diff --git a/.Rbuildignore b/.Rbuildignore
index 7e8674f..66c4508 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,2 +1,8 @@
^gravitree\.Rproj$
^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^sandbox$
+^LICENSE\.md$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..0f2fe08
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'oldrel-1'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..c9f0165
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ # Only restrict concurrency for non-PR jobs
+ concurrency:
+ group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ permissions:
+ contents: write
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::pkgdown, local::.
+ needs: website
+
+ - name: Build site
+ run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+ shell: Rscript {0}
+
+ - name: Deploy to GitHub pages 🚀
+ if: github.event_name != 'pull_request'
+ uses: JamesIves/github-pages-deploy-action@v4.5.0
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..fefc52e
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+ test-coverage:
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::covr, any::xml2
+ needs: coverage
+
+ - name: Test coverage
+ run: |
+ cov <- covr::package_coverage(
+ quiet = FALSE,
+ clean = FALSE,
+ install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+ )
+ covr::to_cobertura(cov)
+ shell: Rscript {0}
+
+ - uses: codecov/codecov-action@v4
+ with:
+ fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+ file: ./cobertura.xml
+ plugin: noop
+ disable_search: true
+ token: ${{ secrets.CODECOV_TOKEN }}
+
+ - name: Show testthat output
+ if: always()
+ run: |
+ ## --------------------------------------------------------------------
+ find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+ shell: bash
+
+ - name: Upload test results
+ if: failure()
+ uses: actions/upload-artifact@v4
+ with:
+ name: coverage-test-failures
+ path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
index accfb7b..c87bf3f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,5 @@
.httr-oauth
.DS_Store
.quarto
+docs
+sandbox
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index 34b06d8..b395f33 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,14 +1,23 @@
Package: gravitree
Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
-Authors@R:
- person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
- comment = c(ORCID = "YOUR-ORCID-ID"))
+Version: 0.1
+Authors@R: c(
+ person("Simon", "Garnier", email = "garnier@njit.edu", role = c("aut", "cre"),
+ comment = c(ORCID = "0000-0002-3886-3974")),
+ person("Graham", "Jason", email = "jason.graham@scranton.edu", role = c("ctb", "cph"))
+ )
Description: What the package does (one paragraph).
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
- license
+License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
-URL: https://github.com/swarm-lab/gravitree
+URL: https://github.com/swarm-lab/gravitree, https://swarm-lab.github.io/gravitree/
BugReports: https://github.com/swarm-lab/gravitree/issues
+LinkingTo:
+ Rcpp,
+ RcppEigen
+Imports:
+ Rcpp,
+ Rfast,
+ fastcluster,
+ stats
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..175443c
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,595 @@
+GNU General Public License
+==========================
+
+_Version 3, 29 June 2007_
+_Copyright © 2007 Free Software Foundation, Inc. <>_
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+## Preamble
+
+The GNU General Public License is a free, copyleft license for software and other
+kinds of works.
+
+The licenses for most software and other practical works are designed to take away
+your freedom to share and change the works. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change all versions of a
+program--to make sure it remains free software for all its users. We, the Free
+Software Foundation, use the GNU General Public License for most of our software; it
+applies also to any other work released this way by its authors. You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our General
+Public Licenses are designed to make sure that you have the freedom to distribute
+copies of free software (and charge for them if you wish), that you receive source
+code or can get it if you want it, that you can change the software or use pieces of
+it in new free programs, and that you know you can do these things.
+
+To protect your rights, we need to prevent others from denying you these rights or
+asking you to surrender the rights. Therefore, you have certain responsibilities if
+you distribute copies of the software, or if you modify it: responsibilities to
+respect the freedom of others.
+
+For example, if you distribute copies of such a program, whether gratis or for a fee,
+you must pass on to the recipients the same freedoms that you received. You must make
+sure that they, too, receive or can get the source code. And you must show them these
+terms so they know their rights.
+
+Developers that use the GNU GPL protect your rights with two steps: **(1)** assert
+copyright on the software, and **(2)** offer you this License giving you legal permission
+to copy, distribute and/or modify it.
+
+For the developers' and authors' protection, the GPL clearly explains that there is
+no warranty for this free software. For both users' and authors' sake, the GPL
+requires that modified versions be marked as changed, so that their problems will not
+be attributed erroneously to authors of previous versions.
+
+Some devices are designed to deny users access to install or run modified versions of
+the software inside them, although the manufacturer can do so. This is fundamentally
+incompatible with the aim of protecting users' freedom to change the software. The
+systematic pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable. Therefore, we have designed
+this version of the GPL to prohibit the practice for those products. If such problems
+arise substantially in other domains, we stand ready to extend this provision to
+those domains in future versions of the GPL, as needed to protect the freedom of
+users.
+
+Finally, every program is threatened constantly by software patents. States should
+not allow patents to restrict development and use of software on general-purpose
+computers, but in those that do, we wish to avoid the special danger that patents
+applied to a free program could make it effectively proprietary. To prevent this, the
+GPL assures that patents cannot be used to render the program non-free.
+
+The precise terms and conditions for copying, distribution and modification follow.
+
+## TERMS AND CONDITIONS
+
+### 0. Definitions
+
+“This License” refers to version 3 of the GNU General Public License.
+
+“Copyright” also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+“The Program” refers to any copyrightable work licensed under this
+License. Each licensee is addressed as “you”. “Licensees” and
+“recipients” may be individuals or organizations.
+
+To “modify” a work means to copy from or adapt all or part of the work in
+a fashion requiring copyright permission, other than the making of an exact copy. The
+resulting work is called a “modified version” of the earlier work or a
+work “based on” the earlier work.
+
+A “covered work” means either the unmodified Program or a work based on
+the Program.
+
+To “propagate” a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for infringement under
+applicable copyright law, except executing it on a computer or modifying a private
+copy. Propagation includes copying, distribution (with or without modification),
+making available to the public, and in some countries other activities as well.
