1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
|
% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/nexus.R
\name{print.nexusDatasetInfo}
\alias{[.nexusDatasetInfoList}
\alias{nexus}
\alias{nexus.get}
\alias{nexus.info}
\alias{nexus.list}
\alias{nexus.search}
\alias{nexusDatasetInfo}
\alias{nexus_get}
\alias{nexus_info}
\alias{nexus_list}
\alias{nexus_search}
\alias{print.nexusDatasetInfo}
\alias{print.nexusDatasetInfoList}
\alias{summary.nexusDatasetInfoList}
\title{Query and download from the Nexus network repository}
\usage{
\method{print}{nexusDatasetInfo}(x, ...)
\method{summary}{nexusDatasetInfoList}(object, ...)
\method{print}{nexusDatasetInfoList}(x, ...)
nexus_list(tags = NULL, offset = 0, limit = 10, operator = c("or",
"and"), order = c("date", "name", "popularity"),
nexus.url = igraph_opt("nexus.url"))
nexus_info(id, nexus.url = igraph_opt("nexus.url"))
nexus_get(id, offset = 0, order = c("date", "name", "popularity"),
nexus.url = igraph_opt("nexus.url"))
nexus_search(q, offset = 0, limit = 10, order = c("date", "name",
"popularity"), nexus.url = igraph_opt("nexus.url"))
\method{[}{nexusDatasetInfoList}(x, i)
}
\arguments{
\item{x,object}{The \code{nexusDatasetInfo} object to print.}
\item{tags}{A character vector, the tags that are searched. If not given (or
\code{NULL}), then all datasets are listed.}
\item{offset}{An offset to select part of the results. Results are listed
from \code{offset}+1.}
\item{limit}{The maximum number of results to return.}
\item{operator}{A character scalar. If \sQuote{or} (the default), then all
datasets that have at least one of the given tags, are returned. If it if
\sQuote{and}, then only datasets that have all the given tags, are returned.}
\item{order}{The ordering of the results, possible values are:
\sQuote{date}, \sQuote{name}, \sQuote{popularity}.}
\item{nexus.url}{The URL of the Nexus server. Don't change this from the
default, unless you set up your own Nexus server.}
\item{id}{The numeric or character id of the data set to query or download.
Instead of the data set ids, it is possible to supply a
\code{nexusDatasetInfo} or \code{nexusDatasetInfoList} object here directly
and then the query is done on the corresponding data set(s).}
\item{q}{Nexus search string. See examples below. For the complete
documentation please see the Nexus homepage at
\url{http://nexus.igraph.org}.}
\item{i}{Index.}
\item{\dots}{Currently ignored.}
}
\value{
\code{nexus_list} and \code{nexus_search} return a list of
\code{nexusDatasetInfo} objects. The list also has these attributes:
\describe{ \item{size}{The number of data sets returned by the query.}
\item{totalsize}{The total number of data sets found for the query.}
\item{offset}{The offset parameter of the query.} \item{limit}{The limit
parameter of the query.} }
\code{nexus_info} returns a single \code{nexusDatasetInfo} object.
\code{nexus_get} returns an igraph graph object, or a list of graph objects,
if the data set consists of multiple networks.
}
\description{
The Nexus network repository is an online collection of network data sets.
These functions can be used to query it and download data from it, directly
as an igraph graph.
}
\details{
Nexus is an online repository of networks, with an API that allow
programatic queries against it, and programatic data download as well.
The \code{nexus_list} and \code{nexus_info} functions query the online
database. They both return \code{nexusDatasetInfo} objects.
\code{nexus_info} returns more information than \code{nexus_list}.
\code{nexus_search} searches Nexus, and returns a list of data sets, as
\code{nexusDatasetInfo} objects. See below for some search examples.
\code{nexus_get} downloads a data set from Nexus, based on its numeric id,
or based on a Nexus search string. For search strings, only the first search
hit is downloaded, but see also the \code{offset} argument. (If there are
not data sets found, then the function returns an error.)
