Website prepared and final changes to the package.

NAMESPACE

@@ -1,3 +1,13 @@
-exportPattern("^[^\\.]")
+# Generated by roxygen2: do not edit by hand
+
+export(direct_graph)
+export(get_all_nodes)
+export(get_shortest_path)
+export(modify_graph_hsu)
+export(modify_graph_vd)
+export(parse_vpath)
 importFrom(foreach,"%dopar%")
-importFrom(magrittr,"%>%")
+importFrom(igraph,E)
+importFrom(igraph,graph_from_data_frame)
+importFrom(igraph,shortest_paths)
+importFrom(magrittr,"%>%")

R/hsu.R

@@ -1,3 +1,4 @@
+#' @export
 #' @title Hsu et al. (2009) Algorithm
 #'
 #' @description It is an implementation of Hsu et al. algorithm to transform a digraph and a known set of
@@ -26,7 +27,11 @@
 #'    original graph, nodes on the new graph are of type
 #'    character. The new nodes names are generated by incrementally concatenating the nodes on a forbidden
 #'    path, but split by a pipe character (\code{|}).
-
+#'    
+#' @importFrom foreach %dopar% 
+#' @importFrom magrittr %>%
+#'     
+#'             
 #' @examples
 #' # Obtain a graph and its forbidden subpaths
 #' graph <- structure(list(from = c("c", "c", "u", "u", "t", "a", "a", "r", "e", "e", "e", "p", "i", "i", "n", "o"),

R/igraph.R

@@ -0,0 +1,55 @@
+#' @export
+#' @title iGraph Shortest Path
+#'
+#' @description A original node N_i can appear on a transformed gStar as different N_i* equivalent nodes. Therefore, 
+#'    this becomes a limitation when searching for a shortest path inside gStar. As a result: all N_i* need to be
+#'    considered as possible destination nodes when looking for the shortest path. This function is a wrapper for this
+#'    behavior, providing a straightforward implementation using iGraph capabilities. However, it aims to provide
+#'    guidance on how to build a similar algorithm for different path-finding algorithms.
+#'    
+#'    It is important to mention that new nodes are only considered as destination nodes, and they are not search
+#'    for origin nodes. This is because N* nodes can only be reached after traveling through gStar nodes. For example,
+#'    a node \code{"f|e|r"} is actually indicating that \code{"r"} has been reached after traveling through the nodes 
+#'    \code{"f"} and \code{"e"}.
+#' 
+#' @family iGraph Integration
+#'
+#' @param g A gStar digraph in data frame format, translated using one of the available functions. The weight or cost attribute
+#'    of each arc of the graph must be stored in a specific column named \code{weight}.
+#' @param origin The name of the starting node from G for the path. It must be written as it appears in G, and it is 
+#'    preferable to use a character format, but this can also be of any simple type. No lists or vectors are allowed.
+#' @param dest The name of the destination node from G for the path. It must be written as it appears in G, and it is 
+#'    preferable to use a character format, but this can also be of any simple type. No lists or vectors are allowed.   
+#'
+#' @return The shortest path from \code{origin} node to \code{dest} node, calculated in G*, to include the forbidden paths.
+#'    It uses iGraph's functionalities.
+#'    
+#' @importFrom igraph graph_from_data_frame
+#' @importFrom igraph shortest_paths
+#' @importFrom igraph E     
+#'
+#' @examples
+#' # Given a specific gStar graph:
+#' gStar <- structure(list(from = c("u|v", "s|u|v", "s|u", "s", "s", "u", "w", "w", "x", "x", 
+#'                                  "v", "v", "y", "y", "s", "s|u", "u", "u|v"), 
+#'                         to = c("t", "u|v|y", "w", "w", "x", "w", "v", "y", "w", "y", "y", "t", 
+#'                                "t", "u", "s|u", "s|u|v", "u|v", "u|v|y"), 
+#'                    weight = c(12L, 3L, 5L, 9L, 7L, 5L, 11L, 10L, 1L, 2L, 3L, 12L, 13L, 0L, 8L, 4L, 4L, 3L)), 
+#'                    class = "data.frame", row.names = c(NA, -18L), .Names = c("from", "to", "weight"))
+#' gStar
+#' 
+#' # Obtain the shortest path
+#' get_shortest_path(gStar, "s", "v")                                                 
+#'
+#'
+get_shortest_path <- function(g, origin, dest) {
+  # Convert the graph
+  g.i <- graph_from_data_frame(g)
+
+  # Get all the shortest paths to each node
+  sp <- shortest_paths(g.i, from = origin, to = get_all_nodes(gStar, dest), weights = E(g.i)$weight, output = "both")
+
+  # Return the shortest path
+  sp$vpath[which.min( lapply(sp$epath, function(y) 
+      ifelse(length(y) != 0, sum(E(g.i)$weight[ y[[1]] ]), 999999999)) )] [[1]]
+}

