prepare first cran release

.Rbuildignore

@@ -4,3 +4,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^cran-comments\.md$

.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 }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: coupling
-Title: Coupling Coordination Analysis
-Version: 0.0.0.9000
+Title: Analysis of Coupling Coordination Degree
+Version: 0.1
 Authors@R: 
     person(given = "Wenbo", family = "Lyu",
            email = "lyu.geosocial@gmail.com", 
@@ -17,7 +17,10 @@ LinkingTo:
     Rcpp,
     RcppThread
 Suggests: 
+    infoxtr,
+    pc,
     Rcpp,
     RcppThread,
+    spEDM
 Config/roxygen2/markdown: TRUE
 Config/roxygen2/version: 8.0.0

NEWS.md

@@ -0,0 +1,3 @@
+# coupling 0.1
+
+* Initial CRAN submission.

README.md

@@ -16,7 +16,7 @@
 
 <a href="https://stscl.github.io/coupling/"><img src="man/figures/coupling.png" align="right" hspace="5" vspace="0" width="15%" alt="coupling website: https://stscl.github.io/coupling/"/></a>
 
-***Coupling** Coordination Analysis*
+*Analysis of Coupling Coordination Degree*
 
 *coupling* is an R package for coupling coordination analysis based on coupling coordination degree (CCD) models. It incorporates metacoupling frameworks to characterize cross-scale linkages, flows, and feedbacks within and among coupled systems.
 

_pkgdown.yml

@@ -18,7 +18,7 @@ navbar:
 
 home:
   title: |
-    ccd | Coupling Coordination Analysis
+    coupling | Analysis of Coupling Coordination Degree
 authors:
   Wenbo Lyu:
     href: https://spatlyu.github.io/

cran-comments.md

@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.

inst/CITATION

@@ -0,0 +1,10 @@
+citHeader("To cite package coupling in publications, please use:")
+
+bibentry(
+  bibtype  = "Manual",
+  title    = "{coupling: Analysis of Coupling Coordination Degree}",
+  author   = "Wenbo Lyu",
+  year     = "2026",
+  note     = "R package version 0.1",
+  doi      = "10.32614/CRAN.package.coupling"
+)

inst/include/coupling/ccd.hpp

@@ -295,6 +295,10 @@ inline std::vector<double> ccd_c(
     if (n_units == 0) return {};
 
     std::vector<double> result(n_units, 0.0);
+
+    if (threads == 0) threads = 1;
+    size_t hw = std::thread::hardware_concurrency();
+    if (hw > 0) threads = std::min(threads, hw);
 
     if (threads <= 1) {
         for (size_t i = 0; i < n_units; ++i) {

inst/include/coupling/metacoupling.hpp

@@ -312,6 +312,13 @@ inline std::vector<std::vector<double>> metacoupling_c(
         result[1][s] = peri_sum;
         result[2][s] = tele_sum;
     };
+
+    // ============================================================
+    // Check for available threads
+    // ============================================================
+    if (threads == 0) threads = 1;
+    size_t hw = std::thread::hardware_concurrency();
+    if (hw > 0) threads = std::min(threads, hw);
 
     // ============================================================
     // Parallel or serial execution
@@ -357,6 +364,13 @@ inline std::vector<std::vector<double>> metacoupling(
 
     size_t full_perm = 1ULL << p;
 
+    // ============================================================
+    // Check for available threads
+    // ============================================================
+    if (threads == 0) threads = 1;
+    size_t hw = std::thread::hardware_concurrency();
+    if (hw > 0) threads = std::min(threads, hw);
+
     // ============================================================
     // Step 1: reuse existing C computation
     // ============================================================
@@ -399,11 +413,7 @@ inline std::vector<std::vector<double>> metacoupling(
         return sum_t / static_cast<double>(count);
     };
 
-    // ============================================================
-    // Step 3: assemble results
-    // ============================================================
-    for (size_t s = 0; s < n_units; ++s) {
-
+    auto worker4D = [&](size_t s) {
         // ---- intra ----
         double C_intra = C_res[0][s];
         double T_intra = compute_T_intra(s);
@@ -442,6 +452,17 @@ inline std::vector<std::vector<double>> metacoupling(
 
         result[4][s] = C_tele;
         result[5][s] = std::sqrt(C_tele * tele_T_sum);
+    };
+
+    // ============================================================
+    // Step 3: assemble results
+    // ============================================================
+    if (threads <= 1) {
+        for (size_t s = 0; s < n_units; ++s) {
+            worker4D(s);
+        }
+    } else {
+        RcppThread::parallelFor(0, n_units, worker4D, threads);
     }
 
     return result;