R Under development (unstable) (2023-12-09 r85665 ucrt) -- "Unsuffered Consequences"
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> #  Part of the statnet package, http://statnetproject.org
> #
> #  This software is distributed under the GPL-3 license.  It is free,
> #  open source, and has the attribution requirements (GPL Section 7) in
> #    http://statnetproject.org/attribution
> #
> #  Copyright 2013 the statnet development team
> ######################################################################
> 
> require(networkDynamic)
Loading required package: networkDynamic
Loading required package: network

'network' 1.18.2 (2023-12-04), part of the Statnet Project
* 'news(package="network")' for changes since last version
* 'citation("network")' for citation information
* 'https://statnet.org' for help, support, and other information


'networkDynamic' 0.11.4 (2023-12-10?), part of the Statnet Project
* 'news(package="networkDynamic")' for changes since last version
* 'citation("networkDynamic")' for citation information
* 'https://statnet.org' for help, support, and other information

> require(testthat)
Loading required package: testthat
> # -------------- activate.vertex.attribute----------------------
> 
> # gives error if argument not a network?
> nd <-list()
> expect_error(activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1),"requires that the first argument be a network")
> 
> nd <- network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.vertex.attribute(nd,"letters","c",onset=2,terminus=3)
> # was the expected structure created?
> if(!all(nd$val[[1]]$letters.active[[1]][[1]] == "a",
+     nd$val[[1]]$letters.active[[1]][[2]] == "b",
+     nd$val[[1]]$letters.active[[1]][[3]] == "c",
+     all(nd$val[[1]]$letters.active[[2]] == matrix(c(0,1, 1,2, 2,3),ncol=2,byrow=TRUE)))){
+   stop("activate.vertex.attribute did not create activity attribute with expected structure")
+ }
> if(!all(nd$val[[2]]$letters.active[[1]][[1]] == "a",
+         nd$val[[2]]$letters.active[[1]][[2]] == "b",
+         nd$val[[2]]$letters.active[[1]][[3]] == "c",
+         all(nd$val[[2]]$letters.active[[2]] == matrix(c(0,1, 1,2, 2,3),ncol=2,byrow=TRUE)))){
+   stop("activate.vertex.attribute did not create activity attribute with expected structure")
+ }
> 
> # sets nD class on argument
> if(!is.networkDynamic(nd)){
+   stop("networkDynamic class was not set on network argument of activate.vertex.attribute")
+ }
> 
> # store and retreive attribute at specific times
> if(!all(get.vertex.attribute.active(nd,"letters",onset=0,terminus=1) == c("a","a","a","a","a"),
+     get.vertex.attribute.active(nd,"letters",onset=2,terminus=5) == c("c","c","c","c","c"))){
+   stop("unexpected values returned for time ranges by get.vertex.attribute.active")
+ }
> 
> # invisably returns argument
> nd2 <- activate.vertex.attribute(nd,"letters","z",onset=-1,terminus=0)
> if(!all(deparse(nd2)==deparse(nd))){
+   stop("activate.vertex.attribute did not return modified network argument or it does not match argument modified in place")
+ }
> 
> # apply to subset of vertices
> activate.vertex.attribute(nd,"letters","d",onset=3,terminus=4,v=1:2)
> if(!all(get.vertex.attribute.active(nd,"letters",onset=3,terminus=4)[1:2] == c("d","d"),
+     is.na(get.vertex.attribute.active(nd,"letters",onset=3,terminus=4)[3:5]))){
+   stop("activate.vertex.attribute did not correctly activate the assigned subset of vertex attributes")
+ }
> 
> # maintain spell order when added out of order?