+
+To “convey” a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user through a computer
+network, with no transfer of a copy, is not conveying.
+
+An interactive user interface displays “Appropriate Legal Notices” to the
+extent that it includes a convenient and prominently visible feature that **(1)**
+displays an appropriate copyright notice, and **(2)** tells the user that there is no
+warranty for the work (except to the extent that warranties are provided), that
+licensees may convey the work under this License, and how to view a copy of this
+License. If the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+### 1. Source Code
+
+The “source code” for a work means the preferred form of the work for
+making modifications to it. “Object code” means any non-source form of a
+work.
+
+A “Standard Interface” means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of interfaces
+specified for a particular programming language, one that is widely used among
+developers working in that language.
+
+The “System Libraries” of an executable work include anything, other than
+the work as a whole, that **(a)** is included in the normal form of packaging a Major
+Component, but which is not part of that Major Component, and **(b)** serves only to
+enable use of the work with that Major Component, or to implement a Standard
+Interface for which an implementation is available to the public in source code form.
+A “Major Component”, in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system (if any) on which
+the executable work runs, or a compiler used to produce the work, or an object code
+interpreter used to run it.
+
+The “Corresponding Source” for a work in object code form means all the
+source code needed to generate, install, and (for an executable work) run the object
+code and to modify the work, including scripts to control those activities. However,
+it does not include the work's System Libraries, or general-purpose tools or
+generally available free programs which are used unmodified in performing those
+activities but which are not part of the work. For example, Corresponding Source
+includes interface definition files associated with source files for the work, and
+the source code for shared libraries and dynamically linked subprograms that the work
+is specifically designed to require, such as by intimate data communication or
+control flow between those subprograms and other parts of the work.
+
+The Corresponding Source need not include anything that users can regenerate
+automatically from other parts of the Corresponding Source.
+
+The Corresponding Source for a work in source code form is that same work.
+
+### 2. Basic Permissions
+
+All rights granted under this License are granted for the term of copyright on the
+Program, and are irrevocable provided the stated conditions are met. This License
+explicitly affirms your unlimited permission to run the unmodified Program. The
+output from running a covered work is covered by this License only if the output,
+given its content, constitutes a covered work. This License acknowledges your rights
+of fair use or other equivalent, as provided by copyright law.
+
+You may make, run and propagate covered works that you do not convey, without
+conditions so long as your license otherwise remains in force. You may convey covered
+works to others for the sole purpose of having them make modifications exclusively
+for you, or provide you with facilities for running those works, provided that you
+comply with the terms of this License in conveying all material for which you do not
+control copyright. Those thus making or running the covered works for you must do so
+exclusively on your behalf, under your direction and control, on terms that prohibit
+them from making any copies of your copyrighted material outside their relationship
+with you.
+
+Conveying under any other circumstances is permitted solely under the conditions
+stated below. Sublicensing is not allowed; section 10 makes it unnecessary.
+
+### 3. Protecting Users' Legal Rights From Anti-Circumvention Law
+
+No covered work shall be deemed part of an effective technological measure under any
+applicable law fulfilling obligations under article 11 of the WIPO copyright treaty
+adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention
+of such measures.
+
+When you convey a covered work, you waive any legal power to forbid circumvention of
+technological measures to the extent such circumvention is effected by exercising
+rights under this License with respect to the covered work, and you disclaim any
+intention to limit operation or modification of the work as a means of enforcing,
+against the work's users, your or third parties' legal rights to forbid circumvention
+of technological measures.
+
+### 4. Conveying Verbatim Copies
+
+You may convey verbatim copies of the Program's source code as you receive it, in any
+medium, provided that you conspicuously and appropriately publish on each copy an
+appropriate copyright notice; keep intact all notices stating that this License and
+any non-permissive terms added in accord with section 7 apply to the code; keep
+intact all notices of the absence of any warranty; and give all recipients a copy of
+this License along with the Program.
+
+You may charge any price or no price for each copy that you convey, and you may offer
+support or warranty protection for a fee.
+
+### 5. Conveying Modified Source Versions
+
+You may convey a work based on the Program, or the modifications to produce it from
+the Program, in the form of source code under the terms of section 4, provided that
+you also meet all of these conditions:
+
+* **a)** The work must carry prominent notices stating that you modified it, and giving a
+relevant date.
+* **b)** The work must carry prominent notices stating that it is released under this
+License and any conditions added under section 7. This requirement modifies the
+requirement in section 4 to “keep intact all notices”.
+* **c)** You must license the entire work, as a whole, under this License to anyone who
+comes into possession of a copy. This License will therefore apply, along with any
+applicable section 7 additional terms, to the whole of the work, and all its parts,
+regardless of how they are packaged. This License gives no permission to license the
+work in any other way, but it does not invalidate such permission if you have
+separately received it.
+* **d)** If the work has interactive user interfaces, each must display Appropriate Legal
+Notices; however, if the Program has interactive interfaces that do not display
+Appropriate Legal Notices, your work need not make them do so.
+
+A compilation of a covered work with other separate and independent works, which are
+not by their nature extensions of the covered work, and which are not combined with
+it such as to form a larger program, in or on a volume of a storage or distribution
+medium, is called an “aggregate” if the compilation and its resulting
+copyright are not used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work in an aggregate
+does not cause this License to apply to the other parts of the aggregate.
+
+### 6. Conveying Non-Source Forms
+
+You may convey a covered work in object code form under the terms of sections 4 and
+5, provided that you also convey the machine-readable Corresponding Source under the
+terms of this License, in one of these ways:
+
+* **a)** Convey the object code in, or embodied in, a physical product (including a
+physical distribution medium), accompanied by the Corresponding Source fixed on a
+durable physical medium customarily used for software interchange.
