diff --git a/R/Koenigsberg.R b/R/Koenigsberg.R index 8dde8c4..09ac3a9 100644 --- a/R/Koenigsberg.R +++ b/R/Koenigsberg.R @@ -2,19 +2,16 @@ #' #' @description #' -#' The Seven Bridges of Koenigsberg is a notable historical problem in -#' mathematics. Its negative resolution by Leonhard Euler in 1735 laid -#' the foundations of graph theory and presaged the idea of topology. +#' The Seven Bridges of Koenigsberg is a notable historical problem in mathematics. +#' Its negative resolution by Leonhard Euler in 1735 laid the foundations of graph theory and presaged the idea of topology. #' -#' The city of Koenigsberg in Prussia (now Kaliningrad, Russia) was set on -#' both sides of the Pregel River, and included two large islands which -#' were connected to each other and the mainland by seven bridges +#' The city of Koenigsberg in Prussia (now Kaliningrad, Russia) was set on both sides of the Pregel River, +#' and included two large islands which were connected to each other and the mainland by seven bridges #' -#' The problem was to find a walk through the city that would cross each -#' bridge once and only once. The islands could not be reached by any route -#' other than the bridges, and every bridge must have been crossed -#' completely every time (one could not walk half way onto the bridge and -#' then turn around and later cross the other half from the other side). +#' The problem was to find a walk through the city that would cross each bridge once and only once. +#' The islands could not be reached by any route other than the bridges, +#' and every bridge must have been crossed completely every time +#' (one could not walk half way onto the bridge and then turn around and later cross the other half from the other side). #' #' Euler proved that the problem has no solution. #' @@ -25,16 +22,13 @@ #' @usage #' Koenigsberg #' @format -#' An undirected `igraph` graph object with vertex attributes -#' \sQuote{name} and \sQuote{Euler_letter}, the latter is the notation -#' from Eulers original paper; and edge attributes \sQuote{name} (the name -#' of the bridge) and \sQuote{Euler_letter}, again, Euler's notation -#' from his paper. +#' An undirected `igraph` graph object with vertex attributes \sQuote{name} and \sQuote{Euler_letter}, +#' the latter is the notation from Eulers original paper; +#' and edge attributes \sQuote{name} (the name of the bridge) and \sQuote{Euler_letter}, again, Euler's notation from his paper. #' #' This dataset is in the public domain. #' @references Leonhard Euler, “Solutio problematis ad geometriam situs pertinensis” #' Commentarii Academiae Scientarum Imperialis Petropolitanae, 8 (1736), 128–140 + Plate VIII. -#' @source Wikipedia, -#' +#' @source Wikipedia, #' @keywords datasets NULL diff --git a/R/UKfaculty.R b/R/UKfaculty.R index f5994d8..9b376b2 100644 --- a/R/UKfaculty.R +++ b/R/UKfaculty.R @@ -1,28 +1,24 @@ #' Friendship network of a UK university faculty #' #' @description -#' The personal friendship network of a faculty of a UK -#' university, consisting of 81 vertices (individuals) and 817 directed -#' and weighted connections. The school affiliation of each individual is -#' stored as a vertex attribute. This dataset can serve as a testbed for -#' community detection algorithms. +#' The personal friendship network of a faculty of a UK university, +#' consisting of 81 vertices (individuals) and 817 directed and weighted connections. +#' The school affiliation of each individual is stored as a vertex attribute. +#' This dataset can serve as a testbed for community detection algorithms. #' #' @name UKfaculty #' @docType data #' @usage #' UKfaculty #' @format -#' A directed `igraph` graph object with vertex attribute -#' \sQuote{Group}, the numeric id of the school affiliation, and edge -#' attribute \sQuote{weight}, i.e. the graph is weighted. +#' A directed `igraph` graph object with vertex attribute \sQuote{Group}, the numeric id of the school affiliation, +#' and edge attribute \sQuote{weight}, i.e. the graph is weighted. #' -#' This dataset is licensed under a Creative Commons -#' Attribution-Share Alike 2.0 UK: England & Wales License, +#' This dataset is licensed under a Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License, #' see for details. #' Please cite the reference below if you use this dataset. -#' @references Nepusz T., Petroczi A., Negyessy L., Bazso F.: Fuzzy -#' communities and the concept of bridgeness in complex -#' networks. Physical Review E 77:016107, 2008. +#' @references Nepusz T., Petroczi A., Negyessy L., Bazso F.: Fuzzy communities and the concept of bridgeness in complex networks. +#' Physical Review E 77:016107, 2008. #' \doi{10.1103/PhysRevE.77.016107} #' @source See reference below. #' @keywords datasets diff --git a/R/USairports.R b/R/USairports.R index 75edf30..2a41fdf 100644 --- a/R/USairports.R +++ b/R/USairports.R @@ -2,12 +2,11 @@ #' #' @description #' -#' The network of passanger flights between airports in the United -#' States. The data set was compiled based on flights in 2010 -#' December. This network is directed and edge directions correspond to -#' flight directions. Each edge is specific to a single carrier aircraft -#' type. Multiple carriers between the same two airports are denoted by -#' multiple edges. +#' The network of passanger flights between airports in the United States. +#' The data set was compiled based on flights in 2010 December. +#' This network is directed and edge directions correspond to flight directions. +#' Each edge is specific to a single carrier aircraft type. +#' Multiple carriers between the same two airports are denoted by multiple edges. #' #' See information about the included meta-data below. #' @@ -18,35 +17,28 @@ #' @usage #' USairports #' @format -#' A directed `igraph` graph object, with multiple edges. It has a -#' \sQuote{name} graph attribute, and several vertex and edge -#' attributes. The vertex attributes: +#' A directed `igraph` graph object, with multiple edges. +#' It has a \sQuote{name} graph attribute, and several vertex and edge attributes. +#' The vertex attributes: #' \describe{ -#' \item{name}{Symbolic vertex name, this is the three letter IATA -#' airport code.} +#' \item{name}{Symbolic vertex name, this is the three letter IATA airport code.} #' \item{City}{City and state, where the airport is located.} #' \item{Position}{Position of the airport, in WGS coordinates.} #' } #' #' Edge attributes: #' \describe{ -#' \item{Carrier}{Name of the airline. The network includes both -#' domestic and international carriers that performed at least one -#' flight in December of 2010.} -#' \item{Departures}{The number of departures (for a given airline and -#' aircraft type.} -#' \item{Seats}{The total number of seats available on the flights -#' carried out by a given airline, using a given aircraft type.} -#' \item{Passengers}{The total number of passangers on the flights -#' carried out by a given airline, using a given aircraft type.} +#' \item{Carrier}{Name of the airline. +#' The network includes both domestic and international carriers that performed at least one flight in December of 2010.} +#' \item{Departures}{The number of departures (for a given airline and aircraft type.} +#' \item{Seats}{The total number of seats available on the flights carried out by a given airline, using a given aircraft type.} +#' \item{Passengers}{The total number of passangers on the flights carried out by a given airline, using a given aircraft type.} #' \item{Aircraft}{Type of the aircraft.} #' \item{Distance}{The distance between the two airports, in miles.} #' } #' @source -#' Most of this information was downloaded from The Research and -#' Innovative Technology Administration (RITA). See -#' for details. The airport -#' position information was collected from Wikipedia and other public -#' online sources. +#' Most of this information was downloaded from The Research and Innovative Technology Administration (RITA). +#' See for details. +#' The airport position information was collected from Wikipedia and other public online sources. #' @keywords datasets NULL diff --git a/R/enron.R b/R/enron.R index b3728de..4ee1407 100644 --- a/R/enron.R +++ b/R/enron.R @@ -14,11 +14,9 @@ #' A directed `igraph` graph object. #' #' Graph attributes: \itemize{ -#' \item \sQuote{LDC_names} The names of the 32 LDC catagories the emails -#' are classfied into by Michael W. Berry +#' \item \sQuote{LDC_names} The names of the 32 LDC catagories the emails are classfied into by Michael W. Berry #' () -#' \item \sQuote{LDC_desc} Longer descriptions of the 32 LDC -#' categories. +#' \item \sQuote{LDC_desc} Longer descriptions of the 32 LDC categories. #' \item \sQuote{Citation} Additionally, see also the references below. #' \item \sQuote{name} #' } @@ -30,60 +28,48 @@ #' } #' #' Edge attributes: \itemize{ -#' \item \sQuote{Time} When the email was sent. Note that some time -#' labels are from 1979, these are certainly wrong and you might want -#' to remove them before analyses that include time. -#' \item \sQuote{Reciptype} Recipient type, \sQuote{to}, \sQuote{cc} or -#' \sQuote{bcc}. -#' \item \sQuote{Topic} Assigned based on 3-means clustering of -#' randomly selected 3,120 out of all 125,409 messages, then NN -#' classification for the whole corpus. Note that topic 0 means an -#' outlier, e.g., too few words or all meaningless numbers in the -#' message body. -#' \item \sQuote{LDC_topic} Assigned based on Michael W. Berry's 2001 -#' \dQuote{Annotated (by Topic) Enron Email Data Set.} +#' \item \sQuote{Time} When the email was sent. +#' Note that some time labels are from 1979, +#' these are certainly wrong and you might want to remove them before analyses that include time. +#' \item \sQuote{Reciptype} Recipient type, \sQuote{to}, \sQuote{cc} or \sQuote{bcc}. +#' \item \sQuote{Topic} Assigned based on 3-means clustering of randomly selected 3,120 out of all 125,409 messages, +#' then NN classification for the whole corpus. +#' Note that topic 0 means an outlier, e.g., too few words or all meaningless numbers in the message body. +#' \item \sQuote{LDC_topic} Assigned based on Michael W. Berry's 2001 \dQuote{Annotated (by Topic) Enron Email Data Set.