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters","c",onset=2,terminus=3)
> if (!all(nd$val[[1]]$letters.active[[2]] == matrix(c(0,1, 1,2, 2,3),ncol=2,byrow=TRUE))){
+   stop("activate.vertex.attribute did not correctly maintain attribute spell ordering when added in non-temporal order")
+ }
> 
> # merge spells when same attribute added in adjoining spell
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters","a",onset=1,terminus=2)
> if (!all(nd$val[[1]]$letters.active[[2]] == matrix(c(0,2),ncol=2,byrow=TRUE))){
+   stop("activate.vertex.attribute did not correctly merge adjoining attribute spells")
+ }
> 
> # overwrite existing spell
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=1,terminus=2)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=3)
> if (!all(nd$val[[1]]$letters.active[[2]] == matrix(c(0,3),ncol=2,byrow=TRUE))){
+   stop("activate.vertex.attribute did not correctly overwrite attribute spells")
+ }
> 
> 
> # store multiple object types
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters",5,onset=1,terminus=2)
> activate.vertex.attribute(nd,"letters",NULL,onset=2,terminus=3)
> activate.vertex.attribute(nd,"letters",list(list(hello="world")),onset=3,terminus=4)
> if (!all(nd$val[[1]]$letters.active[[1]][[1]] == "a",
+          nd$val[[1]]$letters.active[[1]][[2]] == 5,
+          nd$val[[1]]$letters.active[[1]][[3]] == NULL,
+          nd$val[[1]]$letters.active[[1]][[4]]$hello == "world")){
+   stop("activate.vertex.attribute did not correctly store attributes of different types")
+ }
> 
> # replace existing attribute with TEA
> nd <-network.initialize(5)
> set.vertex.attribute(nd,"letters","a")
> activate.vertex.attribute(nd,"letters","b",onset=0,terminus=2)
> if("letters"%in%list.vertex.attributes(nd) | !"letters.active"%in%list.vertex.attributes(nd)){
+   stop("activate.vertex.attribute did not replace non-active attribute with same name")
+ }
> 
> # don't replace existing attribute with TEA if dynamic.only=TRUE
> nd <-network.initialize(5)
> set.vertex.attribute(nd,"letters","a")
> activate.vertex.attribute(nd,"letters","b",onset=0,terminus=2,dynamic.only=TRUE)
> if(!"letters"%in%list.vertex.attributes(nd) | !"letters.active"%in%list.vertex.attributes(nd)){
+   stop("activate.vertex.attribute should not have removed non-active attribute with same name")
+ }
> 
> # test at syntax
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",at=1)
> if(!all(nd$val[[2]]$letters.active[[1]][[1]] == "a",
+         all(nd$val[[2]]$letters.active[[2]] == matrix(c(1,1),ncol=2,byrow=TRUE)))){
+   stop("activate.vertex.attribute did not create activity attribute with expected structure using 'at' parameter")
+ }
> 
> # test onset and length syntax
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=1,length=5.5)
> if(!all(nd$val[[2]]$letters.active[[1]][[1]] == "a",
+         all(nd$val[[2]]$letters.active[[2]] == matrix(c(1,6.5),ncol=2,byrow=TRUE)))){
+   stop("activate.vertex.attribute did not create activity attribute with expected structure using 'onset' nad 'length' parameters")
+ }
> 
> # test terminus and length syntax
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",terminus=7,length=5.5)
> if(!all(nd$val[[2]]$letters.active[[1]][[1]] == "a",
+         all(nd$val[[2]]$letters.active[[2]] == matrix(c(1.5,7),ncol=2,byrow=TRUE)))){
+   stop("activate.vertex.attribute did not create activity attribute with expected structure using 'onset' nad 'length' parameters")
+ }
> 
> 
> # test no time params
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","a")
> if(!all(nd$val[[2]]$letters.active[[1]][[1]] == "a",
+         all(nd$val[[2]]$letters.active[[2]] == matrix(c(-Inf,Inf),ncol=2,byrow=TRUE)))){
+   stop("activate.vertex.attribute did not create activity attribute with expected structure using no time prams")
+ }
> 
> 
> # test assigning multiple values
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters",c("a","b","c","d","e"))
> if(!all(get.vertex.attribute.active(nd,"letters",onset=1,terminus=1)==c("a","b","c","d","e"))){
+   stop("activate.vertex.attribute did not correctly assign multiple values to multiple vertices")
+ }
> 
> 
> # test assigning multiple times
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",at=c(1,2,3,4,5))
> if(!all(all(nd$val[[1]]$letters.active[[2]] == matrix(c(1,1),ncol=2,byrow=TRUE)),
+         all(nd$val[[2]]$letters.active[[2]] == matrix(c(2,2),ncol=2,byrow=TRUE)),
+         all(nd$val[[3]]$letters.active[[2]] == matrix(c(3,3),ncol=2,byrow=TRUE)),
+         all(nd$val[[4]]$letters.active[[2]] == matrix(c(4,4),ncol=2,byrow=TRUE)),
+         all(nd$val[[5]]$letters.active[[2]] == matrix(c(5,5),ncol=2,byrow=TRUE)))){
+   stop("activate.vertex.attribute did not create activity attribute with expected values using multiple input times")
+ }
> 
> # test assigning complex objects (lists)
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',list(list("a","b")),onset=0,terminus=1)
> if(!all(nd$val[[2]]$letters.active[[1]][[1]][[1]]=="a",nd$val[[2]]$letters.active[[1]][[1]][[2]]=="b")){
+   stop("activate.vertex.attribute did not store list object in expected form")
+ }
> 
> activate.vertex.attribute(nd,'letters',list(list("c","d")),onset=1,terminus=2)
> if(!all(nd$val[[2]]$letters.active[[1]][[2]][[1]]=="c",nd$val[[2]]$letters.active[[1]][[2]][[2]]=="d")){
+   stop("activate.vertex.attribute did not store list object in expected form")
