156 Commits

Author SHA1 Message Date
Tong He
3912f3de06
Updates from 1.2.0 cran submission (#6077)
* update for 1.2.0 cran submission

* recover cmakelists

* fix unittest from the shap PR

* trigger CI
2020-09-02 20:50:23 +08:00
Philip Hyunsu Cho
5a2dcd1c33
[R] Provide better guidance for persisting XGBoost model (#5964)
* [R] Provide better guidance for persisting XGBoost model

* Update saving_model.rst

* Add a paragraph about xgb.serialize()
2020-07-31 20:00:26 -07:00
Philip Hyunsu Cho
ace7fd328b
[R] Add a compatibility layer to load Booster object from an old RDS file (#5940)
* [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
2020-07-26 00:06:49 -07:00
Lorenz Walthert
60511a3222
Document more objective parameters in R package (#5682) 2020-05-20 14:00:55 +08:00
Jiaming Yuan
7903286961
Remove silent from R demos. (#5675)
* Remove silent from R demos.

* Vignettes.
2020-05-19 18:20:46 +08:00
Jiaming Yuan
b56c902841
[R] R raw serialization. (#5123)
* Add bindings for serialization.
* Change `xgb.save.raw' into full serialization instead of simple model.
* Add `xgb.load.raw' for unserialization.
* Run devtools.
2020-04-11 17:16:54 +08:00
Jiaming Yuan
ed2465cce4
Add configuration to R interface. (#5217)
* Save and load internal parameter configuration as JSON.
2020-02-16 03:01:58 +08:00
Jiaming Yuan
911a902835
Merge model compatibility fixes from 1.0rc branch. (#5305)
* Port test model compatibility.
* Port logit model fix.

https://github.com/dmlc/xgboost/pull/5248
https://github.com/dmlc/xgboost/pull/5281
2020-02-13 20:41:58 +08:00
Jiaming Yuan
808f61081b
Update R doc by roxygen2. (#5201) 2020-01-15 10:49:17 +08:00
Tong He
7b74b1b64d fix additional files note (#4699)
* fix additional files note

* Trigger CI

* Trigger CI
2019-07-25 00:37:38 -07:00
James Lamb
5e97de6a41 fixed typos in R package docs (#4345)
* fixed typos in R package docs

* updated verbosity parameter in xgb.train docs
2019-04-21 15:54:11 +08:00
Jiaming Yuan
29a1356669
Deprecate reg:linear' in favor of reg:squarederror'. (#4267)
* Deprecate `reg:linear' in favor of `reg:squarederror'.
* Replace the use of `reg:linear'.
* Replace the use of `silent`.
2019-03-17 17:55:04 +08:00
Tong He
84a3af8dc0 Fix CRAN check warnings/notes (#3988)
* fix

* reorder declaration to match initialization
2018-12-12 08:23:20 -06:00
Vadim Khotilovich
5b662cbe1c
[R] R-interface for SHAP interactions (#3636)
* add R-interface for SHAP interactions

* update docs for new roxygen version
2018-08-30 19:06:21 -05:00
Jakob Richter
725f4c36f2 replace nround with nrounds to match actual parameter (#3592) 2018-08-15 11:13:53 -07:00
Tong He
098075b81b
CRAN Submission for 0.71.1 (#3311)
* fix for CRAN manual checks

* fix for CRAN manual checks

* pass local check

* fix variable naming style

* Adding Philip's record
2018-05-14 17:32:39 -07:00
Tong He
ace4016c36
Replace cBind by cbind (#3203)
* modify test_helper.R

* fix noLD

* update desc

* fix solaris test

* fix desc

* improve fix

* fix url

* change Matrix cBind to cbind

* fix

* fix error in demo

* fix examples
2018-03-28 10:05:47 -07:00
Arjan van der Velde
04221a7469 rank_metric: add AUC-PR (#3172)
* rank_metric: add AUC-PR

Implementation of the AUC-PR calculation for weighted data, proposed by Keilwagen, Grosse and Grau (https://doi.org/10.1371/journal.pone.0092209)

* rank_metric: fix lint warnings

* Implement tests for AUC-PR and fix implementation

* add aucpr to documentation for other languages
2018-03-23 10:43:47 -04:00
Vadim Khotilovich
706be4e5d4
Additional improvements for gblinear (#3134)
* fix rebase conflict

* [core] additional gblinear improvements

* [R] callback for gblinear coefficients history

* force eta=1 for gblinear python tests

* add top_k to GreedyFeatureSelector

* set eta=1 in shotgun test

* [core] fix SparsePage processing in gblinear; col-wise multithreading in greedy updater