} #' () -#' There are 32 topics. Topic "0" means an outlier, e.g., too few words -#' or all meaningless numbers in the message body, etc. Topic "-1" -#' means there is no matching topic. +#' There are 32 topics. +#' Topic "0" means an outlier, e.g., too few words or all meaningless numbers in the message body, etc. +#' Topic "-1" means there is no matching topic. #' } #' @references #' C.E. Priebe, J.M. Conroy, D.J. Marchette, and Y. Park, -#' Scan Statistics on Enron Graphs Computational and Mathematical -#' Organization Theory, Volume 11, Number 3, p229 - 247, October 2005, -#' Springer Science+Business Media B.V. \doi{10.1007/s10588-005-5378-z} +#' Scan Statistics on Enron Graphs Computational and Mathematical Organization Theory, +#' Volume 11, Number 3, p229 - 247, October 2005, Springer Science+Business Media B.V. \doi{10.1007/s10588-005-5378-z} #' #' C.E. Priebe, J.M. Conroy, D.J. Marchette, and Y. Park, -#' Scan Statistics on Enron Graphs, SIAM International Conference on -#' Data Mining, Workshop on Link Analysis, Counterterrorism and Security, -#' Newport Beach, California, April 23, 2005. +#' Scan Statistics on Enron Graphs, SIAM International Conference on Data Mining, +#' Workshop on Link Analysis, Counterterrorism and Security, Newport Beach, California, April 23, 2005. #' -#' Gina Kolata, Enron Offers an Unlikely Boost to E-Mail Surveillance, -#' New York Times, Week in Review, May 22, 2005. +#' Gina Kolata, Enron Offers an Unlikely Boost to E-Mail Surveillance, New York Times, Week in Review, May 22, 2005. #' -#' C.E. Priebe, Scan Statistics on Enron Graphs, IPAM Summer Graduate -#' School: Intelligent Extraction of Information from Graphs and High -#' Dimensional Data, UCLA, July 11-29, 2005. +#' C.E. Priebe, Scan Statistics on Enron Graphs, +#' IPAM Summer Graduate School: Intelligent Extraction of Information from Graphs and High Dimensional Data, +#' UCLA, July 11-29, 2005. #' -#' C.E. Priebe, Scan Statistics on Enron Graphs, 2005 Fall Department -#' of Applied Mathematics and Statistics Seminars, September 15, 2005, -#' The Johns Hopkins University. +#' C.E. Priebe, Scan Statistics on Enron Graphs, +#' 2005 Fall Department of Applied Mathematics and Statistics Seminars, September 15, 2005, The Johns Hopkins University. #' -#' Y. Park, C.E. Priebe, D.J. Marchette, Scan Statistics on Enron -#' Hypergraphs, Interface 2008, Durham, North Carolina, May 21, 2008, +#' Y. Park, C.E. Priebe, D.J. Marchette, Scan Statistics on Enron Hypergraphs, Interface 2008, Durham, North Carolina, May 21, 2008, #' -#' Y. Park, C.E. Priebe, D.J. Marchette, Anomaly Detection using Scan -#' Statistics on Enron Graphs and Hypergraphs, The Satellite Workshop of -#' the IASC 2008 Conference, Seoul, Korea, December 1-3, 2008. +#' Y. Park, C.E. Priebe, D.J. Marchette, Anomaly Detection using Scan Statistics on Enron Graphs and Hypergraphs, +#' The Satellite Workshop of the IASC 2008 Conference, Seoul, Korea, December 1-3, 2008. #' -#' Y. Park, C.E. Priebe, D.J. Marchette, A. Youssef, Anomaly Detection -#' using Scan Statistics on Time Series of Hypergraphs, Workshop on Link -#' Analysis, Counterterrorism and Security at the SIAM International -#' Conference on Data Mining, Sparks, Nevada, May 1-3, 2009, +#' Y. Park, C.E. Priebe, D.J. Marchette, A. Youssef, Anomaly Detection using Scan Statistics on Time Series of Hypergraphs, +#' Workshop on Link Analysis, Counterterrorism and Security at the SIAM International Conference on Data Mining, +#' Sparks, Nevada, May 1-3, 2009, #' -#' Y. Park, C.E. Priebe, A. Youssef, Anomaly Detection in Time Series of -#' Graphs using Fusion of Invariants, Computational and Mathematical -#' Organization Theory, submitted, 2010. \doi{10.1109/JSTSP.2012.2233712} +#' Y. Park, C.E. Priebe, A. Youssef, Anomaly Detection in Time Series of Graphs using Fusion of Invariants, +#' Computational and Mathematical Organization Theory, submitted, 2010. \doi{10.1109/JSTSP.2012.2233712} #' @source #' NULL diff --git a/R/foodweb.R b/R/foodweb.R index 8cada05..13ac20b 100644 --- a/R/foodweb.R +++ b/R/foodweb.R @@ -1,8 +1,8 @@ #' A collection of food webs #' #' @description -#' A list of graphs. Each one is a food web, i.e. a directed -#' graph of predator-prey relationships. +#' A list of graphs. +#' Each one is a food web, i.e. a directed graph of predator-prey relationships. #' #' #' @@ -11,13 +11,12 @@ #' @usage #' foodwebs #' @format -#' A named list of directed `igraph` graph objects. Here are the -#' list of the graphs included: +#' A named list of directed `igraph` graph objects. +#' Here are the list of the graphs included: #' \describe{ #' \item{\sQuote{ChesLower}}{Lower Chesapeake Bay in Summer. #' -#' Reference: Hagy, J.D. (2002) Eutrophication, hypoxia and -#' trophic transfer efficiency in Chesapeake Bay PhD Dissertation, +#' Reference: Hagy, J.D. (2002) Eutrophication, hypoxia and trophic transfer efficiency in Chesapeake Bay PhD Dissertation, #' University of Maryland at College Park (USA), 446 pp.} #' \item{\sQuote{ChesMiddle}}{Middle Chesapeake Bay in Summer. #' @@ -27,95 +26,77 @@ #' Reference: same as for \sQuote{ChesLower}.} #' \item{\sQuote{Chesapeake}}{Chesapeake Bay Mesohaline Network. #' -#' Reference: Baird D. & Ulanowicz R.E. (1989) The seasonal dynamics -#' of the Chesapeake Bay ecosystem. Ecological Monographs 59:329-364.} +#' Reference: Baird D. & Ulanowicz R.E. (1989) The seasonal dynamics of the Chesapeake Bay ecosystem. +#' Ecological Monographs 59:329-364.} #' \item{\sQuote{CrystalC}}{Crystal River Creek (Control). #' -#' Reference: Homer, M. and W.M. Kemp. Unpublished Ms. See also -#' Ulanowicz, R.E. 1986. Growth and Development: Ecosystems -#' Phenomenology. Springer, New York. pp 69-79.} +#' Reference: Homer, M. and W.M. Kemp. Unpublished Ms. +#' See also Ulanowicz, R.E. 1986. Growth and Development: Ecosystems Phenomenology. Springer, New York. pp 69-79.} #' \item{\sQuote{CrystalD}}{Crystal River Creek (Delta Temp). #' #' Reference: same as for \sQuote{CrystalD}.} #' \item{\sQuote{Maspalomas}}{Charca de Maspalomas. #' -#' Reference: Almunia, J., G. Basterretxea, J. Aristegui, and -#' R.E. Ulanowicz. (1999) Benthic- Pelagic switching in a coastal -#' subtropical lagoon. Estuarine, Coastal and Shelf Science -#' 49:363-384.} +#' Reference: Almunia, J., G. Basterretxea, J. Aristegui, and R.E. Ulanowicz. (1999) +#' Benthic- Pelagic switching in a coastal subtropical lagoon. Estuarine, Coastal and Shelf Science 49:363-384.} #' \item{\sQuote{Michigan}}{Lake Michigan Control network. #' -#' Reference: Krause, A. and D. Mason. (In preparation.) A. Krause, -#' PhD. Dissertation, Michigan State University. Ann Arbor, MI. USA.} +#' Reference: Krause, A. and D. Mason. (In preparation.) +#' A. Krause, PhD. Dissertation, Michigan State University. Ann Arbor, MI. USA.} #' \item{\sQuote{Mondego}}{Mondego Estuary - Zostrea site. #' -#' Reference: Patricio, J. (In Preparation) Master's -#' Thesis. University of Coimbra, Coimbra, Portugal.} +#' Reference: Patricio, J. (In Preparation) Master's Thesis. University of Coimbra, Coimbra, Portugal.} #' \item{\sQuote{Narragan}}{Narragansett Bay Model. #' -#' Reference: Monaco, M.E. and R.E. Ulanowicz. (1997) Comparative -#' ecosystem trophic structure of three U.S. Mid-Atlantic -#' estuaries. Mar. Ecol. Prog. Ser. 161:239-254.} +#' Reference: Monaco, M.E. and R.E. Ulanowicz. (1997) Comparative ecosystem trophic structure of three U.S. Mid-Atlantic estuaries. +#' Mar. Ecol. Prog. Ser. 161:239-254.} #' \item{\sQuote{Rhode}}{Rhode River Watershed - Water Budget. #' -#' Reference: Correll, D. (Unpublished manuscript) Smithsonian -#' Institute, Chesapeake Bay Center for Environmental Research, +#' Reference: Correll, D. (Unpublished manuscript) Smithsonian Institute, Chesapeake Bay Center for Environmental Research, #' Edgewater, Maryland 21037-0028 USA.} #' \item{\sQuote{StMarks}}{St. Marks River (Florida) Flow network. #' #' Reference: Baird, D., J. Luczkovich and R. R. Christian. (1998) -#' Assessment of spatial and temporal variability in ecosystem -#' attributes of the St Marks National Wildlife Refuge, Apalachee Bay, -#' Florida. Estuarine, Coastal, and Shelf Science 47: 329-349.} +#' Assessment of spatial and temporal variability in ecosystem attributes of the St Marks National Wildlife Refuge, +#' Apalachee Bay, Florida. Estuarine, Coastal, and Shelf Science 47: 329-349.} #' \item{\sQuote{baydry}}{Florida Bay Trophic Exchange Matrix, dry season. #' -#' Reference: Ulanowicz, R. E., C. Bondavalli, and -#' M. S. Egnotovich. 1998. Network analysis of trophic dynamics in -#' South Florida ecosystems, FY 97: the Florida Bay ecosystem. Annual -#' Report to the United States Geological Service Biological Resources -#' Division, University of Miami Coral Gables, \[UM-CES\] CBL 98-123, -#' Maryland System Center for Environmental Science, Chesapeake -#' Biological Laboratory, Maryland, USA.} +#' Reference: Ulanowicz, R. E., C. Bondavalli, and M. S. Egnotovich. 1998. +#' Network analysis of trophic dynamics in South Florida ecosystems, FY 97: the Florida Bay ecosystem. +#' Annual Report to the United States Geological Service Biological Resources Division, University of Miami Coral Gables, +#' \[UM-CES\] CBL 98-123, Maryland System Center for Environmental Science, Chesapeake Biological Laboratory, Maryland, USA.} #' \item{\sQuote{baywet}}{Florida Bay Trophic Exchange Matrix, wet season. #' #' Reference: same as for \sQuote{baydry}.} #' \item{\sQuote{cypdry}}{Cypress, dry season. #' -#' Reference: Ulanowicz, R. E., C. Bondavalli, and -#' M. S. Egnotovich. 1997. Network analysis of trophic dynamics in -#' South Florida ecosystems, FY 96: the cypress wetland -#' ecosystem. Annual Report to the United States Geological Service -#' Biological Resources Division, University of Miami Coral Gables, -#' \[UM-CES\] CBL 97-075, Maryland System Center for Environmental -#' Science, Chesapeake Biological Laboratory.} +#' Reference: Ulanowicz, R. E., C. Bondavalli, and M. S. Egnotovich. 1997. +#' Network analysis of trophic dynamics in South Florida ecosystems, FY 96: the cypress wetland ecosystem. +#' Annual Report to the United States Geological Service Biological Resources Division, University of Miami Coral Gables, +#' \[UM-CES\] CBL 97-075, Maryland System Center for Environmental Science, Chesapeake Biological Laboratory.} #' \item{\sQuote{cypwet}}{Cypress, wet season. #' #' Reference: same as for \sQuote{cypdry}.} #' \item{\sQuote{gramdry}}{Everglades Graminoids - Dry Season. #' -#' Reference: Ulanowicz, R. E., J. J. Heymans, and -#' M. S. Egnotovich. 2000. Network analysis of trophic dynamics in -#' South Florida ecosystems, FY 99: the graminoid ecosystem. Technical -#' Report TS-191-99, Maryland System Center for Environmental Science, -#' Chesapeake Biological Laboratory, Maryland, USA.} +#' Reference: Ulanowicz, R. E., J. J. Heymans, and M. S. Egnotovich. 2000. +#' Network analysis of trophic dynamics in South Florida ecosystems, FY 99: the graminoid ecosystem. +#' Technical Report TS-191-99, Maryland System Center for Environmental Science, Chesapeake Biological Laboratory, Maryland, USA.