+* **b)** Convey the object code in, or embodied in, a physical product (including a
+physical distribution medium), accompanied by a written offer, valid for at least
+three years and valid for as long as you offer spare parts or customer support for
+that product model, to give anyone who possesses the object code either **(1)** a copy of
+the Corresponding Source for all the software in the product that is covered by this
+License, on a durable physical medium customarily used for software interchange, for
+a price no more than your reasonable cost of physically performing this conveying of
+source, or **(2)** access to copy the Corresponding Source from a network server at no
+charge.
+* **c)** Convey individual copies of the object code with a copy of the written offer to
+provide the Corresponding Source. This alternative is allowed only occasionally and
+noncommercially, and only if you received the object code with such an offer, in
+accord with subsection 6b.
+* **d)** Convey the object code by offering access from a designated place (gratis or for
+a charge), and offer equivalent access to the Corresponding Source in the same way
+through the same place at no further charge. You need not require recipients to copy
+the Corresponding Source along with the object code. If the place to copy the object
+code is a network server, the Corresponding Source may be on a different server
+(operated by you or a third party) that supports equivalent copying facilities,
+provided you maintain clear directions next to the object code saying where to find
+the Corresponding Source. Regardless of what server hosts the Corresponding Source,
+you remain obligated to ensure that it is available for as long as needed to satisfy
+these requirements.
+* **e)** Convey the object code using peer-to-peer transmission, provided you inform
+other peers where the object code and Corresponding Source of the work are being
+offered to the general public at no charge under subsection 6d.
+
+A separable portion of the object code, whose source code is excluded from the
+Corresponding Source as a System Library, need not be included in conveying the
+object code work.
+
+A “User Product” is either **(1)** a “consumer product”, which
+means any tangible personal property which is normally used for personal, family, or
+household purposes, or **(2)** anything designed or sold for incorporation into a
+dwelling. In determining whether a product is a consumer product, doubtful cases
+shall be resolved in favor of coverage. For a particular product received by a
+particular user, “normally used” refers to a typical or common use of
+that class of product, regardless of the status of the particular user or of the way
+in which the particular user actually uses, or expects or is expected to use, the
+product. A product is a consumer product regardless of whether the product has
+substantial commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.
+
+“Installation Information” for a User Product means any methods,
+procedures, authorization keys, or other information required to install and execute
+modified versions of a covered work in that User Product from a modified version of
+its Corresponding Source. The information must suffice to ensure that the continued
+functioning of the modified object code is in no case prevented or interfered with
+solely because modification has been made.
+
+If you convey an object code work under this section in, or with, or specifically for
+use in, a User Product, and the conveying occurs as part of a transaction in which
+the right of possession and use of the User Product is transferred to the recipient
+in perpetuity or for a fixed term (regardless of how the transaction is
+characterized), the Corresponding Source conveyed under this section must be
+accompanied by the Installation Information. But this requirement does not apply if
+neither you nor any third party retains the ability to install modified object code
+on the User Product (for example, the work has been installed in ROM).
+
+The requirement to provide Installation Information does not include a requirement to
+continue to provide support service, warranty, or updates for a work that has been
+modified or installed by the recipient, or for the User Product in which it has been
+modified or installed. Access to a network may be denied when the modification itself
+materially and adversely affects the operation of the network or violates the rules
+and protocols for communication across the network.
+
+Corresponding Source conveyed, and Installation Information provided, in accord with
+this section must be in a format that is publicly documented (and with an
+implementation available to the public in source code form), and must require no
+special password or key for unpacking, reading or copying.
+
+### 7. Additional Terms
+
+“Additional permissions” are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions. Additional
+permissions that are applicable to the entire Program shall be treated as though they
+were included in this License, to the extent that they are valid under applicable
+law. If additional permissions apply only to part of the Program, that part may be
+used separately under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+When you convey a copy of a covered work, you may at your option remove any
+additional permissions from that copy, or from any part of it. (Additional
+permissions may be written to require their own removal in certain cases when you
+modify the work.) You may place additional permissions on material, added by you to a
+covered work, for which you have or can give appropriate copyright permission.
+
+Notwithstanding any other provision of this License, for material you add to a
+covered work, you may (if authorized by the copyright holders of that material)
+supplement the terms of this License with terms:
+
+* **a)** Disclaiming warranty or limiting liability differently from the terms of
+sections 15 and 16 of this License; or
+* **b)** Requiring preservation of specified reasonable legal notices or author
+attributions in that material or in the Appropriate Legal Notices displayed by works
+containing it; or
+* **c)** Prohibiting misrepresentation of the origin of that material, or requiring that
+modified versions of such material be marked in reasonable ways as different from the
+original version; or
+* **d)** Limiting the use for publicity purposes of names of licensors or authors of the
+material; or
+* **e)** Declining to grant rights under trademark law for use of some trade names,
+trademarks, or service marks; or
+* **f)** Requiring indemnification of licensors and authors of that material by anyone
+who conveys the material (or modified versions of it) with contractual assumptions of
+liability to the recipient, for any liability that these contractual assumptions
+directly impose on those licensors and authors.
+
+All other non-permissive additional terms are considered “further
+restrictions” within the meaning of section 10. If the Program as you received
+it, or any part of it, contains a notice stating that it is governed by this License
+along with a term that is a further restriction, you may remove that term. If a
+license document contains a further restriction but permits relicensing or conveying
+under this License, you may add to a covered work material governed by the terms of
+that license document, provided that the further restriction does not survive such
+relicensing or conveying.
+
+If you add terms to a covered work in accord with this section, you must place, in
+the relevant source files, a statement of the additional terms that apply to those
+files, or a notice indicating where to find the applicable terms.
+
+Additional terms, permissive or non-permissive, may be stated in the form of a
+separately written license, or stated as exceptions; the above requirements apply
+either way.
+
+### 8. Termination
+
+You may not propagate or modify a covered work except as expressly provided under
+this License. Any attempt otherwise to propagate or modify it is void, and will
+automatically terminate your rights under this License (including any patent licenses
+granted under the third paragraph of section 11).
