* Disable JSON serialization for now.
* Multi-class classification is checkpointing for each iteration.
This brings significant overhead.
Revert: 90355b4f007ae
* Set R tests to use binary.
* Change DefaultEvalMetric of classification from error to logloss
* Change default binary metric in plugin/example/custom_obj.cc
* Set old error metric in python tests
* Set old error metric in R tests
* Fix missed eval metrics and typos in R tests
* Fix setting eval_metric twice in R tests
* Add warning for empty eval_metric for classification
* Fix Dask tests
Co-authored-by: Hyunsu Cho <chohyu01@cs.washington.edu>
* [R] Fix empty empty tests and a test warnings
* [R] Remove stringi dependency (fix#5905)
* Fix R lint check
* [R] Fix automatic conversion to factor in R < 4.0.0 in xgb.model.dt.tree
* Add `R` Makefile variable
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
* add SHAP summary plot using ggplot2
* Update xgb.plot.shap
* Update example in xgb.plot.shap documentation
* update logic, add tests
* whitespace fixes
* whitespace fixes for test_helpers
* namespace for sd function
* explicitly declare variables that are automatically evaluated by data.table
* Fix R lint
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
* [CI] Move lint to a separate script
* [CI] Improved lintr launcher
* Add lintr as a separate action
* Add custom parsing logic to print out logs
* Fix lintr issues in demos
* Run R demos
* Fix CRAN checks
* Install XGBoost into R env before running lintr
* Install devtools (needed to run demos)
* [R] Add a compatibility layer to load Booster from an old RDS
* Modify QuantileHistMaker::LoadConfig() to be backward compatible with 1.1.x
* Add a big warning about compatibility in QuantileHistMaker::LoadConfig()
* Add testing suite
* Discourage use of saveRDS() in CRAN doc
* [R-package] replace uses of T and F with TRUE and FALSE
* enable linting
* Remove skip
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
* Set output margin to True for custom objective in Python and R.
* Add a demo for writing multi-class custom objective function.
* Run tests on selected demos.
* Add bindings for serialization.
* Change `xgb.save.raw' into full serialization instead of simple model.
* Add `xgb.load.raw' for unserialization.
* Run devtools.
* [WIP] Add lower and upper bounds on the label for survival analysis
* Update test MetaInfo.SaveLoadBinary to account for extra two fields
* Don't clear qids_ for version 2 of MetaInfo
* Add SetInfo() and GetInfo() method for lower and upper bounds
* changes to aft
* Add parameter class for AFT; use enum's to represent distribution and event type
* Add AFT metric
* changes to neg grad to grad
* changes to binomial loss
* changes to overflow
* changes to eps
* changes to code refactoring
* changes to code refactoring
* changes to code refactoring
* Re-factor survival analysis
* Remove aft namespace
* Move function bodies out of AFTNormal and AFTLogistic, to reduce clutter
* Move function bodies out of AFTLoss, to reduce clutter
* Use smart pointer to store AFTDistribution and AFTLoss
* Rename AFTNoiseDistribution enum to AFTDistributionType for clarity
The enum class was not a distribution itself but a distribution type
* Add AFTDistribution::Create() method for convenience
* changes to extreme distribution
* changes to extreme distribution
* changes to extreme
* changes to extreme distribution
* changes to left censored
* deleted cout
* changes to x,mu and sd and code refactoring
* changes to print
* changes to hessian formula in censored and uncensored
* changes to variable names and pow
* changes to Logistic Pdf
* changes to parameter
* Expose lower and upper bound labels to R package
* Use example weights; normalize log likelihood metric
* changes to CHECK
* changes to logistic hessian to standard formula
* changes to logistic formula
* Comply with coding style guideline
* Revert back Rabit submodule
* Revert dmlc-core submodule
* Comply with coding style guideline (clang-tidy)
* Fix an error in AFTLoss::Gradient()
* Add missing files to amalgamation
* Address @RAMitchell's comment: minimize future change in MetaInfo interface
* Fix lint
* Fix compilation error on 32-bit target, when size_t == bst_uint
* Allocate sufficient memory to hold extra label info
* Use OpenMP to speed up
* Fix compilation on Windows
* Address reviewer's feedback
* Add unit tests for probability distributions
* Make Metric subclass of Configurable
* Address reviewer's feedback: Configure() AFT metric
* Add a dummy test for AFT metric configuration
* Complete AFT configuration test; remove debugging print
* Rename AFT parameters
* Clarify test comment
* Add a dummy test for AFT loss for uncensored case
* Fix a bug in AFT loss for uncensored labels
* Complete unit test for AFT loss metric
* Simplify unit tests for AFT metric
* Add unit test to verify aggregate output from AFT metric
* Use EXPECT_* instead of ASSERT_*, so that we run all unit tests
* Use aft_loss_param when serializing AFTObj
This is to be consistent with AFT metric
* Add unit tests for AFT Objective
* Fix OpenMP bug; clarify semantics for shared variables used in OpenMP loops
* Add comments
* Remove AFT prefix from probability distribution; put probability distribution in separate source file
* Add comments
* Define kPI and kEulerMascheroni in probability_distribution.h
* Add probability_distribution.cc to amalgamation
* Remove unnecessary diff
* Address reviewer's feedback: define variables where they're used
* Eliminate all INFs and NANs from AFT loss and gradient
* Add demo
* Add tutorial
* Fix lint
* Use 'survival:aft' to be consistent with 'survival:cox'
* Move sample data to demo/data
* Add visual demo with 1D toy data
* Add Python tests
Co-authored-by: Philip Cho <chohyu01@cs.washington.edu>
* Remove f-string, since it's not supported by Python 3.5 (#5330)
* Remove f-string, since it's not supported by Python 3.5
* Add Python 3.5 to CI, to ensure compatibility
* Remove duplicated matplotlib
* Show deprecation notice for Python 3.5
* Fix lint
* Fix lint
* Fix a unit test that mistook MINOR ver for PATCH ver
* Enforce only major version in JSON model schema
* Bump version to 1.1.0-SNAPSHOT
