From 414ec61caee724e42c031020003be1cc2e17dc84 Mon Sep 17 00:00:00 2001 From: "Pavel N. Krivitsky" Date: Wed, 11 Dec 2024 18:00:36 +1100 Subject: [PATCH] Made get.edgeIDs(), get.edges(), get.neighborhood(), has.edges(), is.adjacent(), and network.density() generic. --- NAMESPACE | 6 ++++++ R/access.R | 35 +++++++++++++++++++++++++++------ R/misc.R | 14 +++++++++++-- man/get.edges.Rd | 40 +++++++++++++++++++++++++++++++++++--- man/get.inducedSubgraph.Rd | 6 +++--- man/get.neighborhood.Rd | 7 ++++++- man/has.edges.Rd | 7 ++++++- man/is.adjacent.Rd | 7 ++++++- man/network.density.Rd | 7 ++++++- 9 files changed, 111 insertions(+), 18 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 5c1efcb..402245e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -37,9 +37,14 @@ S3method(get.edge.attribute,list) S3method(get.edge.attribute,network) S3method(get.edge.value,list) S3method(get.edge.value,network) +S3method(get.edgeIDs,network) +S3method(get.edges,network) S3method(get.inducedSubgraph,network) +S3method(get.neighborhood,network) S3method(get.network.attribute,network) S3method(get.vertex.attribute,network) +S3method(has.edges,network) +S3method(is.adjacent,network) S3method(is.bipartite,mixingmatrix) S3method(is.bipartite,network) S3method(is.directed,mixingmatrix) @@ -49,6 +54,7 @@ S3method(list.edge.attributes,network) S3method(list.network.attributes,network) S3method(list.vertex.attributes,network) S3method(mixingmatrix,network) +S3method(network.density,network) S3method(network.dyadcount,network) S3method(network.edgecount,network) S3method(network.naedgecount,network) diff --git a/R/access.R b/R/access.R index af49afe..d5e3a4b 100644 --- a/R/access.R +++ b/R/access.R @@ -731,6 +731,7 @@ get.edge.value.list <- get.edge.value.network #' @param na.omit logical; should we omit missing edges? #' @param tails a vector of vertex ID for the 'tails' (v) side of the dyad #' @param heads a vector of vertex ID for the 'heads' (alter) side of the dyad +#' @param ... additional arguments to methods #' @return For \code{get.edges}, a list of edges. For \code{get.edgeIDs}, a #' vector of edge ID numbers. For \code{get.dyads.eids}, a list of edge IDs #' corresponding to the dyads defined by the vertex ids in \code{tails} and @@ -752,7 +753,11 @@ get.edge.value.list <- get.edge.value.network #' get.edgeIDs(g,1,neighborhood="in") #' #' @export get.edgeIDs -get.edgeIDs<-function(x, v, alter=NULL, neighborhood=c("out","in","combined"), na.omit=TRUE){ +get.edgeIDs <- function(x, v, alter=NULL, neighborhood=c("out","in","combined"), na.omit=TRUE, ...) UseMethod("get.edgeIDs") + +#' @rdname get.edges +#' @export +get.edgeIDs.network <- function(x, v, alter=NULL, neighborhood=c("out","in","combined"), na.omit=TRUE, ...){ #Check to be sure we were called with a network if(!is.network(x)) stop("get.edgeIDs requires an argument of class network.") @@ -780,7 +785,11 @@ get.edgeIDs<-function(x, v, alter=NULL, neighborhood=c("out","in","combined"), n #' @rdname get.edges #' @export get.edges -get.edges<-function(x, v, alter=NULL, neighborhood=c("out","in","combined"), na.omit=TRUE){ +get.edges <- function(x, v, alter=NULL, neighborhood=c("out","in","combined"), na.omit=TRUE, ...) UseMethod("get.edges") + +#' @rdname get.edges +#' @export +get.edges.network <- function(x, v, alter=NULL, neighborhood=c("out","in","combined"), na.omit=TRUE, ...){ #Check to be sure we were called with a network if(!is.network(x)) stop("get.edges requires an argument of class network.") @@ -803,7 +812,11 @@ get.edges<-function(x, v, alter=NULL, neighborhood=c("out","in","combined"), na. # as defined by a vector of tails and heads vertex ids #' @rdname get.edges #' @export get.dyads.eids -get.dyads.eids<-function(x,tails,heads,neighborhood = c("out", "in", "combined"),na.omit = TRUE){ +get.dyads.eids <- function(x, tails, heads, neighborhood = c("out", "in", "combined"), na.omit = TRUE, ...) UseMethod("get.dyad.eids") + +#' @rdname get.edges +#' @export +get.dyads.eids <- function(x, tails, heads, neighborhood = c("out", "in", "combined"), na.omit = TRUE, ...){ if(length(tails)!=length(heads)){ stop('heads and tails vectors must be the same length for get.dyads.eids') } @@ -907,7 +920,7 @@ get.dyads.eids<-function(x,tails,heads,neighborhood = c("out", "in", "combined") #' #' #' @export get.inducedSubgraph -get.inducedSubgraph <- function(x, ...) UseMethod("get.inducedSubgraph") +get.inducedSubgraph <- function(x, v, alters=NULL,...) UseMethod("get.inducedSubgraph") #' @rdname get.inducedSubgraph #' @export @@ -1024,6 +1037,7 @@ get.network.attribute.network <- function(x, attrname, unlist=FALSE, ...) { #' @param type the neighborhood to be computed #' @param na.omit logical; should missing edges be ignored when obtaining #' vertex neighborhoods? +#' @param ... additional arguments to methods #' @return A vector containing the vertex IDs for the chosen neighborhood. #' @author Carter T. Butts \email{buttsc@@uci.edu} #' @seealso \code{\link{get.edges}}, \code{\link{is.adjacent}} @@ -1047,7 +1061,11 @@ get.network.attribute.network <- function(x, attrname, unlist=FALSE, ...) { #' get.neighborhood(g,1,"combined") #' #' @export get.neighborhood -get.neighborhood<-function(x, v, type=c("out","in","combined"), na.omit=TRUE){ +get.neighborhood<-function(x, v, type=c("out","in","combined"), na.omit=TRUE, ...) UseMethod("get.neighborhood") + +#' @rdname get.neighborhood +#' @export +get.neighborhood.network<-function(x, v, type=c("out","in","combined"), na.omit=TRUE, ...){ #Check to be sure we were called with a network if(!is.network(x)) stop("get.neighborhood requires an argument of class network.") @@ -1217,6 +1235,7 @@ has.loops<-function(x){ #' @param vj a second vertex ID #' @param na.omit logical; should missing edges be ignored when assessing #' adjacency? +#' @param ... additional arguments to methods #' @return A logical, giving the status of the (i,j) edge #' @note Prior to version 1.4, \code{na.omit} was set to \code{TRUE} by #' default. @@ -1241,7 +1260,11 @@ has.loops<-function(x){ #' g[2,1]==1 #FALSE #' #' @export is.adjacent -is.adjacent<-function(x,vi,vj,na.omit=FALSE){ +is.adjacent <- function(x, vi, vj, na.omit=FALSE, ...) UseMethod("is.adjacent") + +#' @rdname is.adjacent +#' @export +is.adjacent.network <- function(x, vi, vj, na.omit=FALSE, ...){ if(!is.network(x)) stop("is.adjacent requires an argument of class network.\n") if(length(vi)!=length(vj)){ diff --git a/R/misc.R b/R/misc.R index 19551d1..1805dc7 100644 --- a/R/misc.R +++ b/R/misc.R @@ -344,6 +344,7 @@ print.mixingmatrix <- function(x, ...) { #' density? #' @param discount.bipartite logical; if \code{x} is bipartite, should #' \dQuote{forbidden} edges be excluded from the count of potential edges? +#' @param ... additional arguments to methods #' @return The network density. #' @section Warning : \code{network.density} relies on network attributes (see #' \link{network.indicators}) to determine the properties of the underlying @@ -370,7 +371,11 @@ print.mixingmatrix <- function(x, ...) { #' #' @rdname