convert documentation to roxygen

DESCRIPTION

@@ -19,3 +19,18 @@ Suggests:
 Description: Tools to create and modify network objects.  The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
 License: GPL (>=2)
 URL: http://statnet.org/
+RoxygenNote: 6.1.1
+Collate:
+    'access.R'
+    'as.edgelist.R'
+    'assignment.R'
+    'coercion.R'
+    'constructors.R'
+    'fileio.R'
+    'layout.R'
+    'misc.R'
+    'network-package.R'
+    'operators.R'
+    'plot.R'
+    'printsum.R'
+    'zzz.R'

NAMESPACE

@@ -1,194 +1,177 @@
-#Set up our dynamic library
-useDynLib(network, .registration = TRUE)
-
-#Import some required symbols
-import(utils)
-
-importFrom("grDevices", "colors", "gray")
-importFrom("graphics", "locator", "par", "plot", "polygon", "rect",
-             "strheight", "strwidth", "text")
-importFrom("stats", "rnorm", "na.omit")
-importFrom("tibble", "tibble", "as.tibble", "as_tibble")
-importFrom("magrittr", "%>%", "set_names")
-
-#Export everything except symbols that start with '.' or end with '_R'.
-#exportPattern("^[^\\.].*[^_][^R]$")
-
-# the %c% operator may have already been defined by the sna library if loaded first
-# but we can't figure out a way to conditionally export it
-export("%c%")
+# Generated by roxygen2: do not edit by hand
 