+ }
> 
> 
> # test passing in zero-length list of vertices returns net unmodified
> nd <-network.initialize(5)
> nd2 <-activate.vertex.attribute(nd,'letters',list(list("a","b")),onset=0,terminus=1,v=numeric(0))
> if (!all(deparse(nd)==deparse(nd2))){
+   stop("activate.vertex.attribute did not return network argument unchanged when v is length 0")
+ }
> 
> activate.vertex.attribute(network.initialize(0),"foo",at=2)
> 
> # ----- get.vertex.attribute.active ----------------
> 
> # return appropriate value for structure (allready tested above)
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',"a",onset=0,terminus=1)
> activate.vertex.attribute(nd,'letters',"b",onset=1,terminus=2)
> 
> if (!all(get.vertex.attribute.active(nd,'letters',onset=0,terminus=1)==rep("a",5),
+ get.vertex.attribute.active(nd,'letters',onset=1,terminus=2)==rep("b",5))){
+   stop("get.vertex.attribute.active did not return expected values for simple spell queries")
+ }
> 
> # test query that will return multiple values (should throw warning)
> expect_that(get.vertex.attribute.active(nd,'letters',onset=0,terminus=3),gives_warning("Multiple attribute values matched query spell for attribute"
+   ))
> 
> 
>          
> # test unlist and structure
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',"a",onset=0,terminus=1) 
> result<-get.vertex.attribute.active(nd,"letters",onset=0,terminus=1,unlist=FALSE)         
> if (class(result[[1]])=="list"){
+   stop("get.vertex.attribute.active returned values with unexpected list nesting when unlist=FALSE")
+ }
> 
> 
> 
> 
> # test at param
> if (!all(get.vertex.attribute.active(nd,'letters',at=0)==rep("a",5))){
+      stop("get.vertex.attribute.active did not return expected values for at query")
+ }
>          
> # test length param
> if (!all(get.vertex.attribute.active(nd,'letters',onset=0,length=1)==rep("a",5))){
+  stop("get.vertex.attribute.active did not return expected values for length query")
+ }
> 
> 
> # test storing a list object
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',list(list("a","b")),onset=0,terminus=1) 
> if (!all(get.vertex.attribute.active(nd,"letters",onset=0,terminus=1,unlist=FALSE)[[3]][[1]]=="a",
+          get.vertex.attribute.active(nd,"letters",onset=0,terminus=1,unlist=FALSE)[[3]][[2]]=="b")){
+   stop("get.vertex.attribute.active did not return stored list object correctly")
+ }
> 
> # find non-active version if active not found
> nd <-network.initialize(5)
> set.vertex.attribute(nd,"letters","a")
> if(!all(get.vertex.attribute.active(nd,"letters",onset=1,terminus=2) == rep("a",5))){
+   stop("get.vertex.attribute did not correctly return non-TEA attribute when TEA attribute not found")
+ }
>          
>  # don't find non-active version if dynamic.only = TRUE
> if (!all(is.na(get.vertex.attribute.active(nd,"letters",onset=1,terminus=2,dynamic.only=TRUE)))){
+   stop("get.vertex.attribute failed to return NA instead of matching non-TEA attribute when dynamic.only=TRUE")
+ }
> 
> # return NAs when no attributes match
> nd <-network.initialize(5)
> if(!all(is.na(get.vertex.attribute.active(nd,"letters",onset=1,terminus=2)))){
+   stop("get.vertex.attribute did not return NAs when no attribute found matching name")
+ }
> 
> # test return teas should return truncated spell lists
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',"a",onset=0,terminus=1)
> activate.vertex.attribute(nd,'letters',"b",onset=1,terminus=2)
> activate.vertex.attribute(nd,'letters',"c",onset=2,terminus=3)
> result <-get.vertex.attribute.active(nd,'letters',onset=1,terminus=2,return.tea=TRUE)
> if(!all(result[[1]][[1]]=="b",result[[1]][[2]]==c(1,2),result[[5]][[1]]=="b",result[[5]][[2]]==c(1,2))){
+   stop("get.vertex.attribute.active did not return expected list structures when return.tea=TRUE")
+ }
> 
> # test if some vertices have activity and not others
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',"a",onset=0,terminus=1,v=c(1,2,4,5))
> if(!all(get.vertex.attribute.active(nd,"letters",onset=0,terminus=1)[c(1,2,4,5)]=="a",is.na(get.vertex.attribute.active(nd,"letters",onset=0,terminus=1)[3]))){
+   stop("get.vertex.attribute.active did not return NA for vertices missing the active attribute")
+ }
> 
> # test require.active argument
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',"a",onset=0,terminus=1)
> deactivate.vertices(nd,v=2:3)
> result <-get.vertex.attribute.active(nd,'letters',onset=0,terminus=1,require.active=TRUE)  
> if(!all(result[c(1,4,5)]=="a",is.na(result[2:3]))){
+   stop("get.vertex.attribute.active did not return NA for attributes of inactive vertices when require.active=TRUE")
+ }
> 
> # this was crashing at one point
> get.vertex.attribute.active(network.initialize(3),"test",at=1,require.active=TRUE)
[1] NA NA NA
>          
> # test active.default argument
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',"a",onset=0,terminus=1)
> activate.vertices(nd,v=2:3)
> result <-get.vertex.attribute.active(nd,'letters',onset=0,terminus=1,require.active=TRUE,active.default=FALSE)  
> if(!all(result[2:3]=="a",is.na(result[c(1,4,5)]))){
+    stop("get.vertex.attribute.active did not return NA for attributes of vertices considered inactive when require.active=TRUE and active.default=FALSE")
+ }     
> 
>          
> # test na.omit argument
> nd <-network.initialize(5)
> set.vertex.attribute(nd,'na',TRUE,v=3)
