export unexported documented functions

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: CrossClustering
 Title: A Partial Clustering Algorithm
-Version: 4.1.1
+Version: 4.1.2
 Date: 2024-05-01
 Authors@R: c(
     person("Paola", "Tellaroli", , "paola.tellaroli@gmail.com", role = c("cre", "aut")),
@@ -12,7 +12,7 @@ Authors@R: c(
     person("Corrado", "Lanera", , "corrado.lanera@unipd.it", role = "aut")
   )
 Maintainer: Paola Tellaroli <paola.tellaroli@gmail.com>
-Description: Provide the CrossClustering algorithm (Tellaroli et al.
+Description: Provide the 'CrossClustering' algorithm (Tellaroli et al.
     (2016) <doi:10.1371/journal.pone.0152333>), which is a partial
     clustering algorithm that combines the Ward's minimum variance and
     Complete Linkage algorithms, providing automatic estimation of a

NAMESPACE

@@ -7,6 +7,10 @@ S3method(print,crossclustering)
 export(ari)
 export(cc_crossclustering)
 export(cc_get_cluster)
+export(cc_test_ari)
+export(cc_test_ari_permutation)
+export(consensus_cluster)
+export(is_zero)
 export(prune_zero_tail)
 export(reverse_table)
 importFrom(stats,cutree)

NEWS.md

@@ -1,3 +1,8 @@
+# CrossClustering 4.1.2
+
+* exported `cc_test_ari`, `cc_test_ari_permutation`,
+  `consensus_cluster`, and `is_zero`
+
 # CrossClustering 4.1.1
 
 * Removed `.Random.seed` after CRAN request.

R/cc_test_ari.R

@@ -13,6 +13,8 @@
 #'   \item{nari}{nari}
 #'   \item{p-value}{the p-value of the test}
 #'
+#' @export
+#'
 #' @examples
 #' library(CrossClustering)
 #'
@@ -24,7 +26,7 @@
 #' ground_truth <- iris[[5]] |>
 #'   as.numeric()
 #'
-#' CrossClustering:::cc_test_ari(ground_truth, clusters)
+#' cc_test_ari(ground_truth, clusters)
 #'
 #' @author
 #' Paola Tellaroli, <paola `dot` tellaroli `at` unipd `dot` it>;
@@ -37,8 +39,6 @@
 #'
 #' L. Hubert and p. Arabie (1985) Comparing partitions, Journal of
 #' Classification, 2, 193-218.
-
-
 cc_test_ari <- function(ground_truth, partition) {
 
   checkmate::qassert(ground_truth, "N+")

R/cc_test_ari_permutation.R

@@ -10,6 +10,8 @@
 #'   \item{ari}{the adjusted Rand Index}
 #'   \item{p_value}{the p-value of the test}
 #'
+#' @export
+#'
 #' @examples
 #' library(CrossClustering)
 #'
@@ -21,7 +23,7 @@
 #' ground_truth <- iris[[5]] |>
 #'   as.numeric()
 #'
-#' CrossClustering:::cc_test_ari_permutation(ground_truth, clusters)
+#' cc_test_ari_permutation(ground_truth, clusters)
 #'
 #' @author
 #' Paola Tellaroli, <paola `dot` tellaroli `at` unipd `dot` it>;
@@ -34,7 +36,6 @@
 #'
 #' L. Hubert and P. Arabie (1985) Comparing partitions, Journal of
 #' Classification, 2, 193-218.
-
 cc_test_ari_permutation <- function(ground_truth, partition) {
 
   checkmate::qassert(ground_truth, "N+")

R/consensus_cluster.R

@@ -18,6 +18,7 @@
 #'           \item{a_star}{contingency table of the clustering};
 #'           \item{max_consensus}{maximum clustering consensus}.
 #'
+#' @export
 #'
 #' @examples
 #' library(CrossClustering)
@@ -37,7 +38,7 @@
 #'
 #'
 #' ### consensus_cluster
-#' CrossClustering:::consensus_cluster(
+#' consensus_cluster(
 #'   c(3, 4),
 #'   cluster_ward,
 #'   cluster_other
@@ -53,7 +54,6 @@
 #' Cross-Clustering: A Partial Clustering Algorithm with Automatic
 #' Estimation of the Number of Clusters. PLoS ONE 11(3):   e0152333.
 #' doi:10.1371/journal.pone.0152333
-
 consensus_cluster <- function(k,
   cluster_ward,
   cluster_other

R/utils.R

@@ -50,10 +50,10 @@ prune_zero_tail <- function(diag_mat) {
 #' @param num a numerical vector of length one
 #'
 #' @return a boolean, TRUE if num is 0
-#'
+#' @export
 #' @examples
-#' CrossClustering:::is_zero(1)
-#' CrossClustering:::is_zero(0)
+#' is_zero(1)
+#' is_zero(0)
 is_zero <- function(num) {
   # input check
   checkmate::qassert(num, "N1")

cran-comments.md

@@ -5,7 +5,7 @@
 
 ### Remote (rhub)
 
-* 19/20 [rhub checks](https://github.com/CorradoLanera/CrossClustering/actions/runs/8941514230) passed (all but the [windows on R devel](https://github.com/CorradoLanera/CrossClustering/actions/runs/8941514230/job/24563996554#step:5:5336) one, because of a [known](https://github.com/gagolews/stringi/issues/508) setup issue w/ `{stringi}`):
+* 20/20 [rhub checks](https://github.com/CorradoLanera/CrossClustering/actions/runs/8941514230) passed:
   - [VM] linux          R-* (any version)                     ubuntu-latest on GitHub
   - [VM] macos          R-* (any version)                     macos-13 on GitHub
   - [VM] macos-arm64    R-* (any version)                     macos-latest on GitHub
@@ -70,6 +70,8 @@ In this updated version I have:
 * Switch from Travis and AppVeyor to GitHub-actions for CMD-checks, lint, 
   and coverage.
 * removed `.Random.seed`, after request
+* exported `cc_test_ari`, `cc_test_ari_permutation`,
+  `consensus_cluster`, and `is_zero`
 
 > File 'R/CrossClustering-internal.R' sets .Random.seed.
 >    This is usually neither needed nor wanted.