* set sorted flag within TryInitColData

* gblinear tests: use scale, add external memory test

* fix multiclass for greedy updater

* fix whitespace

* fix typo
2018-03-13 01:27:13 -05:00
Tong He
98be9aef9a
A fix for CRAN submission of version 0.7-0 (#3061)
* modify test_helper.R

* fix noLD

* update desc

* fix solaris test

* fix desc

* improve fix

* fix url
2018-01-27 17:06:28 -08:00
Vadim Khotilovich
76f8f51438
[R] AppVeyor CI for R package (#2954)
* [R] fix finding R.exe with cmake on WIN when it is in PATH

* [R] appveyor config for R package

* [R] wrap the lines to make R check happier

* [R] install only binary dep-packages in appveyor

* [R] for MSVC appveyor, also build a binary for R package and keep as an artifact
2017-12-17 16:37:45 -06:00
Vadim Khotilovich
e8a6597957 [R] maintenance Nov 2017; SHAP plots (#2888)
* [R] fix predict contributions for data with no colnames

* [R] add a render parameter for xgb.plot.multi.trees; fixes #2628

* [R] update Rd's

* [R] remove unnecessary dep-package from R cmake install

* silence type warnings; readability

* [R] silence complaint about incomplete line at the end

* [R] initial version of xgb.plot.shap()

* [R] more work on xgb.plot.shap

* [R] enforce black font in xgb.plot.tree; fixes #2640

* [R] if feature names are available, check in predict that they are the same; fixes #2857

* [R] cran check and lint fixes

* remove tabs

* [R] add references; a test for plot.shap
2017-12-05 09:45:34 -08:00
Vadim Khotilovich
c82276386d [R] xgb.importance: fix for multiclass gblinear, new 'trees' parameter (#2388) 2017-06-07 13:13:21 -05:00
Michaël Benesty
8e2a1ff2bf Improve setinfo documentation on R package (#2357) 2017-05-30 20:08:31 +02:00
Vadim Khotilovich
b52db87d5c adding feature contributions to R and gblinear (#2295)
* [gblinear] add features contribution prediction; fix DumpModel bug

* [gbtree] minor changes to PredContrib

* [R] add feature contribution prediction to R

* [R] bump up version; update NEWS

* [gblinear] fix the base_margin issue; fixes #1969

* [R] list of matrices as output of multiclass feature contributions

* [gblinear] make order of DumpModel coefficients consistent: group index changes the fastest
2017-05-21 07:41:51 -04:00
Vadim Khotilovich
a375ad2822 [R] maintenance Apr 2017 (#2237)
* [R] make sure things work for a single split model; fixes #2191

* [R] add option use_int_id to xgb.model.dt.tree

* [R] add example of exporting tree plot to a file

* [R] set save_period = NULL as default in xgboost() to be the same as in xgb.train; fixes #2182

* [R] it's a good practice after CRAN releases to bump up package version in dev

* [R] allow xgb.DMatrix construction from integer dense matrices

* [R] xgb.DMatrix: silent parameter; improve documentation

* [R] xgb.model.dt.tree code style changes

* [R] update NEWS with parameter changes

* [R] code safety & style; handle non-strict matrix and inherited classes of input and model; fixes #2242

* [R] change to x.y.z.p R-package versioning scheme and set version to 0.6.4.3

* [R] add an R package versioning section to the contributors guide

* [R] R-package/README.md: clean up the redundant old installation instructions, link the contributors guide
2017-05-01 22:51:34 -07:00
Vadim Khotilovich
b4d97d3cb8 R maintenance Feb2017 (#2045)
* [R] better argument check in xgb.DMatrix; fixes #1480

* [R] showsd was a dummy; fixes #2044

* [R] better categorical encoding explanation in vignette; fixes #1989

* [R] new roxygen version docs update
2017-02-20 10:02:40 -08:00
Vadim Khotilovich
2b5b96d760 [R] various R code maintenance (#1964)
* [R] xgb.save must work when handle in nil but raw exists

* [R] print.xgb.Booster should still print other info when handle is nil

* [R] rename internal function xgb.Booster to xgb.Booster.handle to make its intent clear

* [R] rename xgb.Booster.check to xgb.Booster.complete and make it visible; more docs