} #' \item{\sQuote{gramwet}}{Everglades Graminoids - Wet Season. #' #' Reference: same as for \sQuote{gramdry}.} #' \item{\sQuote{mangdry}}{Mangrove Estuary, Dry Season. #' -#' Reference: Ulanowicz, R. E., C. Bondavalli, J. J. Heymans, and -#' M. S. Egnotovich. 1999. Network analysis of trophic dynamics in -#' South Florida ecosystems, FY 98: the mangrove ecosystem. Technical -#' Report TS-191-99, Maryland System Center for Environmental Science, -#' Chesapeake Biological Laboratory, Maryland, USA.} +#' Reference: Ulanowicz, R. E., C. Bondavalli, J. J. Heymans, and M. S. Egnotovich. 1999. +#' Network analysis of trophic dynamics in South Florida ecosystems, FY 98: the mangrove ecosystem. +#' Technical Report TS-191-99, Maryland System Center for Environmental Science, Chesapeake Biological Laboratory, Maryland, USA.} #' \item{\sQuote{mangwet}}{Mangrove Estuary, Wet Season. #' #' Reference: same as for \sQuote{mangdry}.} #' } #' -#' Each graph has the following vertex attributes: \sQuote{name} is the -#' name of the species, \sQuote{ECO} is the type of the node, and -#' integer value between one and five, meaning: +#' Each graph has the following vertex attributes: \sQuote{name} is the name of the species, +#' \sQuote{ECO} is the type of the node, and integer value between one and five, meaning: #' \enumerate{ #' \item Living/producing compartment #' \item Other compartment @@ -123,18 +104,13 @@ #' \item Output #' \item Respiration. #' } -#' The \sQuote{Biomass} vertex attribute contains the biomass of the -#' species. +#' The \sQuote{Biomass} vertex attribute contains the biomass of the species. #' -#' Edges are weighted, and the weights denote energy flux between the -#' species involved. +#' Edges are weighted, and the weights denote energy flux between the species involved. #' -#' The graphs also contain some informative graph attributes: -#' \sQuote{Author}, \sQuote{Citation}, \sQuote{URL}, and -#' \sQuote{name}. +#' The graphs also contain some informative graph attributes: \sQuote{Author}, \sQuote{Citation}, \sQuote{URL}, and \sQuote{name}. #' @references See them above. -#' @source See references for the individual webs above. The data itself -#' was downloaded from -#' . +#' @source See references for the individual webs above. +#' The data itself was downloaded from . #' @keywords datasets NULL diff --git a/R/igraphdata-package.R b/R/igraphdata-package.R index 6d4462c..1586536 100644 --- a/R/igraphdata-package.R +++ b/R/igraphdata-package.R @@ -2,11 +2,9 @@ "_PACKAGE" #' @section How to use the data sets -#' After loading the \pkg{igraphdata} package, the various data sets are available -#' by accessing them directly. +#' After loading the \pkg{igraphdata} package, the various data sets are available by accessing them directly. #' -#' Get a list of data sets included in this package with -#' `data(package = "igraphdata")`. +#' Get a list of data sets included in this package with `data(package = "igraphdata")`. ## usethis namespace: start diff --git a/R/immuno.R b/R/immuno.R index d485c0d..5eb6eea 100644 --- a/R/immuno.R +++ b/R/immuno.R @@ -2,11 +2,10 @@ #' #' @description #' -#' The undirected and connected network of interactions -#' in the immunoglobulin protein. It is made up of 1316 vertices -#' representing amino-acids and an edge is drawn between two -#' amino-acids if the shortest distance between their C_alpha atoms -#' is smaller than the threshold value \eqn{\theta=8}{theta=8} Angstrom. +#' The undirected and connected network of interactions in the immunoglobulin protein. +#' It is made up of 1316 vertices representing amino-acids +#' and an edge is drawn between two amino-acids +#' if the shortest distance between their C_alpha atoms is smaller than the threshold value \eqn{\theta=8}{theta=8} Angstrom. #' #' #' @@ -19,8 +18,8 @@ #' #' Graph attributes: \sQuote{name}, \sQuote{Citation}, \sQuote{Author}. #' @references -#' D. Gfeller, Simplifying complex networks: from a clustering to a -#' coarse graining strategy, *PhD Thesis EPFL*, no 3888, 2007. +#' D. Gfeller, Simplifying complex networks: from a clustering to a coarse graining strategy, +#' *PhD Thesis EPFL*, no 3888, 2007. #' #' @source #' See reference below. diff --git a/R/karate.R b/R/karate.R index 8395582..a4616c6 100644 --- a/R/karate.R +++ b/R/karate.R @@ -2,40 +2,33 @@ #' #' @description #' -#' Social network between members of a university karate club, led by -#' president John A. and karate instructor Mr. Hi (pseudonyms). +#' Social network between members of a university karate club, led by president John A. and karate instructor Mr. Hi (pseudonyms). #' -#' The edge weights are the number of common activities the club -#' members took part of. These activities were: +#' The edge weights are the number of common activities the club members took part of. +#' These activities were: #' \enumerate{ #' \item Association in and between academic classes at the university. -#' \item Membership in Mr. Hi's private karate studio on the east side -#' of the city where Mr. Hi taught nights as a part-time instructor. -#' \item Membership in Mr. Hi's private karate studio on the east side -#' of the city, where many of his supporters worked out on weekends. -#' \item Student teaching at the east-side karate studio referred to in -#' (2). This is different from (2) in that student teachers interacted -#' with each other, but were prohibited from interacting with their -#' students. -#' \item Interaction at the university rathskeller, located in the same -#' basement as the karate club's workout area. -#' \item Interaction at a student-oriented bar located across the -#' street from the university campus. -#' \item Attendance at open karate tournaments held through the area at -#' private karate studios. -#' \item Attendance at intercollegiate karate tournaments held at local -#' universities. Since both open and intercollegiate tournaments were -#' held on Saturdays, attendance at both was impossible. +#' \item Membership in Mr. Hi's private karate studio on the east side of the city +#' where Mr. Hi taught nights as a part-time instructor. +#' \item Membership in Mr. Hi's private karate studio on the east side of the city, +#' where many of his supporters worked out on weekends. +#' \item Student teaching at the east-side karate studio referred to in (2). +#' This is different from (2) in that student teachers interacted with each other, +#' but were prohibited from interacting with their students. +#' \item Interaction at the university rathskeller, located in the same basement as the karate club's workout area. +#' \item Interaction at a student-oriented bar located across the street from the university campus. +#' \item Attendance at open karate tournaments held through the area at private karate studios. +#' \item Attendance at intercollegiate karate tournaments held at local universities. +#' Since both open and intercollegiate tournaments were held on Saturdays, attendance at both was impossible. #' } #' -#' Zachary studied conflict and fission in this network, as the karate -#' club was split into two separate clubs, after long disputes between -#' two factions of the club, one led by John A., the other by Mr. Hi. +#' Zachary studied conflict and fission in this network, +#' as the karate club was split into two separate clubs, after long disputes between two factions of the club, +#' one led by John A., the other by Mr. Hi. #' -#' The \sQuote{Faction} vertex attribute gives the faction memberships of -#' the actors. After the split of the club, club members chose their -#' new clubs based on their factions, except actor no. 9, who was in John -#' A.'s faction but chose Mr. Hi's club. +#' The \sQuote{Faction} vertex attribute gives the faction memberships of the actors. +#' After the split of the club, club members chose their new clubs based on their factions, +#' except actor no. 9, who was in John A.'s faction but chose Mr. Hi's club. #' #' #' @@ -44,19 +37,18 @@ #' @usage #' karate #' @format -#' An undirected `igraph` graph object. Vertex no. 1 is Mr. Hi, -#' vertex no. 34 corresponds to John A. +#' An undirected `igraph` graph object. +#' Vertex no. 1 is Mr. Hi, vertex no. 34 corresponds to John A. #' #' Graph attributes: \sQuote{name}, \sQuote{Citation}, \sQuote{Author}. #' -#' Vertex attributes: \sQuote{name}, \sQuote{Faction}, \sQuote{color} is -#' the same as \sQuote{Faction}, \sQuote{label} are short labels for plotting. +#' Vertex attributes: \sQuote{name}, \sQuote{Faction}, \sQuote{color} is the same as \sQuote{Faction}, +#' \sQuote{label} are short labels for plotting. #' #' Edge attribute: \sQuote{weight}. #' @references -#' Wayne W. Zachary. An Information Flow Model for Conflict and Fission -#' in Small Groups. *Journal of Anthropological Research* Vol. 33, -#' No. 4 452-473 \doi{10.1086/jar.33.4.3629752} +#' Wayne W. Zachary. An Information Flow Model for Conflict and Fission in Small Groups. +#' *Journal of Anthropological Research* Vol. 33, No. 4 452-473 \doi{10.1086/jar.33.4.3629752} #' @source #' See reference below. #' @keywords datasets diff --git a/R/kite.R b/R/kite.R index 8b8afc7..e035576 100644 --- a/R/kite.R +++ b/R/kite.R @@ -3,22 +3,19 @@ #' @description #' #' Krackhardt's kite is a fictional social network with ten actors. -#' It is a small (though not the smallest possible) graph for which the most -#' central actors are different according to the three classic centrality -#' measures: degree, closeness and betweenness. +#' It is a small (though not the smallest possible) graph for which the most central actors are different +#' according to the three classic centrality measures: degree, closeness and betweenness. #' #' @name kite #' @docType data #' @usage #' kite #' @format -#' An undirected igraph graph with graph attributes `name`, -#' `layout`, `Citation`, `Author`, `URL`, and vertex -#' attributes `label`, `name` and `Firstname`. +#' An undirected igraph graph with graph attributes `name`, `layout`, `Citation`, `Author`, `URL`, +#' and vertex attributes `label`, `name` and `Firstname`. #' @references -#' Assessing the Political Landscape: Structure, Cognition, and Power in -#' Organizations. David Krackhardt. *Admin. Sci. Quart.* 35, 342-369, -#' 1990. \doi{10.2307/2393394} +#' Assessing the Political Landscape: Structure, Cognition, and Power in Organizations. +#' David Krackhardt. *Admin. Sci. Quart.