rename simplex tree coercers to specify interfaces

Author: corybrunson

NAMESPACE

@@ -15,17 +15,17 @@ S3method(as_network,default)
 S3method(as_network,gudhi.simplex_tree.SimplexTree)
 S3method(as_network,igraph)
 S3method(as_network,network)
-S3method(as_py_gudhi,Rcpp_SimplexTree)
-S3method(as_py_gudhi,default)
-S3method(as_py_gudhi,igraph)
-S3method(as_py_gudhi,network)
-S3method(as_simplextree,Rcpp_SimplexTree)
-S3method(as_simplextree,default)
-S3method(as_simplextree,gudhi.simplex_tree.SimplexTree)
-S3method(as_simplextree,igraph)
-S3method(as_simplextree,network)
+S3method(as_py_gudhi_simplextree,Rcpp_SimplexTree)
+S3method(as_py_gudhi_simplextree,default)
+S3method(as_py_gudhi_simplextree,igraph)
+S3method(as_py_gudhi_simplextree,network)
+S3method(as_rcpp_simplextree,Rcpp_SimplexTree)
+S3method(as_rcpp_simplextree,default)
+S3method(as_rcpp_simplextree,gudhi.simplex_tree.SimplexTree)
+S3method(as_rcpp_simplextree,igraph)
+S3method(as_rcpp_simplextree,network)
 export(as_cmplx)
 export(as_igraph)
 export(as_network)
-export(as_py_gudhi)
-export(as_simplextree)
+export(as_py_gudhi_simplextree)
+export(as_rcpp_simplextree)

R/as-igraph.r

@@ -65,7 +65,7 @@ as_igraph.Rcpp_SimplexTree <- function(x, index = NULL, ...) {
   res
 }
 
-#' @rdname as_simplextree
+#' @rdname as_igraph
 #' @export
 as_igraph.gudhi.simplex_tree.SimplexTree <- function(x, index = NULL, ...) {
 

R/as-py-gudhi.r

@@ -5,8 +5,8 @@
 #'
 #' @details
 #'
-#' `as_py_gudhi()` is a generic function with specific methods for different
-#' simplicial complex S3 classes. It returns an object of class
+#' `as_py_gudhi_simplextree()` is a generic function with specific methods for
+#' different simplicial complex S3 classes. It returns an object of class
 #' 'gudhi.simplex_tree.SimplexTree', which is a
 #' [reticulate][reticulate::reticulate] accessor to a Python object of class
 #' 'SimplexTree' implemented in GUDHI.
@@ -23,11 +23,11 @@
 #' @author Jason Cory Brunson
 #' @author Yara Skaf
 #' @export
-as_py_gudhi <- function(x, ...) UseMethod("as_py_gudhi")
+as_py_gudhi_simplextree <- function(x, ...) UseMethod("as_py_gudhi_simplextree")
 
-#' @rdname as_py_gudhi
+#' @rdname as_py_gudhi_simplextree
 #' @export
-as_py_gudhi.default <- function(x, ...) {
+as_py_gudhi_simplextree.default <- function(x, ...) {
   x <- ensure_cmplx(x)
   x <- ensure_list(x)
   # import GUDHI
@@ -40,9 +40,9 @@ as_py_gudhi.default <- function(x, ...) {
   res
 }
 
-#' @rdname as_py_gudhi
+#' @rdname as_py_gudhi_simplextree
 #' @export
-as_py_gudhi.Rcpp_SimplexTree <- function(x, ...) {
+as_py_gudhi_simplextree.Rcpp_SimplexTree <- function(x, ...) {
   # import GUDHI
   gd <- reticulate::import("gudhi")
 
@@ -68,9 +68,9 @@ as_py_gudhi.Rcpp_SimplexTree <- function(x, ...) {
   res
 }
 
-#' @rdname as_py_gudhi
+#' @rdname as_py_gudhi_simplextree
 #' @export
-as_py_gudhi.igraph <- function(x, index = NULL, ...) {
+as_py_gudhi_simplextree.igraph <- function(x, index = NULL, ...) {
   if (! is.null(index)) ensure_index(x, index)
   # import GUDHI
   gd <- reticulate::import("gudhi")
@@ -91,13 +91,13 @@ as_py_gudhi.igraph <- function(x, index = NULL, ...) {
   res
 }
 
