Simple Graph Data Types and Basic Algorithms
Simple classic graph algorithms for simple graph classes. Graphs may possess vertex and edge attributes. ‘simplegraph’ has no dependencies and it is written entirely in R, so it is easy to install.
devtools::install_github("gaborcsardi/simplegraph")library(simplegraph)#>
#> Attaching package: 'simplegraph'
#> The following object is masked from 'package:base':
#>
#> ordersimplegraph has two ways of creating graphs from data.
The first one is an adjacency list containing vertex names. Note that
all graphs are directed in simplegraph. Undirected graphs
can be emulated with bidirectional edges.
This is Euler’s famous graph of the bridges of Koenigsberg:
bridges <- graph(list(
"Altstadt-Loebenicht" = c(
"Kneiphof",
"Kneiphof",
"Lomse"
),
"Kneiphof" = c(
"Altstadt-Loebenicht",
"Altstadt-Loebenicht",
"Vorstadt-Haberberg",
"Vorstadt-Haberberg",
"Lomse"
),
"Vorstadt-Haberberg" = c(
"Kneiphof",
"Kneiphof",
"Lomse"
),
"Lomse" = c(
"Altstadt-Loebenicht",
"Kneiphof",
"Vorstadt-Haberberg"
)
))
bridges#> $`Altstadt-Loebenicht`
#> [1] "Kneiphof" "Kneiphof" "Lomse"
#>
#> $Kneiphof
#> [1] "Altstadt-Loebenicht" "Altstadt-Loebenicht" "Vorstadt-Haberberg"
#> [4] "Vorstadt-Haberberg" "Lomse"
#>
#> $`Vorstadt-Haberberg`
#> [1] "Kneiphof" "Kneiphof" "Lomse"
#>
#> $Lomse
#> [1] "Altstadt-Loebenicht" "Kneiphof" "Vorstadt-Haberberg"
#>
#> attr(,"class")
#> [1] "simplegraph_adjlist" "simplegraph" "list"simplegraph supports graph metadata on vertices and
edges. To create a graph with metadata, pass two data frames to
graph, one for vertices, one for edges.
The first column of the vertex data frame must contain the ids of the vertices in a character vector.
The first columns of the edge data frame must contain the edges of the graph, i.e. the tail vertices and the head vertices, given by the vertex ids.
Here is an example for a graph of actors and movies.
vertices <- data.frame(
stringsAsFactors = FALSE,
name = c("Tom Hanks", "Cate Blanchett", "Matt Damon", "Kate Winslet",
"Saving Private Ryan", "Contagion", "The Talented Mr. Ripley"),
what = c("actor", "actor", "actor", "actor", "movie", "movie", "movie"),
born = c("1956-07-09", "1966-05-26", "1970-10-08", "1975-10-05",
NA, NA, NA),
gender = c("M", "F", "M", "F", NA, NA, NA),
year = c(NA, NA, NA, NA, 1998, 2011, 1999)
)
edges <- data.frame(
stringsAsFactors = FALSE,
actor = c("Tom Hanks", "Cate Blanchett", "Matt Damon", "Matt Damon",
"Kate Winslet"),
movie = c("Saving Private Ryan", "The Talented Mr. Ripley",
"Saving Private Ryan", "The Talented Mr. Ripley", "Contagion")
)
actors <- graph(vertices, edges)vertex_ids(actors)#> [1] "Tom Hanks" "Cate Blanchett"
#> [3] "Matt Damon" "Kate Winslet"
#> [5] "Saving Private Ryan" "Contagion"
#> [7] "The Talented Mr. Ripley"vertices(actors)#> name what born gender year
#> 1 Tom Hanks actor 1956-07-09 M NA
#> 2 Cate Blanchett actor 1966-05-26 F NA
#> 3 Matt Damon actor 1970-10-08 M NA
#> 4 Kate Winslet actor 1975-10-05 F NA
#> 5 Saving Private Ryan movie <NA> <NA> 1998
#> 6 Contagion movie <NA> <NA> 2011
#> 7 The Talented Mr. Ripley movie <NA> <NA> 1999edges(actors)#> actor movie
#> 1 Tom Hanks Saving Private Ryan
#> 2 Cate Blanchett The Talented Mr. Ripley
#> 3 Matt Damon Saving Private Ryan
#> 4 Matt Damon The Talented Mr. Ripley
#> 5 Kate Winslet ContagionNumber of vertices and edges:
order(bridges)#> [1] 4size(bridges)#> [1] 14Adjacenct vertices:
adjacent_vertices(bridges)$Lomse#> [1] "Altstadt-Loebenicht" "Kneiphof" "Vorstadt-Haberberg"
#> [4] "Altstadt-Loebenicht" "Kneiphof" "Vorstadt-Haberberg"This is a graph of function calls from the R package
pkgsnap (https://github.com/mangothecat/pkgsnap):
funcs <- graph(list(
drop_internal = character(0),
get_deps = c("get_description", "parse_deps",
"%||%", "drop_internal"),