network.density #' @export network.density -network.density<-function(x,na.omit=TRUE,discount.bipartite=FALSE){ +network.density <- function(x, na.omit=TRUE, discount.bipartite=FALSE, ...) UseMethod("network.density") + +#' @rdname network.density +#' @export +network.density.network <- function(x, na.omit=TRUE, discount.bipartite=FALSE, ...){ if(!is.network(x)) stop("network.density requires a network object.") if(network.size(x)==0){ @@ -413,6 +418,7 @@ network.density<-function(x,na.omit=TRUE,discount.bipartite=FALSE){ #' @aliases is.isolate #' @param net a \code{\link{network}} object to be queried #' @param v integer vector of vertex ids to check +#' @param ... additional arguments to methods #' @return returns a logical vector with the same length as v, with TRUE if the #' vertex is involved in any edges, FALSE if it is an isolate. #' @author skyebend @@ -425,7 +431,11 @@ network.density<-function(x,na.omit=TRUE,discount.bipartite=FALSE){ #' #' @rdname has.edges #' @export has.edges -has.edges<-function(net,v=seq_len(network.size(net))){ +has.edges <- function(net, v=seq_len(network.size(net)), ...) UseMethod("has.edges") + +#' @rdname has.edges +#' @export +has.edges.network <- function(net, v=seq_len(network.size(net)), ...){ if(network.size(net)==0){ return(logical(0)) } diff --git a/man/get.edges.Rd b/man/get.edges.Rd index b72a1f2..a03ad27 100644 --- a/man/get.edges.Rd +++ b/man/get.edges.Rd @@ -3,6 +3,8 @@ \name{get.edges} \alias{get.edges} \alias{get.edgeIDs} +\alias{get.edgeIDs.network} +\alias{get.edges.network} \alias{get.dyads.eids} \title{Retrieve Edges or Edge IDs Associated with a Given Vertex} \usage{ @@ -11,7 +13,17 @@ get.edgeIDs( v, alter = NULL, neighborhood = c("out", "in", "combined"), - na.omit = TRUE + na.omit = TRUE, + ... +) + +\method{get.edgeIDs}{network}( + x, + v, + alter = NULL, + neighborhood = c("out", "in", "combined"), + na.omit = TRUE, + ... ) get.edges( @@ -19,7 +31,26 @@ get.edges( v, alter = NULL, neighborhood = c("out", "in", "combined"), - na.omit = TRUE + na.omit = TRUE, + ... +) + +\method{get.edges}{network}( + x, + v, + alter = NULL, + neighborhood = c("out", "in", "combined"), + na.omit = TRUE, + ... +) + +get.dyads.eids( + x, + tails, + heads, + neighborhood = c("out", "in", "combined"), + na.omit = TRUE, + ... ) get.dyads.eids( @@ -27,7 +58,8 @@ get.dyads.eids( tails, heads, neighborhood = c("out", "in", "combined"), - na.omit = TRUE + na.omit = TRUE, + ... ) } \arguments{ @@ -43,6 +75,8 @@ undirected networks} \item{na.omit}{logical; should we omit missing edges?} +\item{...}{additional arguments to methods} + \item{tails}{a vector of vertex ID for the 'tails' (v) side of the dyad} \item{heads}{a vector of vertex ID for the 'heads' (alter) side of the dyad} diff --git a/man/get.inducedSubgraph.Rd b/man/get.inducedSubgraph.Rd index 9a8ca77..6570d8e 100644 --- a/man/get.inducedSubgraph.Rd +++ b/man/get.inducedSubgraph.Rd @@ -6,7 +6,7 @@ \alias{\%s\%} \title{Retrieve Induced Subgraphs and Cuts} \usage{ -get.inducedSubgraph(x, ...) +get.inducedSubgraph(x, v, alters = NULL, ...) \method{get.inducedSubgraph}{network}(x, v, alters = NULL, eid = NULL, ...) @@ -15,13 +15,13 @@ x \%s\% v \arguments{ \item{x}{an object of class \code{network}.} -\item{...}{additional arguments for methods.} - \item{v}{a vector of vertex IDs, or, for \code{\%s\%}, optionally a list containing two disjoint vectors of vertex IDs (see below).} \item{alters}{optionally, a second vector of vertex IDs. Must be disjoint with \code{v}.} +\item{...