The \code{nexusDatasetInfo} objects returned by \code{nexus_list} have the
following fields: \describe{
\item{id}{The numeric id of the dataset.}
\item{sid}{The character id of the dataset.}
\item{name}{Character scalar, the name of the dataset.}
\item{vertices/edges}{Character, the number of vertices and edges in
the graph(s). Vertices and edges are separated by a slash, and if
the data set consists of multiple networks, then they are separated
by spaces.}
\item{tags}{Character vector, the tags of the dataset. Directed graph
have the tags \sQuote{directed}. Undirected graphs are tagged
as \sQuote{undirected}. Other common tags are: \sQuote{weighted},
\sQuote{bipartite}, \sQuote{social network}, etc.}
\item{networks}{The ids and names of the networks in the data set. The
numeric and character id are separated by a slash, and multiple networks
are separated by spaces.}
}
\code{nexusDatasetInfo} objects returned by \code{nexus_info} have the
following additional fields: \describe{
\item{date}{Character scalar, e.g. \sQuote{2011-01-09}, the date when
the dataset was added to the database.}
\item{formats}{Character vector, the data formats in which the data set is
available. The various formats are separated by semicolons.}
\item{licence}{Character scalar, the licence of the dataset.}
\item{licence url}{Character scalar, the URL of the licence of the
dataset. Pleaase make sure you consult this before using a dataset.}
\item{summary}{Character scalar, the short description of the dataset,
this is usually a single sentence.}
\item{description}{Character scalar, the full description of the
dataset.}
\item{citation}{Character scalar, the paper(s) describing the
dataset. Please cite these papers if you are using the dataset in your
research, the licence of most datasets requires this.}
\item{attributes}{A list of lists, each list entry is a graph, vertex
or edge attribute and has the following entries: \describe{
\item{type}{Type of the attribute, either \sQuote{graph},
\sQuote{vertex} or \sQuote{edge}.}
\item{datatype}{Data type of the attribute, currently it can be
\sQuote{numeric} and \sQuote{string}.}
\item{name}{Character scalar, the name of the attribute.}
\item{description}{Character scalar, the description of the
attribute.}
}
}
}
The results of the Nexus queries are printed to the screen in a consise
format, similar to the format of igraph graphs. A data set list (typically
the result of \code{nexus_list} and \code{nexus_search}) looks like this:
\preformatted{NEXUS 1-5/18 -- data set list
[1] kaptail.4 39/109-223 #18 Kapferer tailor shop
[2] condmatcollab2003 31163/120029 #17 Condensed matter collaborations+
[3] condmatcollab 16726/47594 #16 Condensed matter collaborations+
[4] powergrid 4941/6594 #15 Western US power grid
[5] celegansneural 297/2359 #14 C. Elegans neural network }
Each line here represents a data set, and the following information is
given about them: the character id of the data set (e.g. \code{kaptail}
or \code{powergrid}), the number of vertices and number of edges in the
graph of the data sets. For data sets with multiple graphs, intervals
are given here. Then the numeric id of the data set and the reamining
space is filled with the name of the data set.
Summary information about an individual Nexus data set is printed as
\preformatted{NEXUS B--- 39 109-223 #18 kaptail -- Kapferer tailor shop
+ tags: directed; social network; undirected
+ nets: 1/KAPFTI2; 2/KAPFTS2; 3/KAPFTI1; 4/KAPFTS1}
This is very similar to the header that is used for printing igraph
graphs, but there are some differences as well. The four characters
after the \code{NEXUS} word give the most important properties of the
graph(s): the first is \sQuote{\code{U}} for undirected and
\sQuote{\code{D}} for directed graphs, and \sQuote{\code{B}} if the data
set contains both directed and undirected graphs. The second is
\sQuote{\code{N}} named graphs. The third character is \sQuote{\code{W}}
for weighted graphs, the fourth is \sQuote{\code{B}} if the data set
contains bipartite graphs. Then the number of vertices and number of
edges are printed, for data sets with multiple graphs, the smallest and
the largest values are given. Then comes the numeric id, and the string
id of the data set. The end of the first line contains the name of the
data set. The second row lists the data set tags, and the third row the
networks that are included in the data set.
Detailed data set information is printed similarly, but it contains more
fields.
}
\examples{
\dontrun{nexus_list(tag="weighted")
nexus_list(limit=3, order="name")
nexus_list(limit=3, order="name")[[1]]
nexus_info(2)
g <- nexus_get(2)
summary(g)
## Data sets related to 'US':
nexus_search("US")
## Search for data sets that have 'network' in their name:
nexus_search("name:network")
## Any word can match
nexus_search("blog or US or karate")
}
}
\seealso{
\url{http://nexus.igraph.org}
}
|