+
+However, if you cease all violation of this License, then your license from a
+particular copyright holder is reinstated **(a)** provisionally, unless and until the
+copyright holder explicitly and finally terminates your license, and **(b)** permanently,
+if the copyright holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+Moreover, your license from a particular copyright holder is reinstated permanently
+if the copyright holder notifies you of the violation by some reasonable means, this
+is the first time you have received notice of violation of this License (for any
+work) from that copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+Termination of your rights under this section does not terminate the licenses of
+parties who have received copies or rights from you under this License. If your
+rights have been terminated and not permanently reinstated, you do not qualify to
+receive new licenses for the same material under section 10.
+
+### 9. Acceptance Not Required for Having Copies
+
+You are not required to accept this License in order to receive or run a copy of the
+Program. Ancillary propagation of a covered work occurring solely as a consequence of
+using peer-to-peer transmission to receive a copy likewise does not require
+acceptance. However, nothing other than this License grants you permission to
+propagate or modify any covered work. These actions infringe copyright if you do not
+accept this License. Therefore, by modifying or propagating a covered work, you
+indicate your acceptance of this License to do so.
+
+### 10. Automatic Licensing of Downstream Recipients
+
+Each time you convey a covered work, the recipient automatically receives a license
+from the original licensors, to run, modify and propagate that work, subject to this
+License. You are not responsible for enforcing compliance by third parties with this
+License.
+
+An “entity transaction” is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an organization, or
+merging organizations. If propagation of a covered work results from an entity
+transaction, each party to that transaction who receives a copy of the work also
+receives whatever licenses to the work the party's predecessor in interest had or
+could give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if the predecessor
+has it or can get it with reasonable efforts.
+
+You may not impose any further restrictions on the exercise of the rights granted or
+affirmed under this License. For example, you may not impose a license fee, royalty,
+or other charge for exercise of rights granted under this License, and you may not
+initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging
+that any patent claim is infringed by making, using, selling, offering for sale, or
+importing the Program or any portion of it.
+
+### 11. Patents
+
+A “contributor” is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The work thus
+licensed is called the contributor's “contributor version”.
+
+A contributor's “essential patent claims” are all patent claims owned or
+controlled by the contributor, whether already acquired or hereafter acquired, that
+would be infringed by some manner, permitted by this License, of making, using, or
+selling its contributor version, but do not include claims that would be infringed
+only as a consequence of further modification of the contributor version. For
+purposes of this definition, “control” includes the right to grant patent
+sublicenses in a manner consistent with the requirements of this License.
+
+Each contributor grants you a non-exclusive, worldwide, royalty-free patent license
+under the contributor's essential patent claims, to make, use, sell, offer for sale,
+import and otherwise run, modify and propagate the contents of its contributor
+version.
+
+In the following three paragraphs, a “patent license” is any express
+agreement or commitment, however denominated, not to enforce a patent (such as an
+express permission to practice a patent or covenant not to sue for patent
+infringement). To “grant” such a patent license to a party means to make
+such an agreement or commitment not to enforce a patent against the party.
+
+If you convey a covered work, knowingly relying on a patent license, and the
+Corresponding Source of the work is not available for anyone to copy, free of charge
+and under the terms of this License, through a publicly available network server or
+other readily accessible means, then you must either **(1)** cause the Corresponding
+Source to be so available, or **(2)** arrange to deprive yourself of the benefit of the
+patent license for this particular work, or **(3)** arrange, in a manner consistent with
+the requirements of this License, to extend the patent license to downstream
+recipients. “Knowingly relying” means you have actual knowledge that, but
+for the patent license, your conveying the covered work in a country, or your
+recipient's use of the covered work in a country, would infringe one or more
+identifiable patents in that country that you have reason to believe are valid.
+
+If, pursuant to or in connection with a single transaction or arrangement, you
+convey, or propagate by procuring conveyance of, a covered work, and grant a patent
+license to some of the parties receiving the covered work authorizing them to use,
+propagate, modify or convey a specific copy of the covered work, then the patent
+license you grant is automatically extended to all recipients of the covered work and
+works based on it.
+
+A patent license is “discriminatory” if it does not include within the
+scope of its coverage, prohibits the exercise of, or is conditioned on the
+non-exercise of one or more of the rights that are specifically granted under this
+License. You may not convey a covered work if you are a party to an arrangement with
+a third party that is in the business of distributing software, under which you make
+payment to the third party based on the extent of your activity of conveying the
+work, and under which the third party grants, to any of the parties who would receive
+the covered work from you, a discriminatory patent license **(a)** in connection with
+copies of the covered work conveyed by you (or copies made from those copies), or **(b)**
+primarily for and in connection with specific products or compilations that contain
+the covered work, unless you entered into that arrangement, or that patent license
+was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied
+license or other defenses to infringement that may otherwise be available to you
+under applicable patent law.
+
+### 12. No Surrender of Others' Freedom
+
+If conditions are imposed on you (whether by court order, agreement or otherwise)
+that contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot convey a covered work so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not convey it at all. For example, if you
+agree to terms that obligate you to collect a royalty for further conveying from
+those to whom you convey the Program, the only way you could satisfy both those terms
+and this License would be to refrain entirely from conveying the Program.
+
+### 13. Use with the GNU Affero General Public License
+
+Notwithstanding any other provision of this License, you have permission to link or
+combine any covered work with a work licensed under version 3 of the GNU Affero
+General Public License into a single combined work, and to convey the resulting work.
+The terms of this License will continue to apply to the part which is the covered
+work, but the special requirements of the GNU Affero General Public License, section
+13, concerning interaction through a network will apply to the combination as such.