get_description = "pkg_from_filename",
parse_deps = "str_trim",
cran_file = c("get_pkg_type", "r_minor_version", "cran_file"),
download_urls = c("split_pkg_names_versions", "cran_file"),
filename_from_url = character(0),
get_pkg_type = character(0),
pkg_download = c("dir_exists", "download_urls",
"filename_from_url", "try_download"),
r_minor_version = character(0),
try_download = character(0),
drop_missing_deps = character(0),
install_order = character(0),
restore = c("pkg_download", "drop_missing_deps",
"install_order", "get_deps"),
snap = character(0),
`%||%` = character(0),
data_frame = character(0),
dir_exists = character(0),
pkg_from_filename = character(0),
split_pkg_names_versions = "data_frame",
str_trim = character(0)
))List of vertices:
vertices(funcs)#> name
#> 1 drop_internal
#> 2 get_deps
#> 3 get_description
#> 4 parse_deps
#> 5 cran_file
#> 6 download_urls
#> 7 filename_from_url
#> 8 get_pkg_type
#> 9 pkg_download
#> 10 r_minor_version
#> 11 try_download
#> 12 drop_missing_deps
#> 13 install_order
#> 14 restore
#> 15 snap
#> 16 %||%
#> 17 data_frame
#> 18 dir_exists
#> 19 pkg_from_filename
#> 20 split_pkg_names_versions
#> 21 str_trimList of edges:
edges(funcs)#> from to
#> 1 get_deps get_description
#> 2 get_deps parse_deps
#> 3 get_deps %||%
#> 4 get_deps drop_internal
#> 5 get_description pkg_from_filename
#> 6 parse_deps str_trim
#> 7 cran_file get_pkg_type
#> 8 cran_file r_minor_version
#> 9 cran_file cran_file
#> 10 download_urls split_pkg_names_versions
#> 11 download_urls cran_file
#> 12 pkg_download dir_exists
#> 13 pkg_download download_urls
#> 14 pkg_download filename_from_url
#> 15 pkg_download try_download
#> 16 restore pkg_download
#> 17 restore drop_missing_deps
#> 18 restore install_order
#> 19 restore get_deps
#> 20 split_pkg_names_versions data_frameTransposing a graph changes the directions of all edges to the opposite.
edges(transpose(funcs))#> from to
#> 1 drop_internal get_deps
#> 2 get_deps restore
#> 3 get_description get_deps
#> 4 parse_deps get_deps
#> 5 cran_file cran_file
#> 6 cran_file download_urls
#> 7 download_urls pkg_download
#> 8 filename_from_url pkg_download
#> 9 get_pkg_type cran_file
#> 10 pkg_download restore
#> 11 r_minor_version cran_file
#> 12 try_download pkg_download
#> 13 drop_missing_deps restore
#> 14 install_order restore
#> 15 %||% get_deps
#> 16 data_frame split_pkg_names_versions
#> 17 dir_exists pkg_download
#> 18 pkg_from_filename get_description
#> 19 split_pkg_names_versions download_urls
#> 20 str_trim parse_depsBreadth-first search:
bfs(funcs)#> [1] "drop_internal" "get_deps"
#> [3] "get_description" "parse_deps"
#> [5] "%||%" "pkg_from_filename"
#> [7] "str_trim" "cran_file"
#> [9] "get_pkg_type" "r_minor_version"
#> [11] "download_urls" "split_pkg_names_versions"
#> [13] "data_frame" "filename_from_url"
#> [15] "pkg_download" "dir_exists"
#> [17] "try_download" "drop_missing_deps"
#> [19] "install_order" "restore"
#> [21] "snap"topological_sort(simplify(funcs))#> [1] "snap" "restore"
#> [3] "install_order" "drop_missing_deps"
#> [5] "pkg_download" "try_download"
#> [7] "dir_exists" "filename_from_url"
#> [9] "download_urls" "split_pkg_names_versions"
#> [11] "data_frame" "cran_file"
#> [13] "r_minor_version" "get_pkg_type"
#> [15] "get_deps" "%||%"
#> [17] "parse_deps" "str_trim"
#> [19] "get_description" "pkg_from_filename"
#> [21] "drop_internal"Detecting loop and multiple edges:
is_loopy(funcs)#> [1] TRUEis_multigraph(funcs)#> [1] FALSERemoving loop and multiple edges:
is_loopy(remove_loops(funcs))#> [1] FALSEis_multigraph(remove_multiple(funcs))#> [1] FALSEsimplify removes both loops and multiple edges, so it
creates a simple graph:
is_loopy(simplify(funcs))#> [1] FALSEis_multigraph(simplify(funcs))#> [1] FALSEis_simple(simplify(funcs))#> [1] TRUEMIT © Mango Solutions.