frycast · Oct 1, 2026 · Jun 3, 2026 · Jun 3, 2026 · Jun 4, 2026 · Jun 4, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,5 @@
 ^man/figures$
 ^tests/build-testing.R
 ^CRAN-SUBMISSION$
+^dev$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,82 @@
+# 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:
+
+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
+      RGL_USE_NULL: true
+      _R_CHECK_FORCE_SUGGESTS_: true
+      _R_CHECK_CRAN_INCOMING_: ${{ matrix.config.r == 'devel' && 'true' || 'false' }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - name: Start a virtual display for Tcl/Tk
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install -y xvfb tidy
+          Xvfb :99 -screen 0 1280x1024x24 &
+          echo "DISPLAY=:99" >> "$GITHUB_ENV"
+
+      - name: Install XQuartz and start a virtual display
+        if: runner.os == 'macOS'
+        run: |
+          brew install --cask xquartz
+          /opt/X11/bin/Xvfb :99 -screen 0 1280x1024x24 &
+          echo "DISPLAY=:99" >> "$GITHUB_ENV"
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Install the Courier font used in the PDF manual
+        run: tlmgr install courier makeindex
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, any::V8
+          needs: check
+
+      - name: Use R's LaTeX emulation on Windows
+        if: runner.os == 'Windows'
+        run: |
+          cat('options(texi2dvi = "emulation")\n', file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        env:
+          NOT_CRAN: false
+        with:
+          upload-snapshots: true
+          args: '"--as-cran"'
+          build_args: 'character()'
+          upload-results: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,67 @@
+# 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:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RGL_USE_NULL: true
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Start a virtual display for Tcl/Tk
+        run: |
+          sudo apt-get install -y xvfb
+          Xvfb :99 -screen 0 1280x1024x24 &
+          echo "DISPLAY=:99" >> "$GITHUB_ENV"
+
+      - 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")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: 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@v7
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
@@ -7,10 +7,11 @@ inst/doc
 
 #exploratory
 exploration
+scratch.R
 
 #Rcpp files
 src/*.o
 src/*.so
 src/*.dll
 packrat/lib*/
-CMB_map_smica1024.fits
+CMB_map_smica1024.fits
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: rcosmo
 URL: https://github.com/frycast/rcosmo
 BugReports: https://github.com/frycast/rcosmo/issues
 Title: Cosmic Microwave Background Data Analysis
-Version: 1.1.4
+Version: 1.1.5
 Authors@R: c(person("Daniel", "Fryer", 
                      role = c("aut", "cre"), 
                      email = "d.fryer@latrobe.edu.au",
@@ -18,7 +18,7 @@ Authors@R: c(person("Daniel", "Fryer",
                      role = "aut"))
 Description: Handling and Analysing Spherical, 
       HEALPix and Cosmic Microwave Background data on a HEALPix grid.
-Depends: R (>= 3.4.0)
+Depends: R (>= 4.5.0)
 License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -33,10 +33,7 @@ Imports:
 	  geoR (>= 1.7-5.2.1),
     nnls (>= 1.4)
 Suggests:
-    knitr,
-    rmarkdown,
     testthat,
-    R.rsp,
     gsl
 LinkingTo: Rcpp
-RoxygenNote: 7.2.1
+Config/roxygen2/version: 8.0.0
diff --git a/NEWS.md b/NEWS.md
diff --git a/R/CMBDat.R b/R/CMBDat.R
@@ -4,7 +4,7 @@
 #' These are lists containing header information and other metadata as well
 #' as an element called data, whose columns may include, for example, the
 #' intensity (I), polarisation (Q, U), PMASK and TMASK. It also may contain an
-#' \code{\link{mmap}} object that points to the CMB map data table in the FITS
+#' \code{\link[mmap:mmap]{mmap}} object that points to the CMB map data table in the FITS
 #' file.
 #'
 #'@param filename The path to the fits file.
@@ -16,7 +16,7 @@
 #'If \code{mmap = FALSE} then a \code{data.frame} is
 #'included, named \code{data}, whose columns may include, for
 #'example, the intensity (I), polarisation (Q, U), PMASK and TMASK.
-#'If \code{mmap = TRUE} then a \code{\link{mmap}} object is returned
+#'If \code{mmap = TRUE} then a \code{\link[mmap:mmap]{mmap}} object is returned
 #'that points to the CMB map data table in the FITS file.
 #'
 #'@examples

diff --git a/R/CMBDataFrameGenerics.R b/R/CMBDataFrameGenerics.R
@@ -1119,7 +1119,7 @@ coords.CMBDataFrame <- function( x, new.coords, ... )
 #'@param depth_test The depth test to be applied to the
 #' plotted points. This controls how resistant the plotted
 #' object is to being obscured. See \code{\link[rgl]{rgl.material}}
-#'@param lab_depth_test The \code{\link{rgl}} depth test
+#'@param lab_depth_test The \code{\link[rgl:rgl.material]{rgl}} depth test
 #' to be applied to the labels and pixel boundaries if present.
 #' See \code{\link[rgl]{rgl.material}}
 #'@param ... Arguments passed to rgl::plot3d.
@@ -1352,7 +1352,7 @@ print.summary.CMBDataFrame <- function(x, ...)
 #' This function neatly prints the contents of a CMBDataFrame.
 #'
 #'@param x A \code{\link{CMBDataFrame}}.
-#'@param ... arguments passed to \code{\link{print.tbl_df}}
+#'@param ... arguments passed to \code{\link[tibble:print.tbl_df]{print.tbl_df}}
 #'
 #'@return
 #'Prints contents of the CMB data frame to the console.