> activate.vertex.attribute(nd,"letters",c("a","b","c","d","e"),onset=0,terminus=1)
> if(!all(get.vertex.attribute.active(nd,"letters",onset=0,terminus=1,na.omit=TRUE)==c("a","b","d","e"))){
+   warning("get.vertex.attribute.active did not correctly omit values for missing vertex when na.omit=TRUE")
+ }
> #NOTE: it does the na.omit ok, but is returning attributes in wrong index positions think it is a feature issue in network ticket #174
> 
> # test when all vertices NA (was giving error)
> nd <-network.initialize(5)
> set.vertex.attribute(nd,'na',TRUE)
> activate.vertex.attribute(nd,"letters",c("a","b","c","d","e"),onset=0,terminus=1)
> expect_true(is.null(get.vertex.attribute.active(nd,"letters",at=0,na.omit=TRUE)),info="check when all vertices are NA")
> 
> # test null.na argument
> nd <-network.initialize(3)
> if(!all(is.na(get.vertex.attribute.active(nd,"letters",onset=0,terminus=1,null.na=TRUE)))){
+   stop("get.vertex.attribute.active did not return NA instead of NULL when null.na=TRUE")
+ }
> expect_true(all(sapply(get.vertex.attribute.active(nd,"letters",onset=0,terminus=1,null.na=FALSE,unlist=FALSE),is.null)),info="test null.na=FALSE returns null")
> 
> # test rule (any vs all) argument
> nd <-network.initialize(5)
> activate.vertex.attribute(nd,'letters',"a",onset=0,terminus=1)
> if (!all(is.na(get.vertex.attribute.active(nd,'letters',onset=-1,terminus=2,rule="all")))){
+   stop("get.vertex.attribute.active did not return expected values when rule='all'")
+ }
>      
>          
> # test multiple onsets
> nd<-network.initialize(3)
> activate.vertex.attribute(nd,'letters',c("a","b","c"),onset=c(0,1,2),terminus=c(1,2,3))
> expect_equal(get.vertex.attribute.active(nd,'letters',at=0),c("a",NA,NA),info="test multiple onsets")
> expect_equal(get.vertex.attribute.active(nd,'letters',at=1),c(NA,"b",NA),info="test multiple onsets")
> expect_equal(get.vertex.attribute.active(nd,'letters',at=2),c(NA,NA,"c"),info="test multiple onsets")
> 
> expect_true(is.null(get.vertex.attribute.active(network.initialize(0),'foo',at=1)))
> 
> # -------------------- activate.edge.attribute ---------------------
> # gives error if argument not a network?
> nd <-list()
> expect_error(activate.edge.attribute(nd,"letters","a",onset=0,terminus=1),"activate.edge.attribute requires that the first argument be a network")
> 
> 
> # activate attribute on non existant edge should throw error
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> result <-try(activate.edge.attribute(nd,"letters","a",onset=0,terminus=1,e=2),T)
> if (!"try-error"%in%class(result)){
+   stop("activate.edge.attribute did not throw error when bad edge specified")
+ }
> 
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.edge.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.edge.attribute(nd,"letters","c",onset=2,terminus=3)
> # was the expected structure created?
> if(!all(nd$mel[[1]]$atl$letters.active[[1]][[1]] == "a",
+         nd$mel[[1]]$atl$letters.active[[1]][[2]] == "b",
+         nd$mel[[1]]$atl$letters.active[[1]][[3]] == "c",
+         all(nd$mel[[1]]$atl$letters.active[[2]] == matrix(c(0,1, 1,2, 2,3),ncol=2,byrow=TRUE)))){
+   stop("activate.edge.attribute did not create activity attribute with expected structure")
+ }
> 
> # sets nD class on argument
> if(!is.networkDynamic(nd)){
+   stop("networkDynamic class was not set on network argument of activate.edge.attribute")
+ }
> 
> # store and retreive attribute at specific times
> if(!all(get.edge.value.active(nd,"letters",onset=0,terminus=1) == c("a","a","a"),
+         get.edge.value.active(nd,"letters",onset=2,terminus=5) == c("c","c","c"))){
+   stop("unexpected values returned for time ranges by get.edge.value.active")
+ }
> 
> if(length(get.edge.value.active(nd,"letters",onset=0,terminus=1)) != network.edgecount(nd)){
+   warning("number of values returned by get.edge.value.active does not match number of edges")
+ }
> 
> # invisably returns argument
> nd2 <- activate.edge.attribute(nd,"letters","z",onset=-1,terminus=0)
> if(!all(deparse(nd2)==deparse(nd))){
+   stop("activate.edge.attribute did not return modified network argument or it does not match argument modified in place")
+ }
> 
> # test bug #523 where edge values getting incorrectly permuted when using e argument
> 
> test<-network.initialize(3)
> add.edges.active(test,tail=1,head=2,onset=0,terminus=1)
> add.edges.active(test,tail=2,head=3,onset=2,terminus=3)
> activate.edge.attribute(test,'letter','a',onset=0,terminus=1,e=1)
> activate.edge.attribute(test,'letter','b',onset=2,terminus=3,e=2)
> expect_equal(get.edge.attribute.active(test,'letter',at=0),c("a",NA)) # this was returning c("a","a")
> 
> 
> # test setting multiple spells on a single element with one call
> test<-network.initialize(3)
> test[1,2]<-1
> activate.edge.attribute(test,'letter',c('a','b','c'),onset=c(0,2,4),terminus=c(1,3,5),e=c(1,1,1))
> #expect_equal(test$mel[[1]]$atl$letter.active[[1]],list('a','b','c'))
> 
> # what if an edge is null because it was deleted
> 
> # apply to subset of edge
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","d",onset=3,terminus=4,e=1:2)
> if(!all(get.edge.value.active(nd,"letters",onset=3,terminus=4)[1:2] == c("d","d"), is.na(get.edge.value.active(nd,"letters",onset=3,terminus=4)[3]))){
+   stop("activate.edge.attribute did not correctly activate the assigned subset of vertex attributes")
+ }
> 
> # maintain spell order when added out of order?
