Bayesian Additive Regression Trees

Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) and Sparapani, Logan, McCulloch and Laud (2016) .


News

Changes and New Features in 2.4 (2019-04-10): * change: per CRAN policy, dynamic libraries are no longer "stripped" on Linux

Changes and New Features in 2.3 (2019-03-27): * new feature: adding arguments to surv.pre.bart, surv.bart and mc.surv.bart to fine-tune grid of time points and automate creation of time dependent covariates. These are convenience features to make multi-state models easier to handle; see new demo leuk

* change: arguments to rtnorm and rtgamma more user friendly

* new feature: re-organized vignettes into a single vignette

* new feature: gbart now calculates log pseudo-marginal
likelihood (LPML) for computing pseudo-Bayes factors

* new feature: new Generalized BART Mixed Models, see the
function gbmm

Changes and New Features in 2.2 (2019-01-22):

* bug fix: fix typo in size of theta grid for sparse prior

* new feature: Multinomial BART, mbart2, (suitable for
cases with more categories) based on the original mbart
implementation but inspired by the logit transformation;
nevertheless, both logit and probit are available and, 
of course, probit is much faster

Changes and New Features in 2.1 (2018-11-28):

* to meet current CRAN guidelines, replaced CXX1X and CXX1XSTD 
configure/autoconf macros with CXX11 and CXX11STD respectively

Changes and New Features in 2.0 (2018-11-12):

* new feature: Multinomial BART, mbart, (suitable for cases
with relatively fewer categories) replaced with a new
conditional probability implementation which allows the user
to choose probit or logit BART; of course, probit BART is 
much faster

* new feature: if lambda is specified as 0, then sigma is
considered to be fixed and known at the value sigest 
    and, therefore, not sampled

* bug fix: fixed single column x.test bug

Changes and New Features in 1.9 (2018-08-17):

* bug fix: off by one error fixed in robust Gamma 
generator for sparse Dirichlet prior

    * new feature: abart/mc.abart computes a variant
of the Accelerated Failue Time model based on BART

* new feature: for x.train/x.test with missing data elements, 
gbart will singly impute them with hot decking.  
Since mc.gbart runs multiple gbart threads in parallel, 
mc.gbart performs multiple imputation with hot decking, 
i.e., a separate imputation for each thread.

Changes and New Features in 1.8 (2018-06-30):

* bug fix: fix typo in the recur.pwbart() which
prevented predict() from working when OpenMP
was not available

Changes and New Features in 1.7 (2018-06-08):

* enhancement: generalized, or generic, BART: gbart/mc.gbart
unites continuous and binary BART in one function call
re-based time-to-event BARTs on gbart as well

* enhancement: binaryOffset=NULL specifies 
binaryOffset=qXXXX(mean(y.train)) for pbart/mc.pbart,
lbart/mc.lbart, mbart/mc.mbart; offset=NULL does the
same for gbart/mc.gbart, surv.bart/mc.surv.bart, 
recur.bart/mc.recur.bart, crisk.bart/mc.crisk.bart
and crisk2.bart/mc.crisk2.bart (note: competing 
cause 2 is handled analogously for offset2=NULL)

* enhancement: multinomial BART rebased on probit BART for 
computational efficiency

* bug fix: several corrections in probit and logit BART.
Note that this may change your results for binary and
time-to-event outcomes.  For probit BART, the correction
generally leads to a small change in the results.  However,
the logit BART correction may lead to more substantial
changes.

* doc fix: correct docs for the binary case in pbart/mc.pbart, 
lbart and mbart; and correct docs for the numeric case in
wbart/mc.wbart

* enhancement: robust Gamma generation for small scale parameter

* enhancement: more robust sparse Dirichlet prior implementation

Changes and New Features in 1.6 (2018-03-19):

* for binary outcomes, new default for ntree=50
  (change inadvertently omitted from v1.4 below)

    * enhancement: recur.pre.bart, recur.bart and mc.recur.bart
  can now handle NA entries in the times and delta matrices

* enhancement: for time-to-event outcomes, new optional 
  K parameter which coarsens time per the quantiles
      1/K, 2/K, ..., K/K.

* bug fix: x.test/x.test2 now properly transposed if needed
  for post-processing

* bug fix: sparse Dirichlet prior now corrected for 
  random theta update.  Thanks to Antonio Linero for
  the detailed bug report.

Changes and New Features in 1.5 (2018-02-08):

    * bug fix: ambiguous call of floor surrounding integer division

* bug fix: x.test is not an argument of recur.pre.bart

Changes and New Features in 1.4 (2018-02-02):

* for binary outcomes, new default for ntree=50

    * fixed library bloat on Linux with strip

* x.train and x.test can be supplied as data.frames
  which contain factors as stated in the documentation

* cutpoints now based on data itself, i.e., binary or
  ordinal covariates.  Similarly, you can request 
  quantiles via the usequants setting. 

* sparse variable selection now available with the
  sparse=TRUE argument; see the documentation

* new vignettes

* new function, mc.lbart, for logit BART in parallel

* mbart updated to equivalent functionality as other functions

* new function, mc.mbart, for Multinomial BART in parallel

Changes and New Features in 1.3 (2017-09-18):

    * new examples in demo directory

* return ndpost values rather ndpost/keepevery

* for calling BART directly from C++, you can
  now use the RNG provided by Rmath or the STL random class
  see the improved example in cxx-ex

* new predict S3 methods, see predict.wbart and other
  predict variants

* Added Geweke diagnostics for pbart, surv.bart, etc.
  See gewekediag which is adapted from the coda package

* logit BART added for binary outcomes; see lbart

* Multinomial BART added for categorical outcomes; see mbart

Changes and New Features in 1.2 (2017-04-30):

* you can now call BART directly from C++ with the Rmath library 
  see new header rn.h and the example in cxx-ex

Changes and New Features in 1.1 (2017-04-13):

* No user visible changes: bug-fix release

Changes and New Features in 1.0 (2017-04-07):

* First release on CRAN

Reference manual

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install.packages("BART")

2.6 by Rodney Sparapani, 2 months ago


Browse source code at https://github.com/cran/BART


Authors: Robert McCulloch [aut] , Rodney Sparapani [aut, cre] , Robert Gramacy [aut] , Charles Spanbauer [aut] , Matthew Pratola [aut] , Martyn Plummer [ctb] , Nicky Best [ctb] , Kate Cowles [ctb] , Karen Vines [ctb]


Documentation:   PDF Manual  


Task views: Machine Learning & Statistical Learning, Bayesian Inference


GPL (>= 2) license


Imports Rcpp, parallel, tools

Depends on nlme, nnet, survival

Suggests MASS, knitr, rmarkdown, sbart

Linking to Rcpp


Imported by borrowr.

Suggested by MachineShop, StratifiedMedicine.


See at CRAN