* [R] storing evaluation_log should depend only on watchlist, not on verbose

* [R] reduce the excessive chattiness of unit tests

* [R] only disable some tests in windows when it's not 64-bit

* [R] clean-up xgb.DMatrix

* [R] test xgb.DMatrix loading from libsvm text file

* [R] store feature_names in xgb.Booster, use them from utility functions

* [R] remove non-functional co-occurence computation from xgb.importance

* [R] verbose=0 is enough without a callback

* [R] added forgotten xgb.Booster.complete.Rd; cran check fixes

* [R] update installation instructions
2017-01-21 11:22:46 -08:00
Vadim Khotilovich
d7406e07f3 [R] xgb.plot.tree fixes (#1939)
* [R] a few fixes and improvements to xgb.plot.tree

* [R] deprecate n_first_tree replace with trees; fix types in xgb.model.dt.tree
2017-01-06 11:09:51 -08:00
Tong He
674024c53a [R] Fix for cran submission of xgboost 0.6 (#1875)
fix cran check
2016-12-15 12:04:54 -08:00
Vadim Khotilovich
b21e658a02 [R-package] JSON dump format and a couple of bugfixes (#1855)
* [R-package] JSON tree dump interface

* [R-package] precision bugfix in xgb.attributes

* [R-package] bugfix for cb.early.stop called from xgb.cv

* [R-package] a bit more clarity on labels checking in xgb.cv

* [R-package] test JSON dump for gblinear as well

* whitespace lint
2016-12-11 19:48:39 +01:00
Tong He
2f3958a455 Fix for CRAN Submission (#1826)
* fix cran check

* change required R version because of utils::globalVariables

* temporary commit, monotone not working

* fix test

* fix doc

* fix doc

* fix cran note and warning

* improve checks

* fix urls
2016-12-02 20:19:03 -08:00
Simon DENEL
58aa1129ea Fixing a few typos (#1771)
* Fixing a few typos

* Fixing a few typos
2016-11-13 15:47:52 -08:00
Tong He
4733357278 [R] Monotonic Constraints in Tree Construction (#1557)
* fix cran check

* change required R version because of utils::globalVariables

* temporary commit, monotone not working

* fix test

* fix doc

* fix doc
2016-09-11 22:16:33 -07:00
Vadim Khotilovich
bdfa8c0e09 [R-package] a few fixes for R (#1485)
* [R] fix #1465

* [R] add sanity check to fix #1434

* [R] some clean-ups for custom obj&eval; require maximize only for early stopping
2016-08-20 05:09:03 -05:00
Vadim Khotilovich
d5c143367d [R-package] GPL2 dependency reduction and some fixes (#1401)
* [R] do not remove zero coefficients from gblinear dump

* [R] switch from stringr to stringi

* fix #1399

* [R] separate ggplot backend, add base r graphics, cleanup, more plots, tests

* add missing include in amalgamation - fixes building R package in linux

* add forgotten file

* [R] fix DESCRIPTION

* [R] fix travis check issue and some cleanup
2016-07-27 00:05:04 -07:00
Vadim Khotilovich
11efa038bd [R-package] various fixes for R CMD check (#1328)
* [R] fix xgb.create.features

* [R] fixes for R CMD check
2016-07-04 10:40:35 -07:00
Vadim Khotilovich
e1a52e896c [R] rm renamed CB's docs 2016-06-27 02:01:54 -05:00
Vadim Khotilovich
a0aa305268 [R] docs update - callbacks and parameter style 2016-06-27 01:59:58 -05:00
Vadim Khotilovich
4e1269b522 print.xgb.cv fix - Rd too 2016-06-09 10:12:20 -05:00
Vadim Khotilovich
2e0ffcc303 R-callbacks docs 2016-06-09 02:52:09 -05:00
Vadim Khotilovich
611b317057 make travis happy 2016-05-17 00:24:06 -05:00
Vadim Khotilovich
2b8b18583f some more xgb.model.dt.tree improvements 2016-05-17 00:24:06 -05:00
Vadim Khotilovich
be65949ba2 xgb.model.dt.tree up to x100 faster 2016-05-17 00:24:06 -05:00
Vadim Khotilovich
8664217a5a [R] more attribute handling functionality 2016-05-14 18:19:18 -05:00
Vadim Khotilovich
79c7c9e5bb R accessors for model attributes 2016-05-02 00:20:44 -05:00
Vadim Khotilovich
33131e2e13 make travis happy 2016-03-27 20:28:40 -05:00
Vadim Khotilovich
fb5291271e fix print.xgb.DMatrix doc 2016-03-27 19:42:26 -05:00
Vadim Khotilovich
71f402ac16 convert S4 to S3; add some extra methods to DMatrix 2016-03-27 19:22:22 -05:00
Vadim Khotilovich
d27bfb61b0 consolidated DMatrix&Booster stuff into xgb.DMatrix.R & xgb.Booster.R 2016-03-27 19:17:13 -05:00