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.edge.attribute(nd,"letters","c",onset=2,terminus=3)
> if (!all(nd$mel[[1]]$atl$letters.active[[2]] == matrix(c(0,1, 1,2, 2,3),ncol=2,byrow=TRUE))){
+   stop("activate.vertex.attribute did not correctly maintain attribute spell ordering when added in non-temporal order")
+ }
> 
> 
> # error if onset > terminus?
> result <- try(activate.vertex.attribute(nd,"letters","z",onset=6,terminus=5),T)
> if (!"try-error"%in%class(result)){
+   stop("activate.edge.attribute did not throw error when onset > terminus")
+ }
> 
> # convert existing attribute to TEA
> 
> # test at syntax
> 
> # test length syntax
> 
> expect_warning(activate.edge.attribute(network.initialize(0),"foo","bar"),'network does not contain any edges')
> 
> # test for network.edgecount vs. seq_along(x$mel)
> nd<-add.edges(network.initialize(3),tail=1:3,head=c(2,3,1))
> delete.edges(nd,e=2)
> activate.edge.attribute(nd,'test',as.list(c("a","b","c")),onset=1,terminus=2)
> 
> expect_equal(get.edge.attribute.active(nd,'test',at=1),c("a",NA,"c"),info='check for edgecount vs seq_along mel bug')
> 
> 
> # ------- activate.edge.value ----------------------------
> 
> # try adding with single value
> nd<-add.edges(network.initialize(3),tail=1:3,head=c(2,3,1))
> activate.edge.value(nd,'test',value=5,onset=1,terminus=2)
> expect_equal(get.edge.attribute.active(nd,'test',onset=1,terminus=2),c(5,5,5),info='test activate.edge.value with single value')
> 
> # try with matrix
> emat<-matrix(0,ncol=3,nrow=3)
> emat[1,2]<-"a"
> emat[2,3]<-"b"
> emat[3,1]<-"c"
> nd<-add.edges(network.initialize(3),tail=1:3,head=c(2,3,1))
> activate.edge.value(nd,'test',value=emat,onset=1,terminus=2)
> expect_equal(get.edge.attribute.active(nd,'test',onset=1,terminus=2),c("a","b","c"),info='test activate.edge.value with basic matrix')
> 
> # try with e subset
> nd<-add.edges(network.initialize(3),tail=1:3,head=c(2,3,1))
> activate.edge.value(nd,'test',value=emat,onset=1,terminus=2,e=2)
> expect_equal(get.edge.attribute.active(nd,'test',onset=1,terminus=2),c(NA,"b",NA),info='test activate.edge.value with basic matrix and e subset')
> 
> # try with a deleted edge
> emat<-matrix(0,ncol=3,nrow=3)
> emat[1,2]<-"a"
> emat[2,3]<-"b"
> emat[3,1]<-"c"
> nd<-add.edges(network.initialize(3),tail=1:3,head=c(2,3,1))
> delete.edges(nd,e=2)
> activate.edge.value(nd,'test',value=emat,onset=1,terminus=2)
> expect_equal(get.edge.attribute.active(nd,'test',onset=1,terminus=2),c("a",NA,"c"),info='test activate.edge.value with basic matrix and missing edge')
> 
> # -------- get.edge.attribute.active-----
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","d",onset=3,terminus=4,e=1:2)
> vals <-get.edge.attribute.active(nd,'letters',onset=3,terminus=4,unlist=FALSE)
> expect_true(all(vals[[1]]=="d",vals[[2]]=="d",is.na(vals[[3]])),info='checking get.edge.attribute.active')
> 
> expect_error(get.edge.attribute.active(nd$mel,'letters'),'must be a network object')
> 
> # ----------------- get.edge.value.active ---------------
> 
> # return values when only subset of edges have activated attributes
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","d",onset=3,terminus=4,e=1:2)
> vals <-get.edge.value.active(nd,'letters',onset=3,terminus=4,unlist=FALSE)
> if (!all(vals[[1]]=="d",vals[[2]]=="d",is.na(vals[[3]]))){
+   stop("get.edge.value.active returned unexpected values when some edges did not have activity attribute set")
+ }
> 
> # test return.tea = TRUE
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.edge.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.edge.attribute(nd,"letters","c",onset=2,terminus=3)
> if(!all(get.edge.value.active(nd,"letters",onset=1,terminus=2,return.tea=TRUE)[[3]][[1]][[1]]=="b",get.edge.value.active(nd,"letters",onset=1,terminus=2,return.tea=TRUE)[[3]][[2]]==c(1,2))){