+
+### 14. Revised Versions of this License
+
+The Free Software Foundation may publish revised and/or new versions of the GNU
+General Public License from time to time. Such new versions will be similar in spirit
+to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that
+a certain numbered version of the GNU General Public License “or any later
+version” applies to it, you have the option of following the terms and
+conditions either of that numbered version or of any later version published by the
+Free Software Foundation. If the Program does not specify a version number of the GNU
+General Public License, you may choose any version ever published by the Free
+Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU
+General Public License can be used, that proxy's public statement of acceptance of a
+version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no
+additional obligations are imposed on any author or copyright holder as a result of
+your choosing to follow a later version.
+
+### 15. Disclaimer of Warranty
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER
+EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE
+QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
+DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+### 16. Limitation of Liability
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS
+PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
+WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16
+
+If the disclaimer of warranty and limitation of liability provided above cannot be
+given local legal effect according to their terms, reviewing courts shall apply local
+law that most closely approximates an absolute waiver of all civil liability in
+connection with the Program, unless a warranty or assumption of liability accompanies
+a copy of the Program in return for a fee.
+
+_END OF TERMS AND CONDITIONS_
+
+## How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to
+the public, the best way to achieve this is to make it free software which everyone
+can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them
+to the start of each source file to most effectively state the exclusion of warranty;
+and each file should have at least the “copyright” line and a pointer to
+where the full notice is found.
+
+
+ Copyright (C)
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Copyright (C)
+ This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type 'show c' for details.
+
+The hypothetical commands `show w` and `show c` should show the appropriate parts of
+the General Public License. Of course, your program's commands might be different;
+for a GUI interface, you would use an “about box”.
+
+You should also get your employer (if you work as a programmer) or school, if any, to
+sign a “copyright disclaimer” for the program, if necessary. For more
+information on this, and how to apply and follow the GNU GPL, see
+<>.
+
+The GNU General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may consider it
+more useful to permit linking proprietary applications with the library. If this is
+what you want to do, use the GNU Lesser General Public License instead of this
+License. But first, please read
+<>.
diff --git a/NAMESPACE b/NAMESPACE
index 6ae9268..b0a5dfd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,2 +1,6 @@
# Generated by roxygen2: do not edit by hand
+export(gravitree)
+import(RcppEigen)
+importFrom(Rcpp,evalCpp)
+useDynLib(gravitree, .registration = TRUE)
diff --git a/R/RcppExports.R b/R/RcppExports.R
new file mode 100644
index 0000000..2477f17
--- /dev/null
+++ b/R/RcppExports.R
@@ -0,0 +1,74 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#' @name .wcov
+#'
+#' @title Weighted Covariance Matrix
+#'
+#' @description \code{wcov} computes the estimates of the weighted covariance
+#' matrix and the weighted mean of the data.
+#'
+#' @param x A matrix with \eqn{m} columns and \eqn{n} rows, where each column
+#' represents a different variable and each row a different observation.
+#'
+#' @param w A non-negative and non-zero vector of weights for each observation.
+#' Its length must equal the number of rows of x.
+#'
+#' @return A list with two components:
+#' \itemize{
+#' \item \code{center}: an estimate for the center (mean) of the data.
+#' \item \code{cov}: the estimated (weighted) covariance matrix.
+#' }
+#'
+#' @author Simon Garnier, \email{garnier@@njit.edu}
+#'
+#' @examples
+#' m <- matrix(c(rnorm(500, 6), rnorm(500, 11, 3)), ncol = 2)
+#' w <- runif(500)
+#' gravitree:::.wcov(m, w)
+#'
+.wcov <- function(x, w) {
+ .Call(`_gravitree_wcov`, x, w)
+}
+
+.eigen <- function(cov) {
+ .Call(`_gravitree_eigen`, cov)
+}
+
+#' @name .Mahalanobis
+#'
+#' @title Mahalanobis Distance
+#'
+#' @description \code{Mahalanobis} computes the squared Mahalanobis distance of
+#' all rows in \code{x} and the vector \eqn{\mu}{mu} = \code{center} with
+#' respect to \eqn{\Sigma}{Sigma} = \code{cov}. This is (for vector \code{x})
+#' defined as \deqn{D^2 = (x - \mu)' \Sigma^{-1} (x - \mu)}{D^2 = (x - \mu)'
+#' \Sigma^-1 (x - \mu)}
+#'
+#' @param x A matrix with \eqn{m} columns and \eqn{n} rows, where each column
+#' represents a different variable and each row a different observation.
+#'
+#' @param center The mean vector of the distribution.
+#'
+#' @param cov The covariance matrix (\eqn{p \times p}{p x p}) of the
+#' distribution.
+#'
+#' @return A matrix with 1 column and \eqn{n} rows representing the estimated
+#' distance for each observation.
+#'
+#' @author Simon Garnier, \email{garnier@@njit.edu}
+#'
+#' @examples
+#' m <- matrix(c(rnorm(500, 6), rnorm(500, 11, 3)), ncol = 2)
+#' w <- runif(500)
+#' covar <- gravitree:::.wcov(m, w)
+#' gravitree:::.Mahalanobis(m, covar$center, covar$cov)
+#'
+.Mahalanobis <- function(x, center, cov) {
+ .Call(`_gravitree_Mahalanobis`, x, center, cov)
+}
+
+.as_dist <- function(mat) {
+ .Call(`_gravitree_as_dist`, mat)
+}
+
diff --git a/R/gravitree-package.R b/R/gravitree-package.R
new file mode 100644
index 0000000..6c5fff2
--- /dev/null
+++ b/R/gravitree-package.R
@@ -0,0 +1,23 @@
+#' gravitree: ...
+#'
+#' The \code{gravitree} package provides...