-# explicity export only a subset of functions
-export(
-add.edge,
-add.edge.network,
-add.edges,
-add.edges.network,
-add.vertices,
-add.vertices.network,
-as.color,
-as.matrix.network,
-as.matrix.network.adjacency,
-as.matrix.network.edgelist,
-as.matrix.network.incidence,
-as.network,
-as.network.default,
-as.network.matrix,
-as.network.network,
-as.sociomatrix,
-as.edgelist,
-# TODO: Don't export as.edgelist.matrix once no one depends on it.
-as.edgelist.matrix,
-is.edgelist,
-"%c%.network",
-delete.edge.attribute,
-delete.edges,
-delete.network.attribute,
-delete.vertex.attribute,
-delete.vertices,
-"%e%",
-"%e%<-",
-"%eattr%",
-"%eattr%<-",
-get.edge.attribute,
-get.edgeIDs,
-get.dyads.eids,
-get.edges,
-get.edge.value,
-get.inducedSubgraph,
-get.neighborhood,
-get.network.attribute,
-get.vertex.attribute,
-has.loops,
-is.adjacent,
-is.bipartite,
-is.color,
-is.directed,
-is.discrete,
-is.discrete.character,
-is.discrete.numeric,
-is.hyper,
-is.multiplex,
-is.na.network,
-is.network,
-has.edges,
-list.edge.attributes,
-list.network.attributes,
-list.vertex.attributes,
-mixingmatrix,
-"%n%",
-"%n%<-",
-"%nattr%",
-"%nattr%<-",
-network,
-"<-.network",
-"|.network",
-"-.network",
-"!.network",
-"[<-.network",
-"[.network",
-"*.network",
-"&.network",
-"+.network",
-network.adjacency,
-network.arrow,
-network.bipartite,
-network.copy,
-network.density,
-network.dyadcount,
-network.edgecount,
-network.edgelabel,
-network.edgelist,
-network.incidence,
-network.initialize,
-network.layout.circle,
-network.layout.fruchtermanreingold,
-network.layout.kamadakawai,
-network.loop,
-network.naedgecount,
-#networkOperatorSetup,
-network.size,
-network.vertex,
-network.vertex.names,
-"network.vertex.names<-",
-permute.vertexIDs,
-plot.network,
-plot.network.default,
-plotArgs.network,
-print.mixingmatrix,
-print.network,
-print.summary.character,
-print.summary.network,
-prod.network,
-#readAndVectorizeLine,
-read.paj,
-#read.paj.simplify,
-"%s%",
-set.edge.attribute,
-set.edge.value,
-set.network.attribute,
-set.vertex.attribute,
-summary.character,
-summary.network,
-sum.network,
-#switchArcDirection,
-"%v%",
-"%v%<-",
-valid.eids,
-"%vattr%",
-"%vattr%<-",
-which.matrix.type
-
-)
-
-# register S3 methods
-
-S3method('%c%',network)
-S3method(add.edge, network)
-S3method(add.edges, network) 
-S3method(add.vertices, network)
-S3method(as.network, default)
-S3method(as.network, matrix)
-S3method(as.network, network)
-S3method(as.matrix, network)
-S3method(print,mixingmatrix)
-S3method(print,network)
-S3method(print,summary.network)
-S3method(print,summary.character)
-S3method(summary,character)
-S3method(summary,network)
-S3method(plot,network)
-S3method(plot.network,default)
-S3method(is.na,network)
-S3method('+',network)
-S3method('-',network) 
-S3method('*',network)
-S3method('&',network)
-S3method('|',network)
-S3method('!',network)
-S3method('[',network)
-S3method('[<-',network)
-S3method(prod,network)
-S3method(sum,network)
-S3method(as.edgelist,network)
+S3method("!",network)
+S3method("%c%",network)
+S3method("&",network)
+S3method("*",network)
+S3method("+",network)
+S3method("-",network)
+S3method("[",network)
+S3method("[<-",network)
+S3method("|",network)
+S3method(add.edge,network)
+S3method(add.edges,network)
+S3method(add.vertices,network)
 S3method(as.edgelist,matrix)
+S3method(as.edgelist,network)
 S3method(as.edgelist,tbl_df)
-S3method(mixingmatrix,network)
-
+S3method(as.matrix,network)
+S3method(as.matrix.network,adjacency)
+S3method(as.matrix.network,edgelist)
+S3method(as.matrix.network,incidence)
+S3method(as.network,default)
+S3method(as.network,matrix)
+S3method(as.network,network)
 S3method(as.tibble,network)
 S3method(as_tibble,network)
-
+S3method(get.vertex.attribute,network)
+S3method(is.na,network)
+S3method(list.vertex.attributes,network)
+S3method(mixingmatrix,network)
 S3method(network.dyadcount,network)
 S3method(network.edgecount,network)
 S3method(network.naedgecount,network)
 S3method(network.size,network)
-
-S3method(list.vertex.attributes,network)
-S3method(get.vertex.attribute,network)
-
-# These are not 'real' S3 methods, as there is no corresponding class
-# but they are dispatched by as.matrix.network and are flagged by check if not marked here
-S3method(as.matrix.network,adjacency)
-S3method(as.matrix.network,edgelist)
-S3method(as.matrix.network,incidence)
-
+S3method(plot,network)
+S3method(plot.network,default)
+S3method(print,mixingmatrix)
+S3method(print,network)
+S3method(print,summary.character)
+S3method(print,summary.network)
+S3method(prod,network)
+S3method(sum,network)
+S3method(summary,character)
+S3method(summary,network)
+export("!.network")
+export("%c%")
+export("%c%.network")
+export("%e%")
+export("%e%<-")
+export("%eattr%")
+export("%eattr%<-")
+export("%n%")
+export("%n%<-")
+export("%nattr%")
+export("%nattr%<-")
+export("%s%")
+export("%v%")
+export("%v%<-")
+export("%vattr%")
+export("%vattr%<-")
+export("&.network")
+export("*.network")
+export("+.network")
+export("-.network")
+export("<-.network")
+export("[.network")
+export("[<-.network")
+export("network.vertex.names<-")
+export("|.network")
+export(add.edge)
+export(add.edge.network)
+export(add.edges)
+export(add.edges.network)
+export(add.vertices)
+export(add.vertices.network)
+export(as.color)
+export(as.edgelist)
+export(as.edgelist.matrix)
+export(as.matrix.network)
+export(as.matrix.network.adjacency)
+export(as.matrix.network.edgelist)
+export(as.matrix.network.incidence)
+export(as.network)
+export(as.network.default)
+export(as.network.matrix)
+export(as.network.network)
+export(as.sociomatrix)
+export(delete.edge.attribute)
+export(delete.edges)
+export(delete.network.attribute)
+export(delete.vertex.attribute)
+export(delete.vertices)
+export(get.dyads.eids)
+export(get.edge.attribute)
+export(get.edge.value)
+export(get.edgeIDs)
+export(get.edges)
+export(get.inducedSubgraph)
+export(get.neighborhood)
+export(get.network.attribute)
+export(get.vertex.attribute)
+export(has.edges)
+export(has.loops)
+export(is.adjacent)
+export(is.bipartite)
+export(is.color)
+export(is.directed)
+export(is.discrete)
+export(is.discrete.character)
+export(is.discrete.numeric)
+export(is.edgelist)
+export(is.hyper)
+export(is.multiplex)
+export(is.na.network)
+export(is.network)
+export(list.edge.attributes)
+export(list.network.attributes)
+export(list.vertex.attributes)
+export(mixingmatrix)
+export(network)
+export(network.adjacency)
+export(network.arrow)
+export(network.bipartite)
+export(network.copy)
+export(network.density)
+export(network.dyadcount)
+export(network.edgecount)
+export(network.edgelabel)
+export(network.edgelist)
+export(network.incidence)
+export(network.initialize)
+export(network.layout.circle)
+export(network.layout.fruchtermanreingold)
+export(network.layout.kamadakawai)
+export(network.loop)
+export(network.naedgecount)
+export(network.size)
+export(network.vertex)
+export(network.vertex.names)
+export(permute.vertexIDs)
+export(plot.network)
+export(plot.network.default)
+export(plotArgs.network)
+export(print.mixingmatrix)
+export(print.network)
+export(print.summary.character)
+export(print.summary.network)
+export(prod.network)
+export(read.paj)
+export(set.edge.attribute)
+export(set.edge.value)
+export(set.network.attribute)
+export(set.vertex.attribute)
+export(sum.network)
+export(summary.character)
+export(summary.network)
+export(valid.eids)
+export(which.matrix.type)
+import(utils)
+importFrom(grDevices,colors)
+importFrom(grDevices,gray)
+importFrom(graphics,locator)
+importFrom(graphics,par)
+importFrom(graphics,plot)
+importFrom(graphics,polygon)
+importFrom(graphics,rect)
+importFrom(graphics,strheight)
+importFrom(graphics,strwidth)
+importFrom(graphics,text)
+importFrom(magrittr,"%>%")
+importFrom(magrittr,set_names)
+importFrom(stats,na.omit)
+importFrom(stats,rnorm)
+importFrom(tibble,as.tibble)
+importFrom(tibble,as_tibble)
+importFrom(tibble,tibble)
+useDynLib(network, .registration = TRUE)