-#' @rdname as_py_gudhi
+#' @rdname as_py_gudhi_simplextree
 #' @export
-as_py_gudhi.network <- function(x, index = NULL, ...) {
+as_py_gudhi_simplextree.network <- function(x, index = NULL, ...) {
 
   # coerce to an igraph object
   x <- intergraph::asIgraph(x, ...)
 
   # invoke 'igraph' method
-  as_py_gudhi(x, index = index)
+  as_py_gudhi_simplextree(x, index = index)
 }

R/as-simplextree.r

@@ -5,8 +5,8 @@
 #'
 #' @details
 #'
-#' `as_simplextree()` is a generic function with specific methods for different
-#' simplicial complex S3 classes. It returns an object of class
+#' `as_rcpp_simplextree()` is a generic function with specific methods for
+#' different simplicial complex S3 classes. It returns an object of class
 #' ['Rcpp_SimplexTree'][simplextree::Rcpp_SimplexTree], which is an [Rcpp
 #' Module][Rcpp::Module] that exposes an instance of a C++ instance of a simplex
 #' tree.
@@ -21,11 +21,11 @@
 #'   'Rcpp_SimplexTree'.
 #' @example inst/examples/ex-as-simplextree.r
 #' @export
-as_simplextree <- function(x, ...) UseMethod("as_simplextree")
+as_rcpp_simplextree <- function(x, ...) UseMethod("as_rcpp_simplextree")
 
-#' @rdname as_simplextree
+#' @rdname as_rcpp_simplextree
 #' @export
-as_simplextree.default <- function(x, ...) {
+as_rcpp_simplextree.default <- function(x, ...) {
   x <- ensure_cmplx(x)
   x <- ensure_list(x)
 
@@ -35,13 +35,13 @@ as_simplextree.default <- function(x, ...) {
   res
 }
 
-#' @rdname as_simplextree
+#' @rdname as_rcpp_simplextree
 #' @export
-as_simplextree.Rcpp_SimplexTree <- function(x, ...) x
+as_rcpp_simplextree.Rcpp_SimplexTree <- function(x, ...) x
 
-#' @rdname as_simplextree
+#' @rdname as_rcpp_simplextree
 #' @export
-as_simplextree.gudhi.simplex_tree.SimplexTree <- function(x, ...) {
+as_rcpp_simplextree.gudhi.simplex_tree.SimplexTree <- function(x, ...) {
 
   # initialize simplex tree
   res <- simplextree::simplex_tree()
@@ -51,9 +51,9 @@ as_simplextree.gudhi.simplex_tree.SimplexTree <- function(x, ...) {
   res
 }
 
-#' @rdname as_simplextree
+#' @rdname as_rcpp_simplextree
 #' @export
-as_simplextree.igraph <- function(x, index = NULL, ...) {
+as_rcpp_simplextree.igraph <- function(x, index = NULL, ...) {
   if (! is.null(index)) ensure_index(x, index)
 
   # generate vertex list
@@ -75,13 +75,13 @@ as_simplextree.igraph <- function(x, index = NULL, ...) {
   res
 }
 
-#' @rdname as_simplextree
+#' @rdname as_rcpp_simplextree
 #' @export
-as_simplextree.network <- function(x, index = NULL, ...) {
+as_rcpp_simplextree.network <- function(x, index = NULL, ...) {
 
   # coerce to an igraph object
   x <- intergraph::asIgraph(x, ...)
 
   # invoke 'igraph' method
-  as_simplextree(x, index = index)
+  as_rcpp_simplextree(x, index = index)
 }

cran-comments.md

@@ -28,7 +28,7 @@ The check flagged the same spellings as the R-hub check.
 
 ## Version dependencies
 
-The method `as_py_gudhi.Rcpp_SimplexTree()` operates differently depending on the version of {simplextree} installed. This has not been flagged by documentation and checks but may be important for the maintainers to know.
+The method `as_py_gudhi_simplextree.Rcpp_SimplexTree()` operates differently depending on the version of {simplextree} installed. This has not been flagged by documentation and checks but may be important for the maintainers to know.
 