}{additional arguments for methods.} + \item{eid}{optionally, a numeric vector of valid edge ids in \code{x} that should be retained (cannot be used with \code{v} or \code{alter})} } diff --git a/man/get.neighborhood.Rd b/man/get.neighborhood.Rd index 00ce8c3..c18490b 100644 --- a/man/get.neighborhood.Rd +++ b/man/get.neighborhood.Rd @@ -2,9 +2,12 @@ % Please edit documentation in R/access.R \name{get.neighborhood} \alias{get.neighborhood} +\alias{get.neighborhood.network} \title{Obtain the Neighborhood of a Given Vertex} \usage{ -get.neighborhood(x, v, type = c("out", "in", "combined"), na.omit = TRUE) +get.neighborhood(x, v, type = c("out", "in", "combined"), na.omit = TRUE, ...) + +\method{get.neighborhood}{network}(x, v, type = c("out", "in", "combined"), na.omit = TRUE, ...) } \arguments{ \item{x}{an object of class \code{network}} @@ -15,6 +18,8 @@ get.neighborhood(x, v, type = c("out", "in", "combined"), na.omit = TRUE) \item{na.omit}{logical; should missing edges be ignored when obtaining vertex neighborhoods?} + +\item{...}{additional arguments to methods} } \value{ A vector containing the vertex IDs for the chosen neighborhood. diff --git a/man/has.edges.Rd b/man/has.edges.Rd index 642d676..5b37270 100644 --- a/man/has.edges.Rd +++ b/man/has.edges.Rd @@ -3,15 +3,20 @@ \name{has.edges} \alias{has.edges} \alias{is.isolate} +\alias{has.edges.network} \title{Determine if specified vertices of a network have any edges (are not isolates)} \usage{ -has.edges(net, v = seq_len(network.size(net))) +has.edges(net, v = seq_len(network.size(net)), ...) + +\method{has.edges}{network}(net, v = seq_len(network.size(net)), ...) } \arguments{ \item{net}{a \code{\link{network}} object to be queried} \item{v}{integer vector of vertex ids to check} + +\item{...}{additional arguments to methods} } \value{ returns a logical vector with the same length as v, with TRUE if the diff --git a/man/is.adjacent.Rd b/man/is.adjacent.Rd index 946a160..be7b054 100644 --- a/man/is.adjacent.Rd +++ b/man/is.adjacent.Rd @@ -2,9 +2,12 @@ % Please edit documentation in R/access.R \name{is.adjacent} \alias{is.adjacent} +\alias{is.adjacent.network} \title{Determine Whether Two Vertices Are Adjacent} \usage{ -is.adjacent(x, vi, vj, na.omit = FALSE) +is.adjacent(x, vi, vj, na.omit = FALSE, ...) + +\method{is.adjacent}{network}(x, vi, vj, na.omit = FALSE, ...) } \arguments{ \item{x}{an object of class \code{network}} @@ -15,6 +18,8 @@ is.adjacent(x, vi, vj, na.omit = FALSE) \item{na.omit}{logical; should missing edges be ignored when assessing adjacency?} + +\item{...}{additional arguments to methods} } \value{ A logical, giving the status of the (i,j) edge diff --git a/man/network.density.Rd b/man/network.density.Rd index 397e279..bc03296 100644 --- a/man/network.density.Rd +++ b/man/network.density.Rd @@ -2,9 +2,12 @@ % Please edit documentation in R/misc.R \name{network.density} \alias{network.density} +\alias{network.density.network} \title{Compute the Density of a Network} \usage{ -network.density(x, na.omit = TRUE, discount.bipartite = FALSE) +network.density(x, na.omit = TRUE, discount.bipartite = FALSE, ...) + +\method{network.density}{network}(x, na.omit = TRUE, discount.bipartite = FALSE, ...) } \arguments{ \item{x}{an object of class \code{network}} @@ -14,6 +17,8 @@ density?} \item{discount.bipartite}{logical; if \code{x} is bipartite, should \dQuote{forbidden} edges be excluded from the count of potential edges?} + +\item{...}{additional arguments to methods} } \value{ The network density.