* 35, 342-369, 1990. \doi{10.2307/2393394} #' @source #' #' @keywords datasets diff --git a/R/macaque.R b/R/macaque.R index c56b1e7..b5f05aa 100644 --- a/R/macaque.R +++ b/R/macaque.R @@ -2,9 +2,8 @@ #' #' @description #' -#' Graph model of the visuotactile brain areas and connections of the -#' macaque monkey. The model consists of 45 areas and 463 directed -#' connections. +#' Graph model of the visuotactile brain areas and connections of the macaque monkey. +#' The model consists of 45 areas and 463 directed connections. #' #' #' @@ -13,18 +12,15 @@ #' @usage #' macaque #' @format -#' A directed `igraph` graph object with vertex attributes -#' \sQuote{name} and \sQuote{shape}. +#' A directed `igraph` graph object with vertex attributes \sQuote{name} and \sQuote{shape}. #' -#' This dataset is licensed under a Creative Commons -#' Attribution-Share Alike 2.0 UK: England & Wales License, +#' This dataset is licensed under a Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License, #' see for details. #' Please cite the reference below if you use this dataset. -#' @references Negyessy L., Nepusz T., Kocsis L., Bazso F.: Prediction of -#' the main cortical areas and connections involved in the tactile -#' function of the visual cortex by network analysis. *European -#' Journal of Neuroscience*, 23(7): 1919-1930, 2006. -#' \doi{10.1111/j.1460-9568.2006.04678.x} +#' @references Negyessy L., Nepusz T., Kocsis L., Bazso F.: +#' Prediction of the main cortical areas and connections involved in the tactile function of the visual cortex by network analysis. +#' *European Journal of Neuroscience*, 23(7): 1919-1930, 2006. +#' \doi{10.1111/j.1460-9568.2006.04678.x} #' @source See reference below. #' @keywords datasets NULL diff --git a/R/netzschleuder.R b/R/netzschleuder.R index b431457..a99d514 100644 --- a/R/netzschleuder.R +++ b/R/netzschleuder.R @@ -78,11 +78,12 @@ download_file <- function(zip_url, token = NULL, file, size_limit) { #' \item{`ns_graph()`}{creates an `igraph` object directly from Netzschleuder.} #' } #' -#' @param name Character. The name of the network dataset. To get a network from a collection, -#' use the format `/`. +#' @param name Character. The name of the network dataset. +#' To get a network from a collection, use the format `/`. #' @param collection Logical. If TRUE, get the metadata of a whole collection of networks. #' @param token Character. Some networks have restricted access and require a token. -#' @param size_limit Numeric. Maximum allowed file size in GB. Larger files will be prevented from being downloaded. +#' @param size_limit Numeric. Maximum allowed file size in GB. +#' Larger files will be prevented from being downloaded. #' See . #' #' @return diff --git a/R/rfid.R b/R/rfid.R index bc0d201..565a465 100644 --- a/R/rfid.R +++ b/R/rfid.R @@ -2,14 +2,11 @@ #' #' @description #' -#' Records of contacts among patients and various types of health care -#' workers in the geriatric unit of a hospital in Lyon, France, in -#' 2010, from 1pm on Monday, December 6 to 2pm on Friday, December -#' 10. Each of the 75 people in this study consented to wear RFID -#' sensors on small identification badges during this period, which made -#' it possible to record when any two of them were in face-to-face -#' contact with each other (i.e., within 1-1.5 m of each other) during -#' a 20-second interval of time. +#' Records of contacts among patients and various types of health care workers in the geriatric unit of a hospital in Lyon, France, +#' in 2010, from 1pm on Monday, December 6 to 2pm on Friday, December 10. +#' Each of the 75 people in this study consented to wear RFID sensors on small identification badges during this period, +#' which made it possible to record when any two of them were in face-to-face contact with each other +#' (i.e., within 1-1.5 m of each other) during a 20-second interval of time. #' #' #' @@ -18,21 +15,18 @@ #' @usage #' rfid #' @format -#' An igraph graph with graph attributes \sQuote{name} and -#' \sQuote{Citation}, vertex attribute \sQuote{Status} and edge attribute -#' \sQuote{Time}. +#' An igraph graph with graph attributes \sQuote{name} and \sQuote{Citation}, +#' vertex attribute \sQuote{Status} and edge attribute \sQuote{Time}. #' -#' \sQuote{Status} is the status of the person. Status codes: -#' administrative staff (ADM), medical doctor (MED), paramedical staff, -#' such as nurses or nurses' aides (NUR), and patients (PAT). +#' \sQuote{Status} is the status of the person. +#' Status codes: administrative staff (ADM), medical doctor (MED), +#' paramedical staff, such as nurses or nurses' aides (NUR), and patients (PAT). #' -#' \sQuote{Time} is the time of the encounter, it is the second when the -#' 20 second encounter terminated. +#' \sQuote{Time} is the time of the encounter, it is the second when the 20 second encounter terminated. #' @references -#' P. Vanhems, A. Barrat, C. Cattuto, J.-F. Pinton, N. Khanafer, -#' C. Regis, B.-a. Kim, B. Comte, N. Voirin: Estimating potential -#' infection transmission routes in hospital wards using wearable -#' proximity sensors. PloS One 8(9), e73970 306 (2013). +#' P. Vanhems, A. Barrat, C. Cattuto, J.-F. Pinton, N. Khanafer, C. Regis, B.-a. Kim, B. Comte, N. Voirin: +#' Estimating potential infection transmission routes in hospital wards using wearable proximity sensors. +#' PloS One 8(9), e73970 306 (2013). #' \doi{10.1371/journal.pone.0073970} #' @source #' See the reference below. diff --git a/R/yeast.R b/R/yeast.R index 3628b6d..9583f49 100644 --- a/R/yeast.R +++ b/R/yeast.R @@ -2,13 +2,11 @@ #' #' @description #' -#' Comprehensive protein-protein interaction maps promise to reveal many -#' aspects of the complex regulatory network underlying cellular -#' function. +#' Comprehensive protein-protein interaction maps promise to reveal many aspects +#' of the complex regulatory network underlying cellular function. #' -#' This data set was compiled by von Mering et al. (see reference below), -#' combining various sources. Only the interactions that have -#' \sQuote{high} and \sQuote{medium} confidence are included here. +#' This data set was compiled by von Mering et al. (see reference below), combining various sources. +#' Only the interactions that have \sQuote{high} and \sQuote{medium} confidence are included here. #' #' #' @@ -17,50 +15,38 @@ #' @usage #' yeast #' @format -#' An undirected `igraph` graph object. Its graph attributes: -#' \sQuote{name}, \sQuote{Citation}, \sQuote{Author}, -#' \sQuote{URL}. \sQuote{Classes}. The \sQuote{Classes} -#' attribute contain the key for the classification labels of the -#' proteins, in a data frame, the original MIPS categories are given -#' after the semicolon: +#' An undirected `igraph` graph object. +#' Its graph attributes: \sQuote{name}, \sQuote{Citation}, \sQuote{Author}, \sQuote{URL}. \sQuote{Classes}. +#' The \sQuote{Classes} attribute contain the key for the classification labels of the proteins, +#' in a data frame, the original MIPS categories are given after the semicolon: #' \describe{ #' \item{E}{energy production; energy} #' \item{G}{aminoacid metabolism; aminoacid metabolism} #' \item{M}{other metabolism; all remaining metabolism categories} #' \item{P}{translation; protein synthesis} -#' \item{T}{transcription; transcription, but without subcategory -#' \sQuote{transcriptional control}} -#' \item{B}{transcriptional control; subcategory -#' \sQuote{transcriptional control}} -#' \item{F}{protein fate; protein fate (folding, modification, -#' destination)} -#' \item{O}{cellular organization; cellular transport and transport -#' mechanisms} -#' \item{A}{transport and sensing; categories \sQuote{transport -#' facilitation} and \sQuote{regulation of / interaction with -#' cellular environment}} +#' \item{T}{transcription; transcription, but without subcategory \sQuote{transcriptional control}} +#' \item{B}{transcriptional control; subcategory \sQuote{transcriptional control}} +#' \item{F}{protein fate; protein fate (folding, modification, destination)} +#' \item{O}{cellular organization; cellular transport and transport mechanisms} +#' \item{A}{transport and sensing; +#' categories \sQuote{transport facilitation} and \sQuote{regulation of / interaction with cellular environment}} #' \item{R}{stress and defense; cell rescue, defense and virulence} #' \item{D}{genome maintenance; DNA processing and cell cycle} -#' \item{C}{cellular fate / organization; categories \sQuote{cell fate} -#' and \sQuote{cellular communication / signal transduction} and -#' \sQuote{control of cellular organization}} -#' \item{U}{uncharacterized; categories \sQuote{not yet clear-cut} and -#' \sQuote{uncharacterized}} +#' \item{C}{cellular fate / organization; +#' categories \sQuote{cell fate} and \sQuote{cellular communication / signal transduction} +#' and \sQuote{control of cellular organization}} +#' \item{U}{uncharacterized; categories \sQuote{not yet clear-cut} and \sQuote{uncharacterized}} #' } #' -#' Vertex attributes: \sQuote{name}, \sQuote{Description}, -#' \sQuote{Class}, the last one contains the class of the protein, -#' accoring to the classification above. +#' Vertex attributes: \sQuote{name}, \sQuote{Description}, \sQuote{Class}, +#' the last one contains the class of the protein, accoring to the classification above. #' -#' Note that some proteins in the network did not appear in the -#' annotation files, the \sQuote{Class} and \sQuote{Description} -#' attributes are `NA` for these. +#' Note that some proteins in the network did not appear in the annotation files, +#' the \sQuote{Class} and \sQuote{Description} attributes are `NA` for these. #' @references -#' Comparative assessment of large-scale data sets of protein-protein -#' interactions. Christian von Mering, Roland Krause, Berend Snel, -#' Michael Cornell, Stephen G. Oliver, Stanley Fields and Peer -#' Bork. *Nature* 417, 399-403 (2002) -#' @source The data was downloaded from -#' . +#' Comparative assessment of large-scale data sets of protein-protein interactions. +#' Christian von Mering, Roland Krause, Berend Snel, Michael Cornell, Stephen G. Oliver, Stanley Fields and Peer Bork. +#' *Nature* 417, 399-403 (2002) +#' @source The data was downloaded from . #' @keywords datasets NULL diff --git a/README.Rmd b/README.Rmd index 9ce3198..c5543bc 100644 --- a/README.Rmd +++ b/README.Rmd @@ -3,9 +3,8 @@ output: cynkratemplate::readme_document --- + Edit that file and render it the usual way: rmarkdown::render(), devtools::build_readme(), or the Knit button. + The cynkratemplate package must be installed; it supplies the output format. --> ```{r, setup, echo = FALSE, message = FALSE} @@ -39,8 +38,8 @@ From CRAN: install.packages("igraphdata") ``` -You can install the development version from Github, using the -[devtools package](https://github.com/hadley/devtools): +You can install the development version from