Merge pull request #19 from astamm/nvd-class

Improved nvd constructor and added embedding to graph space

.Rbuildignore

@@ -14,3 +14,5 @@ codecov.yml
 ^CRAN-RELEASE$
 ^data-raw$
 ^CRAN-SUBMISSION$
+^vignettes/\.quarto$
+^vignettes/*_files$

.github/workflows/R-CMD-check.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,9 +42,15 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
+            any::devtools
           needs: check
 
+      - run: devtools::install(build_vignettes = FALSE)
+        shell: Rscript {0}
+
       - 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

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +23,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +42,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,46 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - 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
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            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 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 }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

.gitignore

@@ -5,3 +5,4 @@
 .DS_Store
 inst/doc
 docs
+**/.quarto/

DESCRIPTION

@@ -57,15 +57,17 @@ Imports:
     tsne,
     umap,
     furrr,
-    rgeomstats
-RoxygenNote: 7.2.3
+    rgeomstats,
+    tidygraph
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 URL: https://astamm.github.io/nevada/,
     https://github.com/astamm/nevada/
 BugReports: https://github.com/astamm/nevada/issues/
 Suggests: 
     knitr,
     rmarkdown,
-    covr
-VignetteBuilder: knitr
+    covr,
+    quarto
+VignetteBuilder: quarto
 LinkingTo: Rcpp, RcppArmadillo

NAMESPACE

@@ -18,7 +18,11 @@ export(edge_count_global_variables)
 export(generate_sigma_algebra)
 export(ipro_frobenius)
 export(nvd)
+export(play_binomial)
+export(play_exponential)
+export(play_poisson)
 export(power2)
+export(push_to_graph_space)
 export(rbinom_network)
 export(repr_adjacency)
 export(repr_graphon)
@@ -27,7 +31,6 @@ export(repr_modularity)
 export(repr_nvd)
 export(rexp_network)
 export(rpois_network)
-export(rsbm)
 export(sample2_sbm)
 export(stat_generalized_edge_count)
 export(stat_original_edge_count)
@@ -46,5 +49,6 @@ importFrom(ggplot2,autoplot)
 importFrom(graphics,plot)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)
+importFrom(rlang,`:=`)
 importFrom(tibble,tibble)
 useDynLib(nevada, .registration = TRUE)

R/distances.R

@@ -21,9 +21,9 @@
 #' Root-Euclidean distance can used only with the laplacian matrix
 #' representation.
 #'
-#' @param x An [`igraph::igraph`] object or a matrix representing an underlying
+#' @param x A [`tidygraph::tbl_graph`] object or a matrix representing an underlying
 #'   network.
-#' @param y An [`igraph::igraph`] object or a matrix representing an underlying
+#' @param y A [`tidygraph::tbl_graph`] object or a matrix representing an underlying
 #'   network. Should have the same number of vertices as `x`.
 #' @param representation A string specifying the desired type of representation,
 #'   among: \code{"adjacency"}, \code{"laplacian"}, \code{"modularity"} or
@@ -189,9 +189,9 @@ ipro_frobenius <- function(x, y, representation = "laplacian") {
 #' elements of the two samples put together. The cardinality of the fist sample
 #' is denoted by \eqn{n_1} and that of the second one is denoted by \eqn{n_2}.
 #'
-#' @param x A [`base::list`] of [`igraph::igraph`] objects or matrix
+#' @param x A [`base::list`] of [`tidygraph::tbl_graph`] objects or matrix
 #'   representations of underlying networks from a given first population.
-#' @param y A [`base::list`] of [`igraph::igraph`] objects or matrix
+#' @param y A [`base::list`] of [`tidygraph::tbl_graph`] objects or matrix
 #'   representations of underlying networks from a given second population.
 #' @param representation A string specifying the desired type of representation,
 #'   among: \code{"adjacency"}, \code{"laplacian"}, \code{"modularity"} or
@@ -215,10 +215,10 @@ ipro_frobenius <- function(x, y, representation = "laplacian") {
 #' @export
 #'
 #' @examples
-#' gnp_params <- list(p = 1/3)
-#' k_regular_params <- list(k = 8L)
-#' x <- nvd(model = "gnp", n = 10L, model_params = gnp_params)
-#' y <- nvd(model = "k_regular", n = 10L, model_params = k_regular_params)
+#' gnp_params <- list(n = 24L, p = 1/3)
+#' degree_params <- list(out_degree = rep(2, 24L), method = "configuration")
+#' x <- nvd(sample_size = 10L, model = "gnp", !!!gnp_params)
+#' y <- nvd(sample_size = 10L, model = "degree", !!!degree_params)
 #' dist_nvd(x, y, "adjacency", "spectral")
 dist_nvd <- function(x,
                      y = NULL,

R/embeddings.R

@@ -0,0 +1,40 @@
+#' Graph Sample Embeddings
+#'
+#' A collection of functions to embed a sample of graphs into suitable spaces
+#' for further statistical analysis.
+#'
+#' @param obj An object of class [`nvd`] containing the sample of graphs.
+#'
+#' @return An object of class [`nvd`] containing the sample of graphs in graph space.
+#'
+#' @export
+#' @examples
+#' x <- nvd(sample_size = 5L, model = "gnp", n = 24L, p = 1/3)
+#' x <- push_to_graph_space(x)
+push_to_graph_space <- function(obj) {
+  if (!is_nvd(obj))
+    cli::cli_abort("Input should be an object of class {.cls nvd}.")
+
+  # Here we handle graphs of different orders by adding as many vertices as
+  # necessary to match the order of the largest graph (a.k.a pushing graphs into
+  # graph space structure).
+  num_vertices <- purrr::map_int(obj, igraph::gorder)
+  cli::cli_alert_info("Graphs have the following number of vertices: {num_vertices}")
+  max_num_vertices <- max(num_vertices)
+  n_chars <- nchar(max_num_vertices)
+  obj <- purrr::map2(obj, num_vertices, \(g, n) {
+    g <- dplyr::mutate(
+      g,
+      name = paste0("O", formatC(1:dplyr::n(), width = n_chars, flag = "0"))
+    )
+    n_extra <- max_num_vertices - n
+    if (n_extra == 0)
+      return(g)
+    extra_nodes <- data.frame(
+      name = paste0("V", formatC(1:n_extra, width = n_chars, flag = "0"))
+    )
+    tidygraph::bind_nodes(g, extra_nodes)
+  })
+
+  obj
+}