Merge pull request #2 from swarm-lab/develop

Develop

Author: sjmgarnier

.Rbuildignore

@@ -11,3 +11,4 @@ cran-comments.md
 ^CRAN-SUBMISSION$
 ^codecov\.yml$
 revdep
+.vscode

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -9,3 +9,4 @@ src/models/*.o
 src/models/*.so
 src/models/*.dll
 docs
+.vscode/settings.json

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: CEC
 Type: Package
 Title: Cross-Entropy Clustering
-Version: 0.11.1
-Date: 2024-01-08
+Version: 0.11.2
+Date: 2024-10-10
 Authors@R: c(
     person("Kamieniecki", "Konrad", email = "[email protected]", 
       role = c("aut")),
@@ -30,6 +30,6 @@ Imports:
     utils
 NeedsCompilation: yes
 License: GPL-3
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests: 
     covr

NEWS.md

@@ -1,3 +1,15 @@
+# CEC v0.11.2
+
+## New features
+
+* N/A. 
+
+## Minor improvements and fixes
+
+* Fixing CRAN NO_REMAP error with R > 4.5.0. 
+
+---
+
 # CEC v0.11.1
 
 ## New features

R/CEC-package.R

@@ -14,75 +14,10 @@
 #' 
 #' @seealso \code{\link{cec}}
 #' 
-#' @keywords package multivariate cluster models
+#' @keywords internal package multivariate cluster models
 #' 
-NULL
-
-
-#' @title Four Gaussian Clusters
-#'
-#' @description Matrix of 2-dimensional points forming four Gaussian clusters.
-#'
-#' @name fourGaussians
-#' 
-#' @docType data
-#' 
-#' @keywords datasets
-#' 
-#' @examples
-#' data(fourGaussians)
-#' plot(fourGaussians, cex = 0.5, pch = 19);
-#'
-NULL
-
+"_PACKAGE"
 
-#' @title Three Gaussian Clusters
-#'
-#' @description Matrix of 2-dimensional points forming three Gaussian clusters.
-#'
-#' @name threeGaussians
-#' 
-#' @docType data
-#' 
-#' @keywords datasets
-#' 
-#' @examples
-#' data(threeGaussians)
-#' plot(threeGaussians, cex = 0.5, pch = 19);
-#'
-NULL
-
-
-#' @title Mixed Shapes Clusters 
-#'
-#' @description Matrix of 2-dimensional points that form circular and elliptical 
-#'  patterns.
-#'
-#' @name mixShapes
-#' 
-#' @docType data
-#' 
-#' @keywords datasets
-#' 
-#' @examples
-#' data(mixShapes)
-#' plot(mixShapes, cex = 0.5, pch = 19);
-#'
-NULL
-
-
-#' @title T-Shaped Clusters
-#'
-#' @description Matrix of 2-dimensional points that form the letter T.
-#'
-#' @name Tset
-#' 
-#' @docType data
-#' 
-#' @keywords datasets
-#' 
-#' @examples
-#' data(Tset)
-#' plot(Tset, cex = 0.5, pch = 19);
-#'
+## usethis namespace: start
+## usethis namespace: end
 NULL

R/cec.R

@@ -26,8 +26,8 @@
 #'  Possible values are: "covariance", "fixedr", "spherical", "diagonal",
 #'  "eigenvalues", "all" (default).
 #'
-#'  Currently, if the \code{centers} argument is a vector, only a single type can
-#'  be used.
+#'  Currently, if the \code{centers} argument is a vector, only a single type 
+#'  can be used.
 #'
 #' @param iter.max The maximum number of iterations of the clustering algorithm.
 #'
@@ -62,8 +62,8 @@
 #'  visible in the results as NA in the "centers" matrix (as well as the
 #'  corresponding values in the list of covariances).
 #'
-#' @param interactive If \code{TRUE}, the result of clustering will be plotted after
-#'  every iteration.
+#' @param interactive If \code{TRUE}, the result of clustering will be plotted 
+#'  after every iteration.
 #'
 #' @param threads The number of threads to use or "auto" to use the default
 #'  number of threads (usually the number of available processing units/cores)
@@ -344,7 +344,7 @@ cec <- function(x,
 
     card.min <- max(card.min, n + 1)
     k <- max(var.centers)
-    startTime <- proc.time()
+    # startTime <- proc.time()
 
     centers.r <- list(init.method = init.method.name,
                       var.centers = as.integer(var.centers),
@@ -378,7 +378,7 @@ cec <- function(x,
     }
 
     k.final <- nrow(Z$centers)
-    execution.time <- as.vector((proc.time() - startTime))[3]
+    # execution.time <- as.vector((proc.time() - startTime))[3]
     Z$centers[is.nan(Z$centers)] <- NA
     tab <- tabulate(Z$cluster)
     probability <- vapply(tab, function(c.card) {
@@ -427,7 +427,7 @@ cec <- function(x,
 
     structure(
         list(data = x, cluster = Z$cluster, centers = Z$centers, probability = probability, cost.function = Z$energy,
-             nclusters = Z$nclusters, iterations = Z$iterations, time = execution.time, covariances = Z$covariances,
+             nclusters = Z$nclusters, iterations = Z$iterations, covariances = Z$covariances,
              covariances.model = covariances.model, means.model = means.model),
         class = "cec")
 }

R/utils.R

@@ -127,3 +127,72 @@ mouseset <- function(n = 4000, r.head = 2, r.left.ear = 1.1, r.right.ear = 1.1,
 
     M
 }
+
+
+#' @title Four Gaussian Clusters
+#'
+#' @description Matrix of 2-dimensional points forming four Gaussian clusters.
+#'
+#' @name fourGaussians
+#' 
+#' @docType data
+#' 
+#' @keywords datasets
+#' 
+#' @examples
+#' data(fourGaussians)
+#' plot(fourGaussians, cex = 0.5, pch = 19);
+#'
+NULL
+
+
+#' @title Three Gaussian Clusters
+#'
+#' @description Matrix of 2-dimensional points forming three Gaussian clusters.
+#'
+#' @name threeGaussians
+#' 
+#' @docType data
+#' 
+#' @keywords datasets
+#' 
+#' @examples
+#' data(threeGaussians)
+#' plot(threeGaussians, cex = 0.5, pch = 19);
+#'
+NULL
+
+
+#' @title Mixed Shapes Clusters 
+#'
+#' @description Matrix of 2-dimensional points that form circular and elliptical 
+#'  patterns.
+#'
+#' @name mixShapes
+#' 
+#' @docType data
+#' 
+#' @keywords datasets
+#' 
+#' @examples
+#' data(mixShapes)
+#' plot(mixShapes, cex = 0.5, pch = 19);
+#'
+NULL
+
+
+#' @title T-Shaped Clusters
+#'
+#' @description Matrix of 2-dimensional points that form the letter T.
+#'
+#' @name Tset
+#' 
+#' @docType data
+#' 
+#' @keywords datasets
+#' 
+#' @examples
+#' data(Tset)
+#' plot(Tset, cex = 0.5, pch = 19);
+#'
+NULL