Github, +using the [devtools package](https://github.com/hadley/devtools): ```{r, eval = FALSE} devtools::install_github("igraph/igraphdata") @@ -57,5 +56,4 @@ data(package = "igraphdata") # License -CC BY-SA 4.0, plus see [LICENSE](LICENSE) for the licenses of the -individual data sets. +CC BY-SA 4.0, plus see [LICENSE](LICENSE) for the licenses of the individual data sets. diff --git a/README.md b/README.md index f593f2e..92c3744 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,7 @@ + Edit that file and render it the usual way: rmarkdown::render(), devtools::build_readme(), or the Knit button. + The cynkratemplate package must be installed; it supplies the output format. --> # Data sets for the igraph R package @@ -20,8 +19,8 @@ From CRAN: install.packages("igraphdata") ``` -You can install the development version from Github, using the -[devtools package](https://github.com/hadley/devtools): +You can install the development version from Github, +using the [devtools package](https://github.com/hadley/devtools): ``` r devtools::install_github("igraph/igraphdata") @@ -52,5 +51,4 @@ data(package = "igraphdata") # License -CC BY-SA 4.0, plus see [LICENSE](LICENSE) for the licenses of the -individual data sets. +CC BY-SA 4.0, plus see [LICENSE](LICENSE) for the licenses of the individual data sets. diff --git a/index.md b/index.md index c35c4b6..e09c2ec 100644 --- a/index.md +++ b/index.md @@ -1,9 +1,8 @@ + Edit that file and render it the usual way: rmarkdown::render(), devtools::build_readme(), or the Knit button. + The cynkratemplate package must be installed; it supplies the output format. --> # Data sets for the igraph R package @@ -21,8 +20,8 @@ From CRAN: install.packages("igraphdata") ``` -You can install the development version from Github, using the -[devtools package](https://github.com/hadley/devtools): +You can install the development version from Github, +using the [devtools package](https://github.com/hadley/devtools): ``` r devtools::install_github("igraph/igraphdata") diff --git a/man/Koenigsberg.Rd b/man/Koenigsberg.Rd index 680b522..cb2e263 100644 --- a/man/Koenigsberg.Rd +++ b/man/Koenigsberg.Rd @@ -5,35 +5,29 @@ \alias{Koenigsberg} \title{Bridges of Koenigsberg from Euler's times} \format{ -An undirected \code{igraph} graph object with vertex attributes -\sQuote{name} and \sQuote{Euler_letter}, the latter is the notation -from Eulers original paper; and edge attributes \sQuote{name} (the name -of the bridge) and \sQuote{Euler_letter}, again, Euler's notation -from his paper. +An undirected \code{igraph} graph object with vertex attributes \sQuote{name} and \sQuote{Euler_letter}, +the latter is the notation from Eulers original paper; +and edge attributes \sQuote{name} (the name of the bridge) and \sQuote{Euler_letter}, again, Euler's notation from his paper. This dataset is in the public domain. } \source{ -Wikipedia, -\url{https://en.wikipedia.org/wiki/Seven_Bridges_of_K\%C3\%B6nigsberg} +Wikipedia, \url{https://en.wikipedia.org/wiki/Seven_Bridges_of_K\%C3\%B6nigsberg} } \usage{ Koenigsberg } \description{ -The Seven Bridges of Koenigsberg is a notable historical problem in -mathematics. Its negative resolution by Leonhard Euler in 1735 laid -the foundations of graph theory and presaged the idea of topology. +The Seven Bridges of Koenigsberg is a notable historical problem in mathematics. +Its negative resolution by Leonhard Euler in 1735 laid the foundations of graph theory and presaged the idea of topology. -The city of Koenigsberg in Prussia (now Kaliningrad, Russia) was set on -both sides of the Pregel River, and included two large islands which -were connected to each other and the mainland by seven bridges +The city of Koenigsberg in Prussia (now Kaliningrad, Russia) was set on both sides of the Pregel River, +and included two large islands which were connected to each other and the mainland by seven bridges -The problem was to find a walk through the city that would cross each -bridge once and only once. The islands could not be reached by any route -other than the bridges, and every bridge must have been crossed -completely every time (one could not walk half way onto the bridge and -then turn around and later cross the other half from the other side). +The problem was to find a walk through the city that would cross each bridge once and only once. +The islands could not be reached by any route other than the bridges, +and every bridge must have been crossed completely every time +(one could not walk half way onto the bridge and then turn around and later cross the other half from the other side). Euler proved that the problem has no solution. } diff --git a/man/UKfaculty.Rd b/man/UKfaculty.Rd index 0965cbd..04c2215 100644 --- a/man/UKfaculty.Rd +++ b/man/UKfaculty.Rd @@ -5,12 +5,10 @@ \alias{UKfaculty} \title{Friendship network of a UK university faculty} \format{ -A directed \code{igraph} graph object with vertex attribute -\sQuote{Group}, the numeric id of the school affiliation, and edge -attribute \sQuote{weight}, i.e. the graph is weighted. +A directed \code{igraph} graph object with vertex attribute \sQuote{Group}, the numeric id of the school affiliation, +and edge attribute \sQuote{weight}, i.e. the graph is weighted. -This dataset is licensed under a Creative Commons -Attribution-Share Alike 2.0 UK: England & Wales License, +This dataset is licensed under a Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License, see \url{http://creativecommons.org/licenses/by-sa/2.0/uk/} for details. Please cite the reference below if you use this dataset. } @@ -21,16 +19,14 @@ See reference below. UKfaculty } \description{ -The personal friendship network of a faculty of a UK -university, consisting of 81 vertices (individuals) and 817 directed -and weighted connections. The school affiliation of each individual is -stored as a vertex attribute. This dataset can serve as a testbed for -community detection algorithms. +The personal friendship network of a faculty of a UK university, +consisting of 81 vertices (individuals) and 817 directed and weighted connections. +The school affiliation of each individual is stored as a vertex attribute. +This dataset can serve as a testbed for community detection algorithms. } \references{ -Nepusz T., Petroczi A., Negyessy L., Bazso F.: Fuzzy -communities and the concept of bridgeness in complex -networks. Physical Review E 77:016107, 2008. +Nepusz T., Petroczi A., Negyessy L., Bazso F.: Fuzzy communities and the concept of bridgeness in complex networks. +Physical Review E 77:016107, 2008. \doi{10.1103/PhysRevE.77.016107} } \keyword{datasets} diff --git a/man/USairports.Rd b/man/USairports.Rd index 0f72cc6..8a70d57 100644 --- a/man/USairports.Rd +++ b/man/USairports.Rd @@ -5,48 +5,40 @@ \alias{USairports} \title{US airport network, 2010 December} \format{ -A directed \code{igraph} graph object, with multiple edges. It has a -\sQuote{name} graph attribute, and several vertex and edge -attributes. The vertex attributes: +A directed \code{igraph} graph object, with multiple edges. +It has a \sQuote{name} graph attribute, and several vertex and edge attributes. +The vertex attributes: \describe{ -\item{name}{Symbolic vertex name, this is the three letter IATA -airport code.} +\item{name}{Symbolic vertex name, this is the three letter IATA airport code.} \item{City}{City and state, where the airport is located.} \item{Position}{Position of the airport, in WGS coordinates.} } Edge attributes: \describe{ -\item{Carrier}{Name of the airline. The network includes both -domestic and international carriers that performed at least one -flight in December of 2010.} -\item{Departures}{The number of departures (for a given airline and -aircraft type.} -\item{Seats}{The total number of seats available on the flights -carried out by a given airline, using a given aircraft type.} -\item{Passengers}{The total number of passangers on the flights -carried out by a given airline, using a given aircraft type.} +\item{Carrier}{Name of the airline. +The network includes both domestic and international carriers that performed at least one flight in December of 2010.} +\item{Departures}{The number of departures (for a given airline and aircraft type.} +\item{Seats}{The total number of seats available on the flights carried out by a given airline, using a given aircraft type.} +\item{Passengers}{The total number of passangers on the flights carried out by a given airline, using a given aircraft type.} \item{Aircraft}{Type of the aircraft.} \item{Distance}{The distance between the two airports, in miles.} } } \source{ -Most of this information was downloaded from The Research and -Innovative Technology Administration (RITA). See -\url{http://www.rita.dot.gov/about_rita/} for details. The airport -position information was collected from Wikipedia and other public -online sources. +Most of this information was downloaded from The Research and Innovative Technology Administration (RITA). +See \url{http://www.rita.dot.gov/about_rita/} for details. +The airport position information was collected from Wikipedia and other public online sources. } \usage{ USairports } \description{ -The network of passanger flights between airports in the United -States. The data set was compiled based on flights in 2010 -December. This network is directed and edge directions correspond to -flight directions. Each edge is specific to a single carrier aircraft -type. Multiple carriers between the same two airports are denoted by -multiple edges. +The network of passanger flights between airports in the United States. +The data set was compiled based on flights in 2010 December. +This network is directed and edge directions correspond to flight directions. +Each edge is specific to a single carrier aircraft type. +Multiple carriers between the same two airports are denoted by multiple edges. See information about the included meta-data below. } diff --git a/man/enron.Rd b/man/enron.Rd index 747bd01..abaab97 100644 --- a/man/enron.Rd +++ b/man/enron.Rd @@ -8,11 +8,9 @@ A directed \code{igraph} graph object. Graph attributes: \itemize{ -\item \sQuote{LDC_names} The names of the 32 LDC catagories the emails -are classfied into by Michael W. Berry +\item \sQuote{LDC_names} The names of the 32 LDC catagories the emails are classfied into by Michael W. Berry (\url{http://www.cis.jhu.edu/~parky/Enron/Anno_Topic_exp_LDC.pdf}) -\item \sQuote{LDC_desc} Longer descriptions of the 32 LDC -categories. +\item \sQuote{LDC_desc} Longer descriptions of the 32 LDC categories. \item \sQuote{Citation} Additionally, see also the references below. \item \sQuote{name} } @@ -24,22 +22,18 @@ Vertex attributes: \itemize{ } Edge attributes: \itemize{ -\item \sQuote{Time} When the email was sent. Note that some time -labels are from 1979, these are certainly wrong and you might want -to remove them before analyses that include time. -\item \sQuote{Reciptype} Recipient type, \sQuote{to}, \sQuote{cc} or -\sQuote{bcc}. -\item \sQuote{Topic} Assigned based on 3-means clustering of -randomly selected 3,120 out of all 125,409 messages, then NN -classification for the whole corpus. Note that topic 0 means an -outlier, e.g., too few words or all meaningless numbers in the -message body. -\item \sQuote{LDC_topic} Assigned based on Michael W. Berry's 2001 -\dQuote{Annotated (by Topic) Enron Email Data Set.