R/parsers.R

@@ -1,3 +1,4 @@
+#' @export
 #' @title Parser for G* nodes paths.
 #'
 #' @description Translates a sequence of nodes from a G* graph, generated with any of the available
@@ -37,6 +38,7 @@ parse_vpath <- function(vpath) {
 
 
 
+#' @export
 #' @title Undirected Graph Translator
 #'
 #' @description The SPPFP transformation functions only work with digraphs -i.e. directed graphs. Because in a digraph
@@ -56,6 +58,9 @@ parse_vpath <- function(vpath) {
 #' @return A new graph, with the same columns and data types of the original graph. This new graph is twice as
 #'    big as the original, as new arcs are added to represent that each arc can be traveled in both directions.
 #' 
+#' @importFrom foreach %dopar% 
+#' @importFrom magrittr %>%
+#' 
 #' @examples
 #' # Obtain the graph from any way
 #' graph <- structure(list(from = c("s", "s", "s", "u", "u", "w", "w", "x", "x", "v", "v", "y", "y"), 
@@ -100,3 +105,49 @@ direct_graph <- function(graph, cores = 1L) {
   # Return the value
   rbind(graph, directedGraph)
 }
+
+
+
+
+
+
+
+#' @export
+#' @title Parser for G* nodes.
+#'
+#' @description A original node N_i can appear on a transformed G* as different nodes. This is the result of
+#'    the creation of nodes in the transformation processes. Therefore, it is possible that the original node N
+#'    does not exists on G*, or that multiple N_i* exist. Hence, as all new nodes are generated using a specific
+#'    structure for the name -compiling all previous nodes names, split by pipe-, this function allows searching
+#'    for all the N_i* nodes that are equivalente to N_i. This can be used to find shortest paths to all of them.
+#'
+#' @family Parsers
+#'
+#' @param gStar A graph in data frame format, translated using one of the available functions.
+#' @param originalNode The name of the original node from G, that needs to be searched within G*. It is preferable
+#'    to use a character format, but this can also be of any simple type. No lists or vectors are allowed.
+#'
+#' @return A new vector of character type, whose elements are all the N_i* equivalent to the original N node. This
+#'    also includes the original node.
+#'
+#' @examples
+#' # Given a specific gStar graph:
+#' gStar <- structure(list(from = c("u|v", "s|u|v", "s|u", "s", "s", "u", "w", "w", "x", "x", "v", 
+#'                                  "v", "y", "y", "s", "s|u", "u", "u|v"), 
+#'                         to = c("t", "u|v|y", "w", "w", "x", "w", "v", "y", "w", "y", "y", "t", 
+#'                                "t", "u", "s|u", "s|u|v", "u|v", "u|v|y"), 
+#'                    weight = c(12L, 3L, 5L, 9L, 7L, 5L, 11L, 10L, 1L, 2L, 3L, 12L, 13L, 0L, 8L, 4L, 4L, 3L)), 
+#'                    class = "data.frame", row.names = c(NA, -18L), .Names = c("from", "to", "weight"))
+#' gStar
+#' 
+#' # Obtain all the nodes equivalent to N_i = "v"
+#' get_all_nodes(gStar, "v")                                                   
+#'
+#'
+get_all_nodes <- function(gStar, originalNode) {
+  # Get the list of nodes
+  nodes <- unique(c(gStar$from, gStar$to))
+
+  # Get all the nodes that end on that original node
+  nodes[sapply(paste0("*\\s|", originalNode, "$"), function(y) grepl(y, nodes))]
+}