+#'
+#' @author Simon Garnier
+#' @author Jason Graham
+#'
+#' Maintainer: Simon Garnier
+#'
+#' @details
+#' \tabular{ll}{
+#' Package: \tab gravitree\cr
+#' Type: \tab Package\cr
+#' Version: \tab 0.1\cr
+#' Date: \tab 2024-05-03\cr
+#' License: \tab GPL-3\cr
+#' }
+#'
+#' @name gravitree
+#' @import RcppEigen
+#' @importFrom Rcpp evalCpp
+#' @useDynLib gravitree, .registration = TRUE
+"_PACKAGE"
diff --git a/R/gravitree.R b/R/gravitree.R
new file mode 100644
index 0000000..ee29df0
--- /dev/null
+++ b/R/gravitree.R
@@ -0,0 +1,70 @@
+#' @export
+gravitree <- function(x, m, k = NULL, sample = 1, na_rm = FALSE) {
+ if (!is.matrix(x)) {
+ x <- as.matrix(x)
+ }
+
+ nr <- nrow(x)
+
+ if (nr <= 3) {
+ stop("'x' must contain at least 4 observations.")
+ }
+
+ if (!is.matrix(m)) {
+ m <- as.matrix(m)
+ }
+
+ if (nr != nrow(m)) {
+ stop("The length of 'm' does not equal the number of rows of 'x'.")
+ }
+
+ if (na_rm) {
+ na_ix <- apply(x, 1, function(r) any(is.na(r))) | is.na(m)
+ x <- x[!na_ix, , drop = FALSE]
+ m <- m[!na_ix, , drop = FALSE]
+ }
+
+ if (sample < 1) {
+ ix <- sample(1:nr, nr * sample, prob = m)
+ notix <- which(!(1:nr %in% ix))
+ xx <- x[ix, , drop = FALSE]
+ mm <- m[ix, , drop = FALSE]
+ g <- Rfast::Tcrossprod(mm, mm) / (Rfast::Dist(xx)^ncol(xx))
+ d <- .as_dist(log(1 / g))
+ } else {
+ g <- Rfast::Tcrossprod(m, m) / (Rfast::Dist(x)^ncol(x))
+ d <- .as_dist(log(1 / g))
+ }
+
+ tree <- fastcluster::hclust(d, method = "ward.D2")
+
+ if (is.null(k)) {
+ k <- length(tree$height) - which.max(diff(tree$height)) + 1
+ }
+
+ cluster <- stats::cutree(tree, k)
+
+ if (sample < 1) {
+ centers <- lapply(1:k, function(i) {
+ ix <- cluster == i
+ .wcov(xx[ix, , drop = FALSE], mm[ix])
+ })
+ tmp <- rep(NA, nr)
+ tmp[ix] <- cluster
+ tmp[notix] <- Rfast::rowMins(sapply(1:k, function(i) {
+ .Mahalanobis(x[notix, , drop = FALSE], centers[[i]]$center, centers[[i]]$cov)
+ }))
+ cluster <- tmp
+ } else {
+ centers <- lapply(1:k, function(i) {
+ ix <- cluster == i
+ .wcov(x[ix, , drop = FALSE], m[ix])
+ })
+ }
+
+ list(
+ tree = tree,
+ cluster = cluster,
+ centers = centers
+ )
+}
\ No newline at end of file
diff --git a/README.md b/README.md
index 3e20ee3..eaf5157 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,28 @@
-# gravitree
\ No newline at end of file
+# gravitree
+
+
+[](https://CRAN.R-project.org/package=gravitree)
+[](https://github.com/swarm-lab/gravitree/actions/workflows/R-CMD-check.yaml)
+[](https://github.com/swarm-lab/gravitree/actions/workflows/test-coverage.yaml)
+
+
+The goal of gravitree is to ...
+
+## Installation
+
+You can install the development version of gravitree from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("swarm-lab/gravitree")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(gravitree)
+## basic example code
+```
+
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..e998a56
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: https://swarm-lab.github.io/gravitree/
+template:
+ bootstrap: 5
+
diff --git a/man/dot-Mahalanobis.Rd b/man/dot-Mahalanobis.Rd
new file mode 100644
index 0000000..ac625e5
--- /dev/null
+++ b/man/dot-Mahalanobis.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RcppExports.R
+\name{.Mahalanobis}
+\alias{.Mahalanobis}
+\title{Mahalanobis Distance}
+\usage{
+.Mahalanobis(x, center, cov)
+}
+\arguments{
+\item{x}{A matrix with \eqn{m} columns and \eqn{n} rows, where each column
+represents a different variable and each row a different observation.}
+
+\item{center}{The mean vector of the distribution.}
+
+\item{cov}{The covariance matrix (\eqn{p \times p}{p x p}) of the
+distribution.}
+}
+\value{
+A matrix with 1 column and \eqn{n} rows representing the estimated
+distance for each observation.
+}
+\description{
+\code{Mahalanobis} computes the squared Mahalanobis distance of
+all rows in \code{x} and the vector \eqn{\mu}{mu} = \code{center} with
+respect to \eqn{\Sigma}{Sigma} = \code{cov}. This is (for vector \code{x})
+defined as \deqn{D^2 = (x - \mu)' \Sigma^{-1} (x - \mu)}{D^2 = (x - \mu)'
+ \Sigma^-1 (x - \mu)}
+}
+\examples{
+m <- matrix(c(rnorm(500, 6), rnorm(500, 11, 3)), ncol = 2)
+w <- runif(500)
+covar <- gravitree:::.wcov(m, w)
+gravitree:::.Mahalanobis(m, covar$center, covar$cov)
+
+}
+\author{
+Simon Garnier, \email{garnier@njit.edu}
+}
diff --git a/man/dot-wcov.Rd b/man/dot-wcov.Rd
new file mode 100644
index 0000000..00eb3c3
--- /dev/null
+++ b/man/dot-wcov.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RcppExports.R
+\name{.wcov}
+\alias{.wcov}
+\title{Weighted Covariance Matrix}
+\usage{
+.wcov(x, w)
+}
+\arguments{
+\item{x}{A matrix with \eqn{m} columns and \eqn{n} rows, where each column
+represents a different variable and each row a different observation.}
+
+\item{w}{A non-negative and non-zero vector of weights for each observation.