} +\item \sQuote{Time} When the email was sent. +Note that some time labels are from 1979, +these are certainly wrong and you might want to remove them before analyses that include time. +\item \sQuote{Reciptype} Recipient type, \sQuote{to}, \sQuote{cc} or \sQuote{bcc}. +\item \sQuote{Topic} Assigned based on 3-means clustering of randomly selected 3,120 out of all 125,409 messages, +then NN classification for the whole corpus. +Note that topic 0 means an outlier, e.g., too few words or all meaningless numbers in the message body. +\item \sQuote{LDC_topic} Assigned based on Michael W. Berry's 2001 \dQuote{Annotated (by Topic) Enron Email Data Set.} (\url{http://www.cis.jhu.edu/~parky/Enron/Anno_Topic_exp_LDC.pdf}) -There are 32 topics. Topic "0" means an outlier, e.g., too few words -or all meaningless numbers in the message body, etc. Topic "-1" -means there is no matching topic. +There are 32 topics. +Topic "0" means an outlier, e.g., too few words or all meaningless numbers in the message body, etc. +Topic "-1" means there is no matching topic. } } \source{ @@ -53,39 +47,31 @@ An Enron email dataset has been made public by the U.S. Department of Justice. } \references{ C.E. Priebe, J.M. Conroy, D.J. Marchette, and Y. Park, -Scan Statistics on Enron Graphs Computational and Mathematical -Organization Theory, Volume 11, Number 3, p229 - 247, October 2005, -Springer Science+Business Media B.V. \doi{10.1007/s10588-005-5378-z} +Scan Statistics on Enron Graphs Computational and Mathematical Organization Theory, +Volume 11, Number 3, p229 - 247, October 2005, Springer Science+Business Media B.V. \doi{10.1007/s10588-005-5378-z} C.E. Priebe, J.M. Conroy, D.J. Marchette, and Y. Park, -Scan Statistics on Enron Graphs, SIAM International Conference on -Data Mining, Workshop on Link Analysis, Counterterrorism and Security, -Newport Beach, California, April 23, 2005. +Scan Statistics on Enron Graphs, SIAM International Conference on Data Mining, +Workshop on Link Analysis, Counterterrorism and Security, Newport Beach, California, April 23, 2005. -Gina Kolata, Enron Offers an Unlikely Boost to E-Mail Surveillance, -New York Times, Week in Review, May 22, 2005. +Gina Kolata, Enron Offers an Unlikely Boost to E-Mail Surveillance, New York Times, Week in Review, May 22, 2005. -C.E. Priebe, Scan Statistics on Enron Graphs, IPAM Summer Graduate -School: Intelligent Extraction of Information from Graphs and High -Dimensional Data, UCLA, July 11-29, 2005. +C.E. Priebe, Scan Statistics on Enron Graphs, +IPAM Summer Graduate School: Intelligent Extraction of Information from Graphs and High Dimensional Data, +UCLA, July 11-29, 2005. -C.E. Priebe, Scan Statistics on Enron Graphs, 2005 Fall Department -of Applied Mathematics and Statistics Seminars, September 15, 2005, -The Johns Hopkins University. +C.E. Priebe, Scan Statistics on Enron Graphs, +2005 Fall Department of Applied Mathematics and Statistics Seminars, September 15, 2005, The Johns Hopkins University. -Y. Park, C.E. Priebe, D.J. Marchette, Scan Statistics on Enron -Hypergraphs, Interface 2008, Durham, North Carolina, May 21, 2008, +Y. Park, C.E. Priebe, D.J. Marchette, Scan Statistics on Enron Hypergraphs, Interface 2008, Durham, North Carolina, May 21, 2008, -Y. Park, C.E. Priebe, D.J. Marchette, Anomaly Detection using Scan -Statistics on Enron Graphs and Hypergraphs, The Satellite Workshop of -the IASC 2008 Conference, Seoul, Korea, December 1-3, 2008. +Y. Park, C.E. Priebe, D.J. Marchette, Anomaly Detection using Scan Statistics on Enron Graphs and Hypergraphs, +The Satellite Workshop of the IASC 2008 Conference, Seoul, Korea, December 1-3, 2008. -Y. Park, C.E. Priebe, D.J. Marchette, A. Youssef, Anomaly Detection -using Scan Statistics on Time Series of Hypergraphs, Workshop on Link -Analysis, Counterterrorism and Security at the SIAM International -Conference on Data Mining, Sparks, Nevada, May 1-3, 2009, +Y. Park, C.E. Priebe, D.J. Marchette, A. Youssef, Anomaly Detection using Scan Statistics on Time Series of Hypergraphs, +Workshop on Link Analysis, Counterterrorism and Security at the SIAM International Conference on Data Mining, +Sparks, Nevada, May 1-3, 2009, -Y. Park, C.E. Priebe, A. Youssef, Anomaly Detection in Time Series of -Graphs using Fusion of Invariants, Computational and Mathematical -Organization Theory, submitted, 2010. \doi{10.1109/JSTSP.2012.2233712} +Y. Park, C.E. Priebe, A. Youssef, Anomaly Detection in Time Series of Graphs using Fusion of Invariants, +Computational and Mathematical Organization Theory, submitted, 2010. \doi{10.1109/JSTSP.2012.2233712} } diff --git a/man/foodwebs.Rd b/man/foodwebs.Rd index df0948b..9953028 100644 --- a/man/foodwebs.Rd +++ b/man/foodwebs.Rd @@ -5,13 +5,12 @@ \alias{foodwebs} \title{A collection of food webs} \format{ -A named list of directed \code{igraph} graph objects. Here are the -list of the graphs included: +A named list of directed \code{igraph} graph objects. +Here are the list of the graphs included: \describe{ \item{\sQuote{ChesLower}}{Lower Chesapeake Bay in Summer. -Reference: Hagy, J.D. (2002) Eutrophication, hypoxia and -trophic transfer efficiency in Chesapeake Bay PhD Dissertation, +Reference: Hagy, J.D. (2002) Eutrophication, hypoxia and trophic transfer efficiency in Chesapeake Bay PhD Dissertation, University of Maryland at College Park (USA), 446 pp.} \item{\sQuote{ChesMiddle}}{Middle Chesapeake Bay in Summer. @@ -21,95 +20,77 @@ Reference: same as for \sQuote{ChesLower}.} Reference: same as for \sQuote{ChesLower}.} \item{\sQuote{Chesapeake}}{Chesapeake Bay Mesohaline Network. -Reference: Baird D. & Ulanowicz R.E. (1989) The seasonal dynamics -of the Chesapeake Bay ecosystem. Ecological Monographs 59:329-364.} +Reference: Baird D. & Ulanowicz R.E. (1989) The seasonal dynamics of the Chesapeake Bay ecosystem. +Ecological Monographs 59:329-364.} \item{\sQuote{CrystalC}}{Crystal River Creek (Control). -Reference: Homer, M. and W.M. Kemp. Unpublished Ms. See also -Ulanowicz, R.E. 1986. Growth and Development: Ecosystems -Phenomenology. Springer, New York. pp 69-79.} +Reference: Homer, M. and W.M. Kemp. Unpublished Ms. +See also Ulanowicz, R.E. 1986. Growth and Development: Ecosystems Phenomenology. Springer, New York. pp 69-79.} \item{\sQuote{CrystalD}}{Crystal River Creek (Delta Temp). Reference: same as for \sQuote{CrystalD}.} \item{\sQuote{Maspalomas}}{Charca de Maspalomas. -Reference: Almunia, J., G. Basterretxea, J. Aristegui, and -R.E. Ulanowicz. (1999) Benthic- Pelagic switching in a coastal -subtropical lagoon. Estuarine, Coastal and Shelf Science -49:363-384.} +Reference: Almunia, J., G. Basterretxea, J. Aristegui, and R.E. Ulanowicz. (1999) +Benthic- Pelagic switching in a coastal subtropical lagoon. Estuarine, Coastal and Shelf Science 49:363-384.} \item{\sQuote{Michigan}}{Lake Michigan Control network. -Reference: Krause, A. and D. Mason. (In preparation.) A. Krause, -PhD. Dissertation, Michigan State University. Ann Arbor, MI. USA.} +Reference: Krause, A. and D. Mason. (In preparation.) +A. Krause, PhD. Dissertation, Michigan State University. Ann Arbor, MI. USA.} \item{\sQuote{Mondego}}{Mondego Estuary - Zostrea site. -Reference: Patricio, J. (In Preparation) Master's -Thesis. University of Coimbra, Coimbra, Portugal.} +Reference: Patricio, J. (In Preparation) Master's Thesis. University of Coimbra, Coimbra, Portugal.} \item{\sQuote{Narragan}}{Narragansett Bay Model. -Reference: Monaco, M.E. and R.E. Ulanowicz. (1997) Comparative -ecosystem trophic structure of three U.S. Mid-Atlantic -estuaries. Mar. Ecol. Prog. Ser. 161:239-254.} +Reference: Monaco, M.E. and R.E. Ulanowicz. (1997) Comparative ecosystem trophic structure of three U.S. Mid-Atlantic estuaries. +Mar. Ecol. Prog. Ser. 161:239-254.} \item{\sQuote{Rhode}}{Rhode River Watershed - Water Budget. -Reference: Correll, D. (Unpublished manuscript) Smithsonian -Institute, Chesapeake Bay Center for Environmental Research, +Reference: Correll, D. (Unpublished manuscript) Smithsonian Institute, Chesapeake Bay Center for Environmental Research, Edgewater, Maryland 21037-0028 USA.} \item{\sQuote{StMarks}}{St. Marks River (Florida) Flow network. Reference: Baird, D., J. Luczkovich and R. R. Christian. (1998) -Assessment of spatial and temporal variability in ecosystem -attributes of the St Marks National Wildlife Refuge, Apalachee Bay, -Florida. Estuarine, Coastal, and Shelf Science 47: 329-349.} +Assessment of spatial and temporal variability in ecosystem attributes of the St Marks National Wildlife Refuge, +Apalachee Bay, Florida. Estuarine, Coastal, and Shelf Science 47: 329-349.} \item{\sQuote{baydry}}{Florida Bay Trophic Exchange Matrix, dry season. -Reference: Ulanowicz, R. E., C. Bondavalli, and -M. S. Egnotovich. 1998. Network analysis of trophic dynamics in -South Florida ecosystems, FY 97: the Florida Bay ecosystem. Annual -Report to the United States Geological Service Biological Resources -Division, University of Miami Coral Gables, [UM-CES] CBL 98-123, -Maryland System Center for Environmental Science, Chesapeake -Biological Laboratory, Maryland, USA.} +Reference: Ulanowicz, R. E., C. Bondavalli, and M. S. Egnotovich. 1998. +Network analysis of trophic dynamics in South Florida ecosystems, FY 97: the Florida Bay ecosystem. +Annual Report to the United States Geological Service Biological Resources Division, University of Miami Coral Gables, +[UM-CES] CBL 98-123, Maryland System Center for Environmental Science, Chesapeake Biological Laboratory, Maryland, USA.} \item{\sQuote{baywet}}{Florida Bay Trophic Exchange Matrix, wet season. Reference: same as for \sQuote{baydry}.} \item{\sQuote{cypdry}}{Cypress, dry season. -Reference: Ulanowicz, R. E., C. Bondavalli, and -M. S. Egnotovich. 1997. Network analysis of trophic dynamics in -South Florida ecosystems, FY 96: the cypress wetland -ecosystem. Annual Report to the United States Geological Service -Biological Resources Division, University of Miami Coral Gables, -[UM-CES] CBL 97-075, Maryland System Center for Environmental -Science, Chesapeake Biological Laboratory.