First pass

.Rbuildignore

@@ -1,2 +1,7 @@
 ^wcec\.Rproj$
 ^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^sandbox$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.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.yaml
+
+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")'

.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.yaml
+
+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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.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.yaml
+
+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

.gitignore

@@ -6,3 +6,5 @@
 .httr-oauth
 .DS_Store
 .quarto
+docs
+sandbox

DESCRIPTION

@@ -10,5 +10,13 @@ License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-URL: https://github.com/swarm-lab/wcec
+URL: https://github.com/swarm-lab/wcec, https://swarm-lab.github.io/wcec/
 BugReports: https://github.com/swarm-lab/wcec/issues
+LazyData: true
+LinkingTo: 
+    Rcpp,
+    RcppEigen
+Imports: 
+    Rcpp,
+    RcppEigen,
+    Rfast

NAMESPACE

@@ -1,2 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(wcec)
+import(RcppEigen)
+importFrom(Rcpp,evalCpp)
+useDynLib(wcec, .registration = TRUE)

R/RcppExports.R

@@ -0,0 +1,33 @@
+# 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('_wcec_wcov', PACKAGE = 'wcec', x, w)
+}
+

R/wcec-package.R

@@ -0,0 +1,57 @@
+#' wcec: ...
+#'
+#' The \code{wcec} package provides ...
+#'
+#' @author Simon Garnier <garnier@@njit.edu>
+#' @author Jason Graham <jason.graham@@scranton.edu>
+#'
+#' Maintainer: Simon Garnier <garnier@@njit.edu>
+#'
+#' @details
+#' \tabular{ll}{
+#'  Package: \tab wcec\cr
+#'  Type: \tab Package\cr
+#'  Version: \tab 0.1\cr
+#'  Date: \tab 2024-08-07\cr
+#'  License: \tab GPL-3\cr
+#' }
+#'
+#' @name wcec
+#' @import RcppEigen
+#' @importFrom Rcpp evalCpp
+#' @useDynLib wcec, .registration = TRUE
+"_PACKAGE"
+
+
+#' @title Four Gaussian Clusters
+#'
+#' @description Matrix of 2-dimensional points forming four Gaussian clusters.
+#'
+#' @name four_Gaussians
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @examples
+#' data(four_Gaussians)
+#' plot(four_Gaussians, pch = 19)
+#'
+NULL
+
+
+#' @title Three Gaussian Clusters
+#'
+#' @description Matrix of 2-dimensional points forming three Gaussian clusters.
+#'
+#' @name three_Gaussians
+#'
+#' @docType data
+#'
+#' @keywords datasets
+#'
+#' @examples
+#' data(three_Gaussians)
+#' plot(three_Gaussians, pch = 19)
+#'
+NULL