+Its length must equal the number of rows of x.}
+}
+\value{
+A list with two components:
+\itemize{
+\item \code{center}: an estimate for the center (mean) of the data.
+\item \code{cov}: the estimated (weighted) covariance matrix.
+}
+}
+\description{
+\code{wcov} computes the estimates of the weighted covariance
+matrix and the weighted mean of the data.
+}
+\examples{
+m <- matrix(c(rnorm(500, 6), rnorm(500, 11, 3)), ncol = 2)
+w <- runif(500)
+gravitree:::.wcov(m, w)
+
+}
+\author{
+Simon Garnier, \email{garnier@njit.edu}
+}
diff --git a/man/gravitree.Rd b/man/gravitree.Rd
new file mode 100644
index 0000000..b307ea8
--- /dev/null
+++ b/man/gravitree.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gravitree-package.R
+\docType{package}
+\name{gravitree}
+\alias{gravitree-package}
+\alias{gravitree}
+\title{gravitree: ...}
+\description{
+The \code{gravitree} package provides...
+}
+\details{
+\tabular{ll}{
+Package: \tab gravitree\cr
+Type: \tab Package\cr
+Version: \tab 0.1\cr
+Date: \tab 2024-05-03\cr
+License: \tab GPL-3\cr
+}
+}
+\seealso{
+Useful links:
+\itemize{
+ \item \url{https://github.com/swarm-lab/gravitree}
+ \item \url{https://swarm-lab.github.io/gravitree/}
+ \item Report bugs at \url{https://github.com/swarm-lab/gravitree/issues}
+}
+
+}
+\author{
+Simon Garnier \href{mailto:garnier@njit.edu}{garnier@njit.edu}
+
+Jason Graham \href{mailto:jason.graham@scranton.edu}{jason.graham@scranton.edu}
+
+Maintainer: Simon Garnier \href{mailto:garnier@njit.edu}{garnier@njit.edu}
+}
diff --git a/src/.gitignore b/src/.gitignore
new file mode 100644
index 0000000..22034c4
--- /dev/null
+++ b/src/.gitignore
@@ -0,0 +1,3 @@
+*.o
+*.so
+*.dll
diff --git a/src/Makevars b/src/Makevars
new file mode 100644
index 0000000..6868846
--- /dev/null
+++ b/src/Makevars
@@ -0,0 +1,8 @@
+## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is
+## no user-facing library. The include path to headers is already set by R.
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+
+## With R 3.1.0 or later, you can uncomment the following line to tell R to
+## enable compilation with C++11 (or even C++14) where available
+#CXX_STD = CXX11
diff --git a/src/Makevars.win b/src/Makevars.win
new file mode 100644
index 0000000..6868846
--- /dev/null
+++ b/src/Makevars.win
@@ -0,0 +1,8 @@
+## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is
+## no user-facing library. The include path to headers is already set by R.
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+
+## With R 3.1.0 or later, you can uncomment the following line to tell R to
+## enable compilation with C++11 (or even C++14) where available
+#CXX_STD = CXX11
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
new file mode 100644
index 0000000..819a564
--- /dev/null
+++ b/src/RcppExports.cpp
@@ -0,0 +1,73 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include
+#include
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+// wcov
+Rcpp::List wcov(Eigen::MatrixXd& x, Eigen::VectorXd& w);
+RcppExport SEXP _gravitree_wcov(SEXP xSEXP, SEXP wSEXP) {
+BEGIN_RCPP
+ Rcpp::RObject rcpp_result_gen;
+ Rcpp::RNGScope rcpp_rngScope_gen;
+ Rcpp::traits::input_parameter< Eigen::MatrixXd& >::type x(xSEXP);
+ Rcpp::traits::input_parameter< Eigen::VectorXd& >::type w(wSEXP);
+ rcpp_result_gen = Rcpp::wrap(wcov(x, w));
+ return rcpp_result_gen;
+END_RCPP
+}
+// eigen
+Rcpp::List eigen(Eigen::MatrixXd& cov);
+RcppExport SEXP _gravitree_eigen(SEXP covSEXP) {
+BEGIN_RCPP
+ Rcpp::RObject rcpp_result_gen;
+ Rcpp::RNGScope rcpp_rngScope_gen;
+ Rcpp::traits::input_parameter< Eigen::MatrixXd& >::type cov(covSEXP);
+ rcpp_result_gen = Rcpp::wrap(eigen(cov));
+ return rcpp_result_gen;
+END_RCPP
+}
+// Mahalanobis
+Eigen::MatrixXd Mahalanobis(Eigen::MatrixXd& x, Eigen::VectorXd& center, Eigen::MatrixXd& cov);
+RcppExport SEXP _gravitree_Mahalanobis(SEXP xSEXP, SEXP centerSEXP, SEXP covSEXP) {
+BEGIN_RCPP
+ Rcpp::RObject rcpp_result_gen;
+ Rcpp::RNGScope rcpp_rngScope_gen;
+ Rcpp::traits::input_parameter< Eigen::MatrixXd& >::type x(xSEXP);
+ Rcpp::traits::input_parameter< Eigen::VectorXd& >::type center(centerSEXP);
+ Rcpp::traits::input_parameter< Eigen::MatrixXd& >::type cov(covSEXP);
+ rcpp_result_gen = Rcpp::wrap(Mahalanobis(x, center, cov));
+ return rcpp_result_gen;
+END_RCPP
+}
+// as_dist
+Rcpp::NumericVector as_dist(const Rcpp::NumericMatrix& mat);
+RcppExport SEXP _gravitree_as_dist(SEXP matSEXP) {
+BEGIN_RCPP
+ Rcpp::RObject rcpp_result_gen;
+ Rcpp::RNGScope rcpp_rngScope_gen;
+ Rcpp::traits::input_parameter< const Rcpp::NumericMatrix& >::type mat(matSEXP);
+ rcpp_result_gen = Rcpp::wrap(as_dist(mat));
+ return rcpp_result_gen;
+END_RCPP
+}
+
+static const R_CallMethodDef CallEntries[] = {
+ {"_gravitree_wcov", (DL_FUNC) &_gravitree_wcov, 2},
+ {"_gravitree_eigen", (DL_FUNC) &_gravitree_eigen, 1},
+ {"_gravitree_Mahalanobis", (DL_FUNC) &_gravitree_Mahalanobis, 3},
+ {"_gravitree_as_dist", (DL_FUNC) &_gravitree_as_dist, 1},
+ {NULL, NULL, 0}
+};
+
+RcppExport void R_init_gravitree(DllInfo *dll) {
+ R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+ R_useDynamicSymbols(dll, FALSE);
+}
diff --git a/src/fast.cpp b/src/fast.cpp
new file mode 100644
index 0000000..bdf6824
--- /dev/null
+++ b/src/fast.cpp
@@ -0,0 +1,119 @@
+#include
+// [[Rcpp::depends(RcppEigen)]]
+
+//' @name .wcov
+//'
+//' @title Weighted Covariance Matrix
+//'
+//' @description \code{wcov} computes the estimates of the weighted covariance
+//' matrix and the weighted mean of the data.
