Mp codemerge

README.md

@@ -1,142 +1,58 @@
-# Open Bayesian Trees Project
-This repository includes new developments with Bayesian Additive Regression Trees and extends the original OpenBT repository created by Matt Pratola (https://bitbucket.org/mpratola/openbt/src/master/).
-Such extensions include Bayesian Model Mixing and Bayesian Calibration. 
-All of the Bayesian Tree code is written in C++. User interfaces constructed in R and Python allow one to easily run the software.
-The BART Model Mixing software has been implemented in the [Taweret](https://github.com/bandframework/Taweret/tree/main) Python package in conjunction with the [BAND](https://bandframework.github.io/) collaboration.
-
-
-# Installation
-The heart of OpenBT is a set of C++ tools that can be used directly via
-the command line or indirectly through the Python and R packages, which wrap
-them.  Typically these tools are built with an implementation of the Message
-Passing Interface (MPI) such as [Open MPI](https://www.open-mpi.org) or
-[MPICH](https://www.mpich.org) to enable distributed parallelization of
-computations.  In particular, the Python wrapper package is always built with
-MPI support.
-
-The software and its distribution scheme have been developed to allow users to
-use OpenBT with the MPI installation of their choice.  For instance, it
-can be built with MPI installations on leadership class platforms and clusters
-that were installed by experts and optimized for their specific platform.  As a
-result, however, the software is not distributed as prebuilt binaries or wheels,
-but rather must be built for each case with the compiler suite and matching MPI
-implementation provided by the user.
-
-## Requirements
-Before building and installing the Python package, users
-must provide
-* a compiler suite that includes a C++ compiler that supports the C++14
-  standard,
-* an MPI installation that is compatible with the compiler suite, and
-* optionally the [Eigen software package](https://gitlab.com/libeigen/eigen).
-
-Note that if installing MPI using a package manager, related developer library
-packages such as ``libopenmpi-dev`` or ``libmpich-dev`` might need to be
-installed in addition to the base MPI packages such as ``openmpi-bin`` or
-``mpich``.
-
-To build and install just the bare C++ tools, users must provide in addition to
-the above
-* the [Meson build system](https://mesonbuild.com) and its prerequisites such as
-  Python 3 and [ninja](https://ninja-build.org).
-
-While both Meson and ninja are used internally to build the Python package, they
-are installed automatically just for building the package.
-
-The Meson build system is setup to automatically detect the compiler suite and
-MPI installation to use.  If Eigen already exists in the system and Meson can
-find it, then Meson will use it for the build.  Otherwise, Meson will
-automatically obtain a copy of Eigen for internal use.
-
-We presently test OpenBT with both Open MPI and MPICH.  In addition, we
-have successfully tested with the Intel MPI implementation and have used the
-Python package with MPI implementations installed
-* via package managers such as Ubuntu's Advanced Packaging Tool (`apt`) and
-  [homebrew](https://brew.sh) on macOS;
-* by experts on clusters and that are available as modules; and
-* with `conda` from the prebuilt conda forge
-  [openmpi](https://anaconda.org/conda-forge/openmpi) package.
-
-## Meson installation
-The Meson build system documentation suggests installing Meson via package
-manager when possible.  Please refer to that documentation for detailed and
-up-to-date installation information.
-
-If Meson cannot be installed by package manager or the manager's version is too
-old, the following is contrary to Meson suggestions but has been used
-successfully to install Meson with Python into a dedicated virtual environment
-as well as to install `meson` in the `PATH` for use without needing to activate
-that virtual environment.
-```
-$ /path/to/target/python -m venv ~/local/venv/meson
-$ . ~/local/venv/meson/bin/activate
-$ which python
-$ python -m pip install --upgrade pip
-$ python -m pip install meson
-$ python -m pip list
-$ ln -s ~/local/venv/meson/bin/meson ~/local/bin
-<add ~/local/bin to PATH if desired and appropriate>
-$ deactivate
-$ which meson
-$ meson --version
-```
-Note that this `meson` virtual environment is for installing **just** the Meson
-build system.  Attempts to install `openbt` into this virtual environment
-will likely fail with an error that the `mesonbuild` module cannot be found.
-
-## Python package
-The OpenBT Python package is **not** currently distributed on PyPI since the
-[PyPI OpenBT package](https://pypi.org/project/openbt/) already exists.  This
-package will eventually be transferred to this project so that distribution of
-modern versions of this package will be enabled by PyPI under the name `openbt`.
-
-<!--
-The OpenBTMixing Python package is distributed on
-[PyPI](https://pypi.org/project/openbtmixing/) as a source distribution that
-contains the C++ code and files needed by Meson to build the dedicated,
-standalone command line tools that the package will use.  The tools are built
-and installed automatically by Meson as part of executing
-```
-python -m pip install openbt
-```
-By default, `pip install` does not show any of Meson's progress.  Users and
-developers interested in seeing how Meson satisfies dependencies and reviewing
-compiler output should pass `-v` to `pip install`.
--->
+# OpenBT
 