 ## Reverse dependencies
 

inst/examples/ex-as-py-gudhi.r

@@ -16,35 +16,35 @@ rf <- TDA::ripsFiltration(
   maxdimension = 2L, maxscale = 1.7
 )
 print(rf$cmplx)
-gd_rf <- as_py_gudhi(rf)
+gd_rf <- as_py_gudhi_simplextree(rf)
 print_py_gudhi(gd_rf)
-gd_rf2 <- as_py_gudhi(rf$cmplx)
+gd_rf2 <- as_py_gudhi_simplextree(rf$cmplx)
 print_py_gudhi(gd_rf2)
 
 # convert a simplextree object
 st <- simplextree::simplex_tree()
 st$insert(list(3:5, 5:6, 8))
-gd_st <- as_py_gudhi(st)
+gd_st <- as_py_gudhi_simplextree(st)
 print_py_gudhi(gd_st)
 
 # convert an igraph object
 ig <- igraph::graph(c(1,2, 2,3, 1,3, 3,4))
 print(ig)
-gd_ig <- as_py_gudhi(ig)
+gd_ig <- as_py_gudhi_simplextree(ig)
 print_py_gudhi(gd_ig)
 
 # specify 0-simplex indices
 set.seed(0L)
 ig <- igraph::set_vertex_attr(ig, "id", value = sample(igraph::vcount(ig)) + 1L)
 igraph::V(ig)$id
 igraph::as_edgelist(ig)
-gd_ig2 <- as_py_gudhi(ig, index = "id")
+gd_ig2 <- as_py_gudhi_simplextree(ig, index = "id")
 print_py_gudhi(gd_ig2)
 
 # convert a network object
 el <- data.frame(tails = c(1, 2, 1, 3), heads = c(2, 3, 3, 4))
 nw <- network::network.edgelist(el, network::network.initialize(4))
 print(nw)
-gd_nw <- as_py_gudhi(nw)
+gd_nw <- as_py_gudhi_simplextree(nw)
 print_py_gudhi(gd_nw)
 }

inst/examples/ex-as-simplextree.r

@@ -5,9 +5,9 @@ rf <- TDA::ripsFiltration(
   maxdimension = 2L, maxscale = 1.7
 )
 print(rf$cmplx)
-st_rf <- as_simplextree(rf)
+st_rf <- as_rcpp_simplextree(rf)
 print(st_rf)
-st_rf2 <- as_simplextree(rf$cmplx)
+st_rf2 <- as_rcpp_simplextree(rf$cmplx)
 print(st_rf2)
 
 \dontrun{
@@ -16,28 +16,28 @@ print(st_rf2)
 gd <- reticulate::import("gudhi")
 gd_st <- gd$SimplexTree()
 for (s in list(3:5, 5:6, 8)) gd_st$insert(as.list(s))
-st_gd <- as_simplextree(gd_st)
+st_gd <- as_rcpp_simplextree(gd_st)
 st_gd$as_list()
 }
 
 # convert an igraph object
 ig <- igraph::graph(c(1,2, 2,3, 1,3, 3,4))
 print(ig)
-st_ig <- as_simplextree(ig)
+st_ig <- as_rcpp_simplextree(ig)
 print(st_ig)
 
 # specify 0-simplex indices
 set.seed(0L)
 ig <- igraph::set_vertex_attr(ig, "id", value = sample(igraph::vcount(ig)) + 1L)
 igraph::V(ig)$id
 igraph::as_edgelist(ig)
-st_ig <- as_simplextree(ig, index = "id")
+st_ig <- as_rcpp_simplextree(ig, index = "id")
 st_ig$vertices
 st_ig$edges
 
 # convert a network object
 el <- data.frame(tails = c(1, 2, 1, 3), heads = c(2, 3, 3, 4))
 nw <- network::network.edgelist(el, network::network.initialize(4))
 print(nw)
-st_nw <- as_simplextree(nw)
+st_nw <- as_rcpp_simplextree(nw)
 print(st_nw)