+//'
+//' @param x A matrix with \eqn{m} columns and \eqn{n} rows, where each column
+//' represents a different variable and each row a different observation.
+//'
+//' @param w A non-negative and non-zero vector of weights for each observation.
+//' Its length must equal the number of rows of x.
+//'
+//' @return A list with two components:
+//' \itemize{
+//' \item \code{center}: an estimate for the center (mean) of the data.
+//' \item \code{cov}: the estimated (weighted) covariance matrix.
+//' }
+//'
+//' @author Simon Garnier, \email{garnier@@njit.edu}
+//'
+//' @examples
+//' m <- matrix(c(rnorm(500, 6), rnorm(500, 11, 3)), ncol = 2)
+//' w <- runif(500)
+//' gravitree:::.wcov(m, w)
+//'
+// [[Rcpp::export(.wcov)]]
+Rcpp::List wcov(Eigen::MatrixXd &x, Eigen::VectorXd &w)
+{
+ Eigen::VectorXd center(x.cols());
+ double ws = w.sum();
+ for (int i = 0; i < x.cols(); i++)
+ {
+ center(i) = (x.col(i).array() * w.array()).sum() / ws;
+ }
+
+ int p = x.cols();
+ Eigen::VectorXd sqw = (w.array() / ws).cwiseSqrt();
+ Eigen::MatrixXd X = x.array().rowwise() - center.transpose().array();
+ Eigen::MatrixXd cov = Eigen::MatrixXd(p, p).setZero().selfadjointView().rankUpdate(X.transpose() * sqw.asDiagonal());
+
+ return Rcpp::List::create(
+ Rcpp::_["center"] = center,
+ Rcpp::_["cov"] = cov);
+}
+
+// [[Rcpp::export(.eigen)]]
+Rcpp::List eigen(Eigen::MatrixXd &cov)
+{
+ Eigen::SelfAdjointEigenSolver eigensolver(cov);
+
+ return Rcpp::List::create(
+ Rcpp::_["values"] = eigensolver.eigenvalues().reverse().real(),
+ Rcpp::_["vectors"] = -eigensolver.eigenvectors().colwise().reverse().transpose().real());
+}
+
+//' @name .Mahalanobis
+//'
+//' @title Mahalanobis Distance
+//'
+//' @description \code{Mahalanobis} computes the squared Mahalanobis distance of
+//' all rows in \code{x} and the vector \eqn{\mu}{mu} = \code{center} with
+//' respect to \eqn{\Sigma}{Sigma} = \code{cov}. This is (for vector \code{x})
+//' defined as \deqn{D^2 = (x - \mu)' \Sigma^{-1} (x - \mu)}{D^2 = (x - \mu)'
+//' \Sigma^-1 (x - \mu)}
+//'
+//' @param x A matrix with \eqn{m} columns and \eqn{n} rows, where each column
+//' represents a different variable and each row a different observation.
+//'
+//' @param center The mean vector of the distribution.
+//'
+//' @param cov The covariance matrix (\eqn{p \times p}{p x p}) of the
+//' distribution.
+//'
+//' @return A matrix with 1 column and \eqn{n} rows representing the estimated
+//' distance for each observation.
+//'
+//' @author Simon Garnier, \email{garnier@@njit.edu}
+//'
+//' @examples
+//' m <- matrix(c(rnorm(500, 6), rnorm(500, 11, 3)), ncol = 2)
+//' w <- runif(500)
+//' covar <- gravitree:::.wcov(m, w)
+//' gravitree:::.Mahalanobis(m, covar$center, covar$cov)
+//'
+// [[Rcpp::export(.Mahalanobis)]]
+Eigen::MatrixXd Mahalanobis(Eigen::MatrixXd &x, Eigen::VectorXd ¢er,
+ Eigen::MatrixXd &cov)
+{
+ Eigen::MatrixXd cx = x.rowwise() - center.transpose();
+ Eigen::MatrixXd out = (cx * cov.inverse()).array() * cx.array();
+ return out.rowwise().sum();
+}
+
+// [[Rcpp::export(.as_dist)]]
+Rcpp::NumericVector as_dist(const Rcpp::NumericMatrix& mat) {
+ int nrow = mat.nrow();
+ int ncol = mat.ncol();
+ int size = nrow * (nrow - 1) / 2;
+ Rcpp::NumericVector out(size);
+
+ if (nrow > 1) {
+ int k = 0;
+ for (int j = 0; j < ncol; j++) {
+ for (int i = j + 1; i < nrow; i++) {
+ out[k++] = mat(i,j);
+ }
+ }
+ }
+
+ out.attr("Size") = nrow;
+ out.attr("class") = "dist";
+ out.attr("Diag") = false;
+ out.attr("Upper") = false;
+ return out;
+}
\ No newline at end of file