diff --git a/R/HPDataFrame.R b/R/HPDataFrame.R
@@ -418,7 +418,7 @@ nside.HPDataFrame <- function( x ) {
 #'@param depth_test The depth test to be applied to the
 #' plotted points. This controls how resistant the plotted
 #' object is to being obscured. This controls how resistant the plotted
-#'@param lab_depth_test The \code{\link{rgl}} depth test
+#'@param lab_depth_test The \code{\link[rgl:rgl.material]{rgl}} depth test
 #' to be applied to the labels and pixel boundaries
 #' if present. See \code{\link[rgl]{rgl.material}}
 #'@param ... arguments passed to rgl::plot3d
@@ -783,7 +783,7 @@ is.HPDataFrame <- function(hpdf) {
 #' This function neatly prints the contents of a HPDataFrame.
 #'
 #'@param x A HPDataFrame.
-#'@param ... arguments passed to \code{\link{print.tbl_df}}
+#'@param ... arguments passed to \code{\link[tibble:print.tbl_df]{print.tbl_df}}
 #'
 #'@return
 #'Prints contents of the HPDataFrame to the console.

diff --git a/R/NestSearch.R b/R/NestSearch.R
@@ -424,7 +424,7 @@ onBPBoundary <- function(se, so, j)
 
 #' Border pattern is resolution independent
 #'
-#' @param pype is the output of onBPBoundary
+#' @param ptype is the output of onBPBoundary
 #'
 #' @return the output is useful as an index
 #' to the output of baseNeighbours. It will

diff --git a/R/Statistics.R b/R/Statistics.R
@@ -866,20 +866,20 @@ qqnormWin <- function(cmbdf, win, intensities = "I")
 #'
 #'This function returns an estimated entropy for the specified
 #'\code{\link{CMBDataFrame}} column  \code{intensities} and \code{\link{CMBWindow}}
-#'region. The functions employs the function \link{entropy} and uses histogram
+#'region. The functions employs the function \link[entropy:entropy]{entropy} and uses histogram
 #'counts of \code{intensities} for computations. All arguments of the standard
-#'\link{entropy} can be used.
+#'\link[entropy:entropy]{entropy} can be used.
 #'
 #'@param cmbdf A \code{\link{CMBDataFrame}}.
 #'@param win A \code{\link{CMBWindow}}
 #'@param intensities A \code{\link{CMBDataFrame}} column with measured values.
-#'@param method	 A method to estimate entropy, see \link{entropy}
+#'@param method	 A method to estimate entropy, see \link[entropy:entropy]{entropy}
 #'
 #'@return
 #'
 #'Estimated Shannon entropy for observations in \code{\link{CMBWindow}}
 #'
-#'@references \link{entropy}
+#'@references \link[entropy:entropy]{entropy}
 #'
 #'@examples
 #' ## Download the map first
@@ -911,7 +911,7 @@ entropyCMB <- function(cmbdf, win, intensities = "I", method)
 #'
 #'This function returns the empirical chi-squared statistic for \code{intensities}
 #'observations from two \code{\link{CMBWindow}}s of the specified
-#'\code{\link{CMBDataFrame}}. The functions employs the function \link{chi2.empirical} and uses histogram
+#'\code{\link{CMBDataFrame}}. The functions employs the function \link[entropy:chi2.empirical]{chi2.empirical} and uses histogram
 #'counts of \code{intensities} for computations.
 #'
 #'@param cmbdf A \code{\link{CMBDataFrame}}.
@@ -925,7 +925,7 @@ entropyCMB <- function(cmbdf, win, intensities = "I", method)
 #'\code{\link{CMBWindow}}s.  For small sample sizes and many zero counts
 #'Chi-squared statistic is inefficient.
 #'
-#'@references \link{chi2.empirical}
+#'@references \link[entropy:chi2.empirical]{chi2.empirical}
 #'
 #'@examples
 #' ## Download the map first

diff --git a/R/rcosmo.R b/R/rcosmo.R
@@ -28,10 +28,9 @@
 #'@author Daniel Fryer \email{d.fryer@latrobe.edu.au},
 #'Andriy Olenko \email{a.olenko@latrobe.edu.au}, Ming Li \email{Ming.Li@latrobe.edu.au},
 #'Yuguang Wang.
-#'@docType package
 #'@name rcosmo
 #'@importFrom Rcpp evalCpp
 #'@useDynLib rcosmo, .registration = TRUE
 #'@aliases rcosmo-package
-NULL
+"_PACKAGE"
 
diff --git a/README.md b/README.md