} +Reference: Ulanowicz, R. E., C. Bondavalli, and M. S. Egnotovich. 1997. +Network analysis of trophic dynamics in South Florida ecosystems, FY 96: the cypress wetland ecosystem. +Annual Report to the United States Geological Service Biological Resources Division, University of Miami Coral Gables, +[UM-CES] CBL 97-075, Maryland System Center for Environmental Science, Chesapeake Biological Laboratory.} \item{\sQuote{cypwet}}{Cypress, wet season. Reference: same as for \sQuote{cypdry}.} \item{\sQuote{gramdry}}{Everglades Graminoids - Dry Season. -Reference: Ulanowicz, R. E., J. J. Heymans, and -M. S. Egnotovich. 2000. Network analysis of trophic dynamics in -South Florida ecosystems, FY 99: the graminoid ecosystem. Technical -Report TS-191-99, Maryland System Center for Environmental Science, -Chesapeake Biological Laboratory, Maryland, USA.} +Reference: Ulanowicz, R. E., J. J. Heymans, and M. S. Egnotovich. 2000. +Network analysis of trophic dynamics in South Florida ecosystems, FY 99: the graminoid ecosystem. +Technical Report TS-191-99, Maryland System Center for Environmental Science, Chesapeake Biological Laboratory, Maryland, USA.} \item{\sQuote{gramwet}}{Everglades Graminoids - Wet Season. Reference: same as for \sQuote{gramdry}.} \item{\sQuote{mangdry}}{Mangrove Estuary, Dry Season. -Reference: Ulanowicz, R. E., C. Bondavalli, J. J. Heymans, and -M. S. Egnotovich. 1999. Network analysis of trophic dynamics in -South Florida ecosystems, FY 98: the mangrove ecosystem. Technical -Report TS-191-99, Maryland System Center for Environmental Science, -Chesapeake Biological Laboratory, Maryland, USA.} +Reference: Ulanowicz, R. E., C. Bondavalli, J. J. Heymans, and M. S. Egnotovich. 1999. +Network analysis of trophic dynamics in South Florida ecosystems, FY 98: the mangrove ecosystem. +Technical Report TS-191-99, Maryland System Center for Environmental Science, Chesapeake Biological Laboratory, Maryland, USA.} \item{\sQuote{mangwet}}{Mangrove Estuary, Wet Season. Reference: same as for \sQuote{mangdry}.} } -Each graph has the following vertex attributes: \sQuote{name} is the -name of the species, \sQuote{ECO} is the type of the node, and -integer value between one and five, meaning: +Each graph has the following vertex attributes: \sQuote{name} is the name of the species, +\sQuote{ECO} is the type of the node, and integer value between one and five, meaning: \enumerate{ \item Living/producing compartment \item Other compartment @@ -117,27 +98,22 @@ integer value between one and five, meaning: \item Output \item Respiration. } -The \sQuote{Biomass} vertex attribute contains the biomass of the -species. +The \sQuote{Biomass} vertex attribute contains the biomass of the species. -Edges are weighted, and the weights denote energy flux between the -species involved. +Edges are weighted, and the weights denote energy flux between the species involved. -The graphs also contain some informative graph attributes: -\sQuote{Author}, \sQuote{Citation}, \sQuote{URL}, and -\sQuote{name}. +The graphs also contain some informative graph attributes: \sQuote{Author}, \sQuote{Citation}, \sQuote{URL}, and \sQuote{name}. } \source{ -See references for the individual webs above. The data itself -was downloaded from -\url{http://vlado.fmf.uni-lj.si/pub/networks/data/bio/foodweb/foodweb.htm}. +See references for the individual webs above. +The data itself was downloaded from \url{http://vlado.fmf.uni-lj.si/pub/networks/data/bio/foodweb/foodweb.htm}. } \usage{ foodwebs } \description{ -A list of graphs. Each one is a food web, i.e. a directed -graph of predator-prey relationships. +A list of graphs. +Each one is a food web, i.e. a directed graph of predator-prey relationships. } \references{ See them above. diff --git a/man/immuno.Rd b/man/immuno.Rd index e8e0e08..1d7a2ab 100644 --- a/man/immuno.Rd +++ b/man/immuno.Rd @@ -16,15 +16,14 @@ See reference below. immuno } \description{ -The undirected and connected network of interactions -in the immunoglobulin protein. It is made up of 1316 vertices -representing amino-acids and an edge is drawn between two -amino-acids if the shortest distance between their C_alpha atoms -is smaller than the threshold value \eqn{\theta=8}{theta=8} Angstrom. +The undirected and connected network of interactions in the immunoglobulin protein. +It is made up of 1316 vertices representing amino-acids +and an edge is drawn between two amino-acids +if the shortest distance between their C_alpha atoms is smaller than the threshold value \eqn{\theta=8}{theta=8} Angstrom. } \references{ -D. Gfeller, Simplifying complex networks: from a clustering to a -coarse graining strategy, \emph{PhD Thesis EPFL}, no 3888, 2007. +D. Gfeller, Simplifying complex networks: from a clustering to a coarse graining strategy, +\emph{PhD Thesis EPFL}, no 3888, 2007. \url{http://library.epfl.ch/theses/?nr=3888} } \keyword{datasets} diff --git a/man/karate.Rd b/man/karate.Rd index 0c4dcf6..6db9ac7 100644 --- a/man/karate.Rd +++ b/man/karate.Rd @@ -5,13 +5,13 @@ \alias{karate} \title{Zachary's karate club network} \format{ -An undirected \code{igraph} graph object. Vertex no. 1 is Mr. Hi, -vertex no. 34 corresponds to John A. +An undirected \code{igraph} graph object. +Vertex no. 1 is Mr. Hi, vertex no. 34 corresponds to John A. Graph attributes: \sQuote{name}, \sQuote{Citation}, \sQuote{Author}. -Vertex attributes: \sQuote{name}, \sQuote{Faction}, \sQuote{color} is -the same as \sQuote{Faction}, \sQuote{label} are short labels for plotting. +Vertex attributes: \sQuote{name}, \sQuote{Faction}, \sQuote{color} is the same as \sQuote{Faction}, +\sQuote{label} are short labels for plotting. Edge attribute: \sQuote{weight}. } @@ -22,44 +22,36 @@ See reference below. karate } \description{ -Social network between members of a university karate club, led by -president John A. and karate instructor Mr. Hi (pseudonyms). +Social network between members of a university karate club, led by president John A. and karate instructor Mr. Hi (pseudonyms). -The edge weights are the number of common activities the club -members took part of. These activities were: +The edge weights are the number of common activities the club members took part of. +These activities were: \enumerate{ \item Association in and between academic classes at the university. -\item Membership in Mr. Hi's private karate studio on the east side -of the city where Mr. Hi taught nights as a part-time instructor. -\item Membership in Mr. Hi's private karate studio on the east side -of the city, where many of his supporters worked out on weekends. -\item Student teaching at the east-side karate studio referred to in -(2). This is different from (2) in that student teachers interacted -with each other, but were prohibited from interacting with their -students. -\item Interaction at the university rathskeller, located in the same -basement as the karate club's workout area. -\item Interaction at a student-oriented bar located across the -street from the university campus. -\item Attendance at open karate tournaments held through the area at -private karate studios. -\item Attendance at intercollegiate karate tournaments held at local -universities. Since both open and intercollegiate tournaments were -held on Saturdays, attendance at both was impossible. +\item Membership in Mr. Hi's private karate studio on the east side of the city +where Mr. Hi taught nights as a part-time instructor. +\item Membership in Mr. Hi's private karate studio on the east side of the city, +where many of his supporters worked out on weekends. +\item Student teaching at the east-side karate studio referred to in (2). +This is different from (2) in that student teachers interacted with each other, +but were prohibited from interacting with their students. +\item Interaction at the university rathskeller, located in the same basement as the karate club's workout area. +\item Interaction at a student-oriented bar located across the street from the university campus. +\item Attendance at open karate tournaments held through the area at private karate studios. +\item Attendance at intercollegiate karate tournaments held at local universities. +Since both open and intercollegiate tournaments were held on Saturdays, attendance at both was impossible. } -Zachary studied conflict and fission in this network, as the karate -club was split into two separate clubs, after long disputes between -two factions of the club, one led by John A., the other by Mr. Hi. +Zachary studied conflict and fission in this network, +as the karate club was split into two separate clubs, after long disputes between two factions of the club, +one led by John A., the other by Mr. Hi. -The \sQuote{Faction} vertex attribute gives the faction memberships of -the actors. After the split of the club, club members chose their -new clubs based on their factions, except actor no. 9, who was in John -A.'s faction but chose Mr. Hi's club. +The \sQuote{Faction} vertex attribute gives the faction memberships of the actors. +After the split of the club, club members chose their new clubs based on their factions, +except actor no. 9, who was in John A.'s faction but chose Mr. Hi's club. } \references{ -Wayne W. Zachary. An Information Flow Model for Conflict and Fission -in Small Groups. \emph{Journal of Anthropological Research} Vol. 33, -No. 4 452-473 \doi{10.1086/jar.33.4.3629752} +Wayne W. Zachary. An Information Flow Model for Conflict and Fission in Small Groups. +\emph{Journal of Anthropological Research} Vol. 33, No. 4 452-473 \doi{10.1086/jar.33.4.3629752} } \keyword{datasets} diff --git a/man/kite.Rd b/man/kite.Rd index 6af187b..127a408 100644 --- a/man/kite.Rd +++ b/man/kite.Rd @@ -5,9 +5,8 @@ \alias{kite} \title{Krackhardt's kite} \format{ -An undirected igraph graph with graph attributes \code{name}, -\code{layout}, \code{Citation}, \code{Author}, \code{URL}, and vertex -attributes \code{label}, \code{name} and \code{Firstname}. +An undirected igraph graph with graph attributes \code{name}, \code{layout}, \code{Citation}, \code{Author}, \code{URL}, +and vertex attributes \code{label}, \code{name} and \code{Firstname}. } \source{ \url{http://www.orgnet.com/sna.html} @@ -17,13 +16,11 @@ kite } \description{ Krackhardt's kite is a fictional social network with ten actors. -It is a small (though not the smallest possible) graph for which the most -central actors are different according to the three classic centrality -measures: degree, closeness and betweenness. +It is a small (though not the smallest possible) graph for which the most central actors are different +according to the three classic centrality measures: degree, closeness and betweenness. } \references{ -Assessing the Political Landscape: Structure, Cognition, and Power in -Organizations. David Krackhardt. \emph{Admin. Sci. Quart.