Merge branch 'master' into v1.17

Author: CarterButts

ChangeLog

@@ -13,6 +13,8 @@ v1.17
   - mixingmatrix() now produces output inheriting from "table" rather than a list; its printing, handling of missing attributes, bipartite networks, and other scenarios has been improved.
   - as.mixingmatrix() has been added.
   - network now uses statnet::statnetStartupMessage().
+  - Updated constructor code per Kurt Hornik's suggestion to future proof versus upcoming sapply() changes.
+  - network.edgelist() now automagically prunes loops and redundant edges for networks that should not have them; previously, the function trusted the user not to supply such things (and would go ahead and make edges if asked to do so).
 v1.16
   - Converted get.vertex.attribute and list.vertex.attributes to generics for greater extensibility.
   - Updated tests to fix a color-related issue.

DESCRIPTION

@@ -11,8 +11,19 @@ Authors@R: c(
     person("Li", "Wang", role=c("ctb"), email="lxwang@uw.edu"),
     person("Pavel N.", "Krivitsky", role=c("ctb"), email="pavel@statnet.org", comment=c(ORCID="0000-0002-9101-3362")),
     person("Brendan", "Knapp", role=c("ctb"), email="brendan.g.knapp@gmail.com", comment=c(ORCID="0000-0003-3284-4972")),
-    person("Michał", " Bojanowski", role=c("ctb"), email="mbojanowski@kozminski.edu.pl"),
+    person("Michał", "Bojanowski", role=c("ctb"), email="mbojanowski@kozminski.edu.pl"),
     person("Chad", "Klumb", role=c("ctb"), email="cklumb@gmail.com"))
+Author: Carter T. Butts [aut, cre],
+    David Hunter [ctb],
+    Mark Handcock [ctb],
+    Skye Bender-deMoll [ctb],
+    Jeffrey Horner [ctb],
+    Li Wang [ctb],
+    Pavel N. Krivitsky [ctb] (<https://orcid.org/0000-0002-9101-3362>),
+    Brendan Knapp [ctb] (<https://orcid.org/0000-0003-3284-4972>),
+    Michał Bojanowski [ctb],
+    Chad Klumb [ctb]
+Maintainer: Carter T. Butts <buttsc@uci.edu>
 Depends: R (>= 2.10), utils
 Imports: tibble, magrittr, statnet.common (>= 4.4.1), stats
 Suggests: 

R/coercion.R

@@ -6,7 +6,7 @@
 # David Hunter <dhunter@stat.psu.edu> and Mark S. Handcock
 # <handcock@u.washington.edu>.
 #
-# Last Modified 02/26/13
+# Last Modified 06/05/21
 # Licensed under the GNU General Public License version 2 (June, 1991)
 # or greater
 #

R/constructors.R

@@ -6,7 +6,7 @@
 # David Hunter <dhunter@stat.psu.edu> and Mark S. Handcock
 # <handcock@u.washington.edu>.
 #
-# Last Modified 02/26/13
+# Last Modified 06/05/21
 # Licensed under the GNU General Public License version 2 (June, 1991)
 # or greater
 #
@@ -305,6 +305,23 @@ network.edgelist<-function(x, g, ignore.eval=TRUE, names.eval=NULL, ...){
   #Set things up to edit g in place
   gn<-substitute(g)
   l<-dim(x)[2]
+  #Remove loops if has.loops==FALSE
+  if(!has.loops(g)){
+    cn<-colnames(x)
+    x<-x[x[,1]!=x[,2],,drop=FALSE]  #Remove loops
+    colnames(x)<-cn
+  }
+  #Remove redundant edges if is.multiplex==FALSE
+  if(!is.multiplex(g)){
+    cn<-colnames(x)
+    if(is.directed(g)){
+      x<-x[!duplicated(x[,1:2]),,drop=FALSE]
+    }else{
+      x[,1:2]<-t(apply(x[,1:2],1,sort))
+      x<-x[!duplicated(x[,1:2]),,drop=FALSE]
+    }
+    colnames(x)<-cn
+  }
   #Traverse the edgelist matrix, adding edges as we go.
   if((l>2)&&(!ignore.eval)){		#Use values if present...
     #if names not given, try to use the names from data frame
@@ -441,9 +458,9 @@ network.initialize<-function(n,directed=TRUE,hyper=FALSE,loops=FALSE,multiple=FA
   g$gal$bipartite<-bipartite
   #Populate the vertex attribute lists, endpoint lists, etc.
   if(n>0){
-    g$val<-replicate(n,list())
-    g$iel<-replicate(n,vector(mode="integer"))
-    g$oel<-replicate(n,vector(mode="integer"))
+    g$val<-rep(list(list()), n)
+    g$iel<-rep(list(integer()), n)
+    g$oel<-rep(list(integer()), n)
   }else{
     g$val<-vector(length=0,mode="list")
     g$iel<-vector(length=0,mode="list")