained an argument `x_variable` that controls what is
  plotted on the x axis.
- A warning is now thrown if the maximum number of passes was reached anywhere
  along the path (and prints where as well).
- If the `max_variables` criterion is hit, the solution path returned will now
  include also the last solution (which was not the case before). Thanks,
  @straw-boy.

## Bug fixes

- Plotting models that are completely sparse no longer throws an error.
- `rho` instead of `1` is now used in the factorization part for the ADMM
  solver.

# SLOPE 0.2.1

## Minor changes

- A few examples in `deviance()` and `SLOPE()` that were taking too long to
  execute have been removed or modified.

# SLOPE 0.2.0

This version of SLOPE represents a major change to the package. We have merged
functionality from the owl package into this package, which means there are
several changes to the API, including deprecated functions.

## Major changes

- `SLOPE_solver()`, `SLOPE_solver_matlab()`, `prox_sorted_L1()`, and
  `create_lambda()` have been deprecated (and will be defunct in the next
  version of SLOPE)
- arguments `X`, `fdr`, and `normalize` have been deprecated in `SLOPE()` and
  replaced by `x`, `q`, `scale` and `center`, respectively
- options `"default"` and `"matlab"` to argument `solver` in `SLOPE()` have been
  deprecated and replaced with `"fista"` and `"admm"`, which uses the
  accelerated proximal gradient method FISTA and alternating direction of
  multipliers method (ADMM) respectively
- ADMM has been implemented as a solver for `family = "gaussian"`
- binomial, poisson, and multinomial families are now supported (using `family`
  argument in `SLOPE()`)
- input to `lambda` is now scaled (divided by) the number of observations (rows)
  in `x`
- predictor screening rules have been implemented and are activated by calling
  `screen = TRUE` in `SLOPE()`. The type of algorithm can also be set via
  `screen_alg`.
- `SLOPE()` now returns an object of class `"SLOPE"` (and an additional class
  depending on input to `family` in `SLOPE()`
- `SLOPE` objects gain `coef()` and `plot()` methods.
- `SLOPE` now uses screening rules to speed up model fitting in the
  high-dimensional regime
- most of the code is now written in C++ using the **Rcpp** and
  **RcppArmadillo** packages
- a new function `trainSLOPE()` trains SLOPE with repeated k-folds
  cross-validation
- a new function `caretSLOPE()` enables model-tuning using the **caret** package
- `SLOPE()` now fits an entire path of regularization sequences by default
- the `normalize` option to `SLOPE()` has been replaced by `scale` and `center`,
  which allows granular options for standardization
- sparse matrices (from the **Matrix** package) can now be used as input
- there are now five datasets included in the package
- the introductory vignette has been replaced

## Minor changes

- a new function `deviance()` returns the deviance from the fit
- a new function `score()` can be used to assess model performance against new
  data
- a new function `plotDiagnostics()` has been included to visualize data from
  the solver (if `diagnostics = TRUE` in the call to `SLOPE()`)
- OSCAR-type penalty sequences can be used by setting
  `lambda = "oscar" in the call to`SLOPE()`
- the test suite for the package has been greatly extended