+   stop("get.edge.value.active did not return expected structure when return.tea=TRUE")
+ }
> # test query spell includes multiple values
> expect_that(
+ if(!all(get.edge.value.active(nd,"letters",onset=0,terminus=3)=="a")){
+   stop("get.edge.value.active did not return earliest values when query spell matched multiple")
+ }, gives_warning("Multiple attribute values matched query spell"))
> 
> if(!all(get.edge.value.active(nd,"letters",onset=0,terminus=3,return.tea=TRUE)[[3]][[2]]== matrix(c(0,1, 1,2, 2,3), ncol=2,byrow=TRUE),
+         get.edge.value.active(nd,"letters",onset=0,terminus=3,return.tea=TRUE)[[3]][[1]][[1]]=="a",
+         get.edge.value.active(nd,"letters",onset=0,terminus=3,return.tea=TRUE)[[3]][[1]][[2]]=="b",
+         get.edge.value.active(nd,"letters",onset=0,terminus=3,return.tea=TRUE)[[3]][[1]][[3]]=="c")){
+   stop("get.edge.value.active did not return multiple values when query spell matched multiple and return.tea=TRUE")
+ }
> 
> 
> # test unlist
> 
> # test not return value if edge not active and require.active = TRUE
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> activate.edges(nd,e=1,onset=0,terminus=2)
> deactivate.edges(nd,e=2,onset=0,terminus=2)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1)
> if(!all(get.edge.value.active(nd,"letters",onset=0,terminus=1,require.active=TRUE)[1]=="a",is.na(get.edge.value.active(nd,"letters",onset=0,terminus=1,require.active=TRUE)[2]))){
+   stop("get.edge.value.active did not return expected values for inactive edge when require.active=TRUE")
+ }
> 
> # test deleted edge
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters",list("a","b","c"),onset=0,terminus=1)
> delete.edges(nd,eid=2)
> if (!all(get.edge.value.active(nd,"letters",onset=0,terminus=1)[c(1,3)]==c("a","c"),
+          is.na(get.edge.value.active(nd,"letters",onset=0,terminus=1)[2]))){
+   stop('get.edge.value.active did not return expected values when edge was deleted')
+ }
>          
> # find non-active version if active not found
> 
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> set.edge.attribute(nd,"letters",list("a","b","c"))
> if(!all(get.edge.value.active(nd,"letters",onset=1,terminus=2) == c("a","b","c"))){
+   stop("get.vertex.attribute did not correctly return non-TEA attribute")
+ }
> 
> # don't find non-active version if dynamic.only = TRUE
> if (!all(is.na(get.edge.value.active(nd,"letters",onset=1,terminus=2,dynamic.only=TRUE)))){
+   stop("get.vertex.attribute failed to return NA instead of matching non-TEA attribute when dynamic.only=TRUE")
+ }
> 
> # return NAs if no matching attribute
> nd <-network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> get.edge.value.active(nd,"letters",onset=1,terminus=2,unlist=FALSE)
[[1]]
NULL

[[2]]
NULL

> 
> # what if network has no edges?
> nd <-network.initialize(5)
> expect_that(activate.edge.attribute(nd,"letters","a",onset=0,terminus=1),gives_warning("network does not contain any edges"))
> 
> expect_true(is.null(get.edge.value.active(network.initialize(0),"foo",at=0)))
> 
> # --------- activate.network.attribute ------------------------
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",onset=1,terminus=2)
> 
> # expected structure?
> if(!all(nd$gal$test.active[[1]][[1]]=="a",nd$gal$test.active[[2]]==c(1,2))){
+   stop("activate.network.attribute did not store attribute and activity spell in expected structure")
+ }
> 
> activate.network.attribute(nd,"test","b",onset=2,terminus=3)
> if(!all(nd$gal$test.active[[1]][[2]]=="b",nd$gal$test.active[[2]][2,]==c(2,3))){
+   stop("activate.network.attribute did not store attribute and activity spell in expected structure")
+ }
> 
> # got nd class?