R/villeneuve.R

@@ -1,3 +1,4 @@
+#' @export
 #' @title Villeneuve and Desaulniers (2005) Algorithm
 #'
 #' @description It is an implementation of Villeneuve and Desaulniers' algorithm to transform a digraph
@@ -27,7 +28,10 @@
 #'    character. The new nodes names are generated by incrementally concatenating the nodes on a forbidden
 #'    path, but split by a pipe character (\code{|}). The new graph includes all of the additional attributes
 #'    that the original graph had.
-#'
+#'    
+#' @importFrom foreach %dopar% 
+#' @importFrom magrittr %>%
+#' 
 #' @examples
 #' # Obtain a graph and its forbidden subpaths
 #'   graph <- structure(list(from = c("s", "s", "s", "u", "u", "w", "w", "x", "x", "v", "v", "y", "y"),
@@ -121,7 +125,7 @@ modify_graph_vd <- function(g, f, cores = 1L) {
       if(!identical(newTo, character(0))) {
         # ...add it using the new node, if it needs attributes
         if(ncol > 2) {
-          tempNewArcs[nrow(tempNewArcs) + 1,] <- list(nn, newTo, .get_arc_attributes(g, nn, toNode))
+          tempNewArcs[nrow(tempNewArcs) + 1,] <- list(nn, newTo, .get_arc_attributes(g, nsName, toNode))
         }
         # Or without the attributes
         else tempNewArcs[nrow(tempNewArcs) + 1,] <- list(nn, newTo)
@@ -133,7 +137,7 @@ modify_graph_vd <- function(g, f, cores = 1L) {
 
         # Add the new link, but with the original node
         if(ncol > 2) {
-          tempNewArcs[nrow(tempNewArcs) + 1,] <- list(nn, toNode, .get_arc_attributes(g, nn, toNode))
+          tempNewArcs[nrow(tempNewArcs) + 1,] <- list(nn, toNode, .get_arc_attributes(g, nsName, toNode))
         }
         # Or without the attributes
         else tempNewArcs[nrow(tempNewArcs) + 1,] <- list(nn, toNode)

README.Rmd

@@ -1,17 +1,3 @@
----
-output: github_document
----
-
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
-```{r, echo = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>",
-  fig.path = "README-"
-)
-```
-
 # R-SPPFP
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/rsppfp)](https://cran.r-project.org/package=rsppfp)
 [![Travis-CI Build Status](https://travis-ci.org/melvidoni/rsppfp.svg?branch=master)](https://travis-ci.org/melvidoni/rsppfp)

README.md

@@ -1,17 +1,3 @@
----
-output: github_document
----
-
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
-```{r, echo = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>",
-  fig.path = "README-"
-)
-```
-
 # R-SPPFP
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/rsppfp)](https://cran.r-project.org/package=rsppfp)
 [![Travis-CI Build Status](https://travis-ci.org/melvidoni/rsppfp.svg?branch=master)](https://travis-ci.org/melvidoni/rsppfp)

_pkgdown.yaml

@@ -7,13 +7,19 @@ reference:
     contents:
       - '`parse_vpath`'
       - '`direct_graph`'
+      - '`get_all_nodes`'
 
   - title: Digraphs Transformations
     desc: Implementations of algorithms to transform a graph and its set of forbidden paths.
     contents:
       - '`modify_graph_vd`'
       - '`modify_graph_hsu`'
 
+  - title: Integrations
+    desc: Functions that simplify the integration with other R-Packages.
+    contents:
+      - '`get_shortest_path`'
+
 
 navbar:
   type: inverse