-Instead the package should be built and installed from a clone of this repository with
-```
-$ cd /path/to/OpenBT/openbt_pypkg
-$ python -m pip install .
-```
-Developers can install in developer/editable mode with verbose logging of the
-build process and installation with
-```
-$ cd /path/to/OpenBT/openbt_pypkg
-$ python -m pip install -v -e .
-```
-In this latter case, the command line tools are built automatically and
-installed at `/path/to/OpenBT/openbt_pypkg/src/openbt/bin`.  The
-Python package is hardcoded to use those tools so that the existence of another
-set of tools in the system and in `PATH` should not cause issues.
+TODO: Copy info from landing page of sphinx docs here.
 
-OpenBT package installations can be minimally tested with
-```
-$ python
->>> import openbt
->>> openbt.__version__
-'<version>'
->>> openbt.test()
-```
+### Repository
+TODO: Add general badges
+
+### Python
+TODO: Add Python-specific badges
+
+## License & Copyright
 
-## C++ library & command line tool interface
-Developers and C++ users can directly build and install the command line tools,
-an OpenBT library, and library tests with `tools/build_openbt_clt.sh`.
-Note that these do **not** need to be built in order to use the Python package.
+TODO: Copy license & copyright info from landing page of sphinx docs here
 
-## R package
-**TODO**: Needs to be written based on current state of affairs.
+## Support
 
-# Examples
+To
 
-The examples from the article "Model Mixing Using Bayesian Additive Regression Trees" are reproduced in the jupyter notebook BART_BMM_Technometrics.ipynb. This notebook can be run locally or in a virtual environment such as google colab.
+* report potential problems with OpenBT or any of the packages derived from it,
+* propose a change, or
+* request a new feature,
+
+please check if a related [Issue](https://github.com/bandframework/OpenBT/issues)
+already exists before creating a new issue.  For all other communication, please
+send an email to the OpenBT development team
+
+ * TODO: Matt's contact info
+ * TODO: John's contact info
+
+## Documentation
+
+[User and Developer Guides](https://openbt.readthedocs.io) are hosted on
+ReadTheDocs.  Please refer to those documents for information regarding
+examples.
+
+## Installation & Testing
+
+Refer to the getting started sections in the User Guide related to the tool or
+package that you intend to use.
+
+## Contributing to IBCDFO
+
+Contributions are welcome in a variety of forms; see
+[Contributing](https://openbt.readthedocs.io/en/latest/contributing.html) in the
+Developer Guide.
+
+## Cite OpenBT
+
+```
+@techreport{openbt2026,
+  author      = {Matt Pratola and John Yannotty},
+  title       = {{OpenBT 1.2.0} Users Manual},
+  institution = {TBD},
+  number      = {Version 1.2.0},
+  year        = {2026},
+  url         = {https://openbt.readthedocs.io/}
+}
+```

Ropenbt/DESCRIPTION

@@ -0,0 +1,15 @@
+Package: Ropenbt
+Type: Package
+Title: The Open Bayesian Trees Project
+Version: 0.0.0
+Date: 2026-06-23
+Authors@R: c(person('Matthew', 'Pratola', role=c('aut','cre','cph'),email='mpratola@iu.edu'))
+URL: http://www.github.com/bandframework/OpenBT
+Description: 
+    This R package provides and R interface to the OpenBT library of Bayesian Tree models (http://www.github.com/bandframework/OpenBT).  For more information and examples, refer to the README  page at http://www.github.com/bandframework/OpenBT/README.md.
+License: GPL (>= 2)
+Depends: R (>= 2.10)
+Imports: data.table, zip, emoa, Hmisc
+Suggests: 
+SystemRequirements: 
+NeedsCompilation: no

Ropenbt/NAMESPACE

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+export(openbt)
+S3method(predict, openbt)
+export(vartivity.openbt)
+export(sobol.openbt)
+export(mopareto.openbt)
+export(openbt.save)
+export(openbt.load)
+export(makecuts.openbt)
+export(setvarcuts.openbt)
+export(calcMBD)
+export(calcRS)
+importFrom(stats,cor)
+importFrom("graphics", "boxplot", "par")
+importFrom("graphics", "abline", "lines", "plot", "points")
+importFrom("stats", "quantile", "sd","qqplot")
+importFrom("stats", "rnorm", "runif")
+importFrom("stats","dist")
+importFrom("utils","read.table")
+importFrom("stats","qnorm")
+importFrom("zip","unzip")
+importFrom("zip","zipr")
+importFrom("graphics","title")
+importFrom("graphics","rect")
+importFrom("grDevices","gray")
+importFrom("utils","combn")
+importFrom("Hmisc","wtd.mean")
+importFrom("Hmisc","wtd.var")
+importFrom("Hmisc","wtd.quantile")
+