> if(!is.networkDynamic(nd)){
+   stop("activate.network.attribute did not set networkDynamic class")
+ }
> 
> #store list
> activate.network.attribute(nd,"test",list("c","d"),onset=3,terminus=4)
> if(!all(unlist(nd$gal$test.active[[1]][[3]])==c("c","d"),nd$gal$test.active[[2]][3,]==c(3,4))){
+   stop("activate.network.attribute did not store attribute and activity spell in expected structure")
+ }
> 
> # test length
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",onset=1,length=2)
> if(!all(nd$gal$test.active[[1]][[1]]=="a",nd$gal$test.active[[2]]==c(1,3))){
+   stop("activate.network.attribute did not store attribute and activity spell in expected structure when using 'length' param")
+ }
> 
> 
> # test at
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",at=2)
> if(!all(nd$gal$test.active[[1]][[1]]=="a",nd$gal$test.active[[2]]==c(2,2))){
+   stop("activate.network.attribute did not store attribute and activity spell in expected structure when using 'at' param")
+ }
> 
> # test dynamic only 
> nd <-network.initialize(5)
> set.network.attribute(nd,"test","a")
> activate.network.attribute(nd,"test","b",onset=1,terminus=2)
> if ("test"%in%list.network.attributes(nd)){
+   stop("same-named non-active attribute was not replaced by activate.network.attribute ")
+ }
> 
> # test dynamic.only = TRUE
> nd <-network.initialize(5)
> set.network.attribute(nd,"test","a")
> activate.network.attribute(nd,"test","b",onset=1,terminus=2,dynamic.only=TRUE)
> if (!"test"%in%list.network.attributes(nd)){
+   stop("same-named non-active attribute was wrongly replaced by activate.network.attribute when dynamic.only=TRUE")
+ }
> 
> activate.network.attribute(network.initialize(0),"foo","bar")
> 
> # ---- get.network.attribute.active --------------
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",onset=1,terminus=2)
> 
> 
> 
> # expected structure?
> if(!get.network.attribute.active(nd,"test",onset=1,terminus=1)=="a"){
+   stop("get.network.attribute.active did not return expected attribute value")
+ }
> 
> activate.network.attribute(nd,"test","b",onset=2,terminus=3)
> if(!get.network.attribute.active(nd,"test",onset=2,terminus=3)=="b"){
+   stop("get.network.attribute.active did not return expected attribute value")
+ }
> 
> 
> #store list
> activate.network.attribute(nd,"test",list("c","d"),onset=3,terminus=4)
> if(!all(unlist(get.network.attribute.active(nd,"test",onset=3,terminus=4))==c("c","d"))){
+   stop("get.network.attribute.active did not return expected attribute value")
+ }
> 
> # return multiple values with warning
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",onset=1,terminus=2)
> activate.network.attribute(nd,"test","b",onset=2,terminus=3)
> activate.network.attribute(nd,"test","c",onset=3,terminus=4)
> expect_that(
+ if(!get.network.attribute.active(nd,"test",onset=2,terminus=4)=="b"){
+   stop("get.network.attribute.active did not return appropriate value when multiple attributes matched query spell")
+ }
+ , gives_warning("Multiple attribute values matched query spell"))
> 
> 
> # return appropriate value for return.tea = T
> returned <-get.network.attribute.active(nd,"test",onset=2,terminus=4,return.tea=TRUE)
> if(!all(returned[[1]][[1]]=="b",returned[[1]][[2]]=="c",returned[[2]][1,]==c(2,3),returned[[2]][2,]==c(3,4))){
+   stop("get.network.attribute.active did not return appropriate value when multiple attributes matched query spell")
+ }
> 
> 
> # test dynamic only fall through
> nd <-network.initialize(5)
> set.network.attribute(nd,"test","a")
> if (!get.network.attribute.active(nd,"test",onset=2,terminus=4)=="a"){
+   stop("get.network.attribute.active did not return non-dynamic attribute when TEA not found")
+ }
> 
> # test dynamic only not fall through
> if (!is.null(get.network.attribute.active(nd,"test",onset=2,terminus=4,dynamic.only=TRUE))){
+   stop("get.network.attribute.active did not return NULL instead non-dynamic attribute when TEA not found and dynamic.only=TRUE")
+ }
> 
> # test unlist
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test",list("a","b"),onset=1,terminus=2)
> if(!all(get.network.attribute.active(nd,"test",onset=1,terminus=2)==c("a","b"))){
+   stop("get.network.attribute.active did not unlist returned attribute correctly")
+ }
>                            
> if(!all(is.list(get.network.attribute.active(nd,"test",onset=1,terminus=2,unlist=FALSE)),get.network.attribute.active(nd,"test",onset=1,terminus=2,unlist=FALSE)[[1]]=="a",get.network.attribute.active(nd,"test",onset=1,terminus=2,unlist=FALSE)[[2]]=="b")){
+   stop("get.network.attribute.active did not return attribute correctly in list when unlist=FALSE")
+ }      
> 
> # test at
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",onset=1,terminus=2)
> activate.network.attribute(nd,"test","b",onset=2,terminus=3)
> activate.network.attribute(nd,"test","c",onset=5,terminus=6)
> 
> if(get.network.attribute.active(nd,"test",at=2)!="b"){
+   stop("get.network.attribute.active did not return expected value when using 'at' parameter")
+ }
> 
> # test length
> if(get.network.attribute.active(nd,"test",onset=0,length=1.5)!="a"){
+   stop("get.network.attribute.active did not return expected value when using 'length' parameter")
+ }
> 
> # test rule
> 
> if(!is.na(get.network.attribute.active(nd,"test",onset=2,terminus=4,rule="all"))){