} 35, 342-369, -1990. \doi{10.2307/2393394} +Assessing the Political Landscape: Structure, Cognition, and Power in Organizations. +David Krackhardt. \emph{Admin. Sci. Quart.} 35, 342-369, 1990. \doi{10.2307/2393394} } \keyword{datasets} diff --git a/man/macaque.Rd b/man/macaque.Rd index 272e270..e8637eb 100644 --- a/man/macaque.Rd +++ b/man/macaque.Rd @@ -5,11 +5,9 @@ \alias{macaque} \title{Visuotactile brain areas and connections} \format{ -A directed \code{igraph} graph object with vertex attributes -\sQuote{name} and \sQuote{shape}. +A directed \code{igraph} graph object with vertex attributes \sQuote{name} and \sQuote{shape}. -This dataset is licensed under a Creative Commons -Attribution-Share Alike 2.0 UK: England & Wales License, +This dataset is licensed under a Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License, see \url{http://creativecommons.org/licenses/by-sa/2.0/uk/} for details. Please cite the reference below if you use this dataset. } @@ -20,15 +18,13 @@ See reference below. macaque } \description{ -Graph model of the visuotactile brain areas and connections of the -macaque monkey. The model consists of 45 areas and 463 directed -connections. +Graph model of the visuotactile brain areas and connections of the macaque monkey. +The model consists of 45 areas and 463 directed connections. } \references{ -Negyessy L., Nepusz T., Kocsis L., Bazso F.: Prediction of -the main cortical areas and connections involved in the tactile -function of the visual cortex by network analysis. \emph{European -Journal of Neuroscience}, 23(7): 1919-1930, 2006. +Negyessy L., Nepusz T., Kocsis L., Bazso F.: +Prediction of the main cortical areas and connections involved in the tactile function of the visual cortex by network analysis. +\emph{European Journal of Neuroscience}, 23(7): 1919-1930, 2006. \doi{10.1111/j.1460-9568.2006.04678.x} } \keyword{datasets} diff --git a/man/netzschleuder.Rd b/man/netzschleuder.Rd index c5a30a0..5118cd0 100644 --- a/man/netzschleuder.Rd +++ b/man/netzschleuder.Rd @@ -13,14 +13,15 @@ ns_df(name, token = NULL, size_limit = 1) ns_graph(name, token = NULL, size_limit = 1) } \arguments{ -\item{name}{Character. The name of the network dataset. To get a network from a collection, -use the format \verb{/}.} +\item{name}{Character. The name of the network dataset. +To get a network from a collection, use the format \verb{/}.} \item{collection}{Logical. If TRUE, get the metadata of a whole collection of networks.} \item{token}{Character. Some networks have restricted access and require a token.} -\item{size_limit}{Numeric. Maximum allowed file size in GB. Larger files will be prevented from being downloaded. +\item{size_limit}{Numeric. Maximum allowed file size in GB. +Larger files will be prevented from being downloaded. See \url{https://networks.skewed.de/restricted}.} } \value{ diff --git a/man/rfid.Rd b/man/rfid.Rd index 1213831..84c5955 100644 --- a/man/rfid.Rd +++ b/man/rfid.Rd @@ -5,16 +5,14 @@ \alias{rfid} \title{Hospital encounter network data} \format{ -An igraph graph with graph attributes \sQuote{name} and -\sQuote{Citation}, vertex attribute \sQuote{Status} and edge attribute -\sQuote{Time}. +An igraph graph with graph attributes \sQuote{name} and \sQuote{Citation}, +vertex attribute \sQuote{Status} and edge attribute \sQuote{Time}. -\sQuote{Status} is the status of the person. Status codes: -administrative staff (ADM), medical doctor (MED), paramedical staff, -such as nurses or nurses' aides (NUR), and patients (PAT). +\sQuote{Status} is the status of the person. +Status codes: administrative staff (ADM), medical doctor (MED), +paramedical staff, such as nurses or nurses' aides (NUR), and patients (PAT). -\sQuote{Time} is the time of the encounter, it is the second when the -20 second encounter terminated. +\sQuote{Time} is the time of the encounter, it is the second when the 20 second encounter terminated. } \source{ See the reference below. @@ -24,20 +22,16 @@ Please cite it if you use this dataset in your work. rfid } \description{ -Records of contacts among patients and various types of health care -workers in the geriatric unit of a hospital in Lyon, France, in -2010, from 1pm on Monday, December 6 to 2pm on Friday, December -10. Each of the 75 people in this study consented to wear RFID -sensors on small identification badges during this period, which made -it possible to record when any two of them were in face-to-face -contact with each other (i.e., within 1-1.5 m of each other) during -a 20-second interval of time. +Records of contacts among patients and various types of health care workers in the geriatric unit of a hospital in Lyon, France, +in 2010, from 1pm on Monday, December 6 to 2pm on Friday, December 10. +Each of the 75 people in this study consented to wear RFID sensors on small identification badges during this period, +which made it possible to record when any two of them were in face-to-face contact with each other +(i.e., within 1-1.5 m of each other) during a 20-second interval of time. } \references{ -P. Vanhems, A. Barrat, C. Cattuto, J.-F. Pinton, N. Khanafer, -C. Regis, B.-a. Kim, B. Comte, N. Voirin: Estimating potential -infection transmission routes in hospital wards using wearable -proximity sensors. PloS One 8(9), e73970 306 (2013). +P. Vanhems, A. Barrat, C. Cattuto, J.-F. Pinton, N. Khanafer, C. Regis, B.-a. Kim, B. Comte, N. Voirin: +Estimating potential infection transmission routes in hospital wards using wearable proximity sensors. +PloS One 8(9), e73970 306 (2013). \doi{10.1371/journal.pone.0073970} } \keyword{datasets} diff --git a/man/yeast.Rd b/man/yeast.Rd index 4d5e484..a98d788 100644 --- a/man/yeast.Rd +++ b/man/yeast.Rd @@ -5,65 +5,51 @@ \alias{yeast} \title{Yeast protein interaction network} \format{ -An undirected \code{igraph} graph object. Its graph attributes: -\sQuote{name}, \sQuote{Citation}, \sQuote{Author}, -\sQuote{URL}. \sQuote{Classes}. The \sQuote{Classes} -attribute contain the key for the classification labels of the -proteins, in a data frame, the original MIPS categories are given -after the semicolon: +An undirected \code{igraph} graph object. +Its graph attributes: \sQuote{name}, \sQuote{Citation}, \sQuote{Author}, \sQuote{URL}. \sQuote{Classes}. +The \sQuote{Classes} attribute contain the key for the classification labels of the proteins, +in a data frame, the original MIPS categories are given after the semicolon: \describe{ \item{E}{energy production; energy} \item{G}{aminoacid metabolism; aminoacid metabolism} \item{M}{other metabolism; all remaining metabolism categories} \item{P}{translation; protein synthesis} -\item{T}{transcription; transcription, but without subcategory -\sQuote{transcriptional control}} -\item{B}{transcriptional control; subcategory -\sQuote{transcriptional control}} -\item{F}{protein fate; protein fate (folding, modification, -destination)} -\item{O}{cellular organization; cellular transport and transport -mechanisms} -\item{A}{transport and sensing; categories \sQuote{transport -facilitation} and \sQuote{regulation of / interaction with -cellular environment}} +\item{T}{transcription; transcription, but without subcategory \sQuote{transcriptional control}} +\item{B}{transcriptional control; subcategory \sQuote{transcriptional control}} +\item{F}{protein fate; protein fate (folding, modification, destination)} +\item{O}{cellular organization; cellular transport and transport mechanisms} +\item{A}{transport and sensing; +categories \sQuote{transport facilitation} and \sQuote{regulation of / interaction with cellular environment}} \item{R}{stress and defense; cell rescue, defense and virulence} \item{D}{genome maintenance; DNA processing and cell cycle} -\item{C}{cellular fate / organization; categories \sQuote{cell fate} -and \sQuote{cellular communication / signal transduction} and -\sQuote{control of cellular organization}} -\item{U}{uncharacterized; categories \sQuote{not yet clear-cut} and -\sQuote{uncharacterized}} +\item{C}{cellular fate / organization; +categories \sQuote{cell fate} and \sQuote{cellular communication / signal transduction} +and \sQuote{control of cellular organization}} +\item{U}{uncharacterized; categories \sQuote{not yet clear-cut} and \sQuote{uncharacterized}} } -Vertex attributes: \sQuote{name}, \sQuote{Description}, -\sQuote{Class}, the last one contains the class of the protein, -accoring to the classification above. +Vertex attributes: \sQuote{name}, \sQuote{Description}, \sQuote{Class}, +the last one contains the class of the protein, accoring to the classification above. -Note that some proteins in the network did not appear in the -annotation files, the \sQuote{Class} and \sQuote{Description} -attributes are \code{NA} for these. +Note that some proteins in the network did not appear in the annotation files, +the \sQuote{Class} and \sQuote{Description} attributes are \code{NA} for these. } \source{ -The data was downloaded from -\url{http://www.nature.com/nature/journal/v417/n6887/suppinfo/nature750.html}. +The data was downloaded from \url{http://www.nature.com/nature/journal/v417/n6887/suppinfo/nature750.html}. } \usage{ yeast } \description{ -Comprehensive protein-protein interaction maps promise to reveal many -aspects of the complex regulatory network underlying cellular -function. +Comprehensive protein-protein interaction maps promise to reveal many aspects +of the complex regulatory network underlying cellular function. -This data set was compiled by von Mering et al. (see reference below), -combining various sources. Only the interactions that have -\sQuote{high} and \sQuote{medium} confidence are included here. +This data set was compiled by von Mering et al. (see reference below), combining various sources. +Only the interactions that have \sQuote{high} and \sQuote{medium} confidence are included here. } \references{ -Comparative assessment of large-scale data sets of protein-protein -interactions. Christian von Mering, Roland Krause, Berend Snel, -Michael Cornell, Stephen G. Oliver, Stanley Fields and Peer -Bork. \emph{Nature} 417, 399-403 (2002) +Comparative assessment of large-scale data sets of protein-protein interactions. +Christian von Mering, Roland Krause, Berend Snel, Michael Cornell, Stephen G. Oliver, Stanley Fields and Peer Bork. +\emph{Nature} 417, 399-403 (2002) } \keyword{datasets}