+   stop("get.network.attribute.active did not return expected value when using rule='all' parameter")
+ }
> if(get.network.attribute.active(nd,"test",onset=2,terminus=4,rule="any")!="b"){
+   stop("get.network.attribute.active did not return expected value when using rule='any' parameter")
+ }
> 
> # test out of range
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",onset=1,terminus=2)
> if(!is.na(get.network.attribute.active(nd,"test",onset=3,terminus=4))){
+   stop("get.network.attribute.active did not return NA when query spell did not match any attributes")
+ }
> 
> ##########################################################################
> # ------list.vertex.attributes.active ----
> ######################################################################################
> nd <- network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=3)
> activate.vertex.attribute(nd,"letters","b",onset=4,terminus=5)
> activate.vertex.attribute(nd,"letters","a",onset=5,terminus=7)
> activate.vertex.attribute(nd,"numbers","1",onset=2,terminus=3)
> activate.vertex.attribute(nd,"numbers","2",onset=4,terminus=8)
> activate.vertex.attribute(nd,"numbers","3",onset=8,terminus=10)
> if(!all(list.vertex.attributes.active(nd,onset=-Inf,terminus=Inf)==c("na","vertex.names","letters.active","numbers.active"))){
+   stop("list.vertex.attributes.active did not return expected values")
+ }
> 
> if(!all(list.vertex.attributes.active(nd,onset=-Inf,terminus=Inf,dynamic.only=TRUE)==c("letters.active","numbers.active"))){
+   stop("list.vertex.attributes.active did not return expected values when dynamic.only=TRUE")
+ }
> 
> # give error if not called with nD object
> 
> expect_error(list.vertex.attributes.active(list()),"requires that the first argument be a network")
> 
> net<-network.initialize(3)
> activate.vertices(net,onset=1,terminus=2)
> # if no dynamic attributes, should just return static ones
> expect_equal(list.vertex.attributes.active(net,onset=-Inf, terminus=Inf),list.vertex.attributes(net))
> 
> expect_true(is.null(list.vertex.attributes.active(network.initialize(0))))
> 
> 
> ##########################################################################
> ##########################################################################
> #----- list.edge.attriubtes.active----
> ######################################################################################
> 
> 
> 
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=3)
> activate.edge.attribute(nd,"letters","b",onset=4,terminus=5)
> activate.edge.attribute(nd,"letters","a",onset=5,terminus=7)
> activate.edge.attribute(nd,"numbers","1",onset=2,terminus=3)
> activate.edge.attribute(nd,"numbers","2",onset=4,terminus=8)
> activate.edge.attribute(nd,"numbers","3",onset=8,terminus=10)
> 
> if(!all(list.edge.attributes.active(nd,onset=-Inf,terminus=Inf)==c('na','letters.active','numbers.active'))){
+   stop("list.edge.attributes.active returned unexpected values")
+ }
> 
> # test dynamic only
> if(!all(list.edge.attributes.active(nd,onset=-Inf,terminus=Inf,dynamic.only=TRUE)==c('letters.active','numbers.active'))){
+   stop("list.edge.attributes.active returned unexpected values when dynamic.only=TRUE")
+ }
> 
> # test time range
> if(!all(list.edge.attributes.active(nd,onset=8,terminus=10)==c('na','numbers.active'))){
+   stop("list.edge.attributes.active returned unexpected values")
+ }
> 
> # check if called on network with no edges
> # this hits a bug in network
> # https://statnet.csde.washington.edu/trac/ticket/181
> net <- network.initialize(2)
> list.edge.attributes.active(net,onset=-Inf,terminus=Inf)
character(0)
> 
> # check if called on network with no active attributes
> add.edges.active(net,tail=1,head=2,onset=1,terminus=2)
> expect_equal(list.edge.attributes.active(net,onset=-Inf,terminus=Inf),list.edge.attributes(net))
> 
> expect_equal(list.edge.attributes.active(network.initialize(0),at=1),character(0))
> 
> 
> ##########################################################################
> ##########################################################################
> # ------list.network.attributes.active-------
> ######################################################################################
> 
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",onset=1,terminus=4)
> if(!all(list.network.attributes.active(nd,onset=-Inf,terminus=Inf) ==c("bipartite","directed","hyper"     ,"loops","mnext","multiple","n","test.active"))){
+   stop("list.network.attributes.active did not return expected results")
+ }
> 
> # check at param (was giving error)
> list.network.attributes.active(net,at=2)
[1] "bipartite" "directed"  "hyper"     "loops"     "mnext"     "multiple" 
[7] "n"        
> 
> # outside of range
> if(!all(list.network.attributes.active(nd,onset=-Inf,terminus=0) ==c("bipartite","directed","hyper"     ,"loops","mnext","multiple","n"))){
+   stop("list.network.attributes.active did not return expected results for query that should miss attributes")
+ }
> 
> # dynamic only
> if(!all(list.network.attributes.active(nd,onset=-Inf,terminus=Inf,dynamic.only=TRUE) =="test.active")){
+   stop("list.network.attributes.active did not return expected results for dynamic.only=TRUE")
+ }
> 
> # also add a more complex attribute
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test",c("a","b"),onset=1,terminus=4)
> if(list.network.attributes.active(nd,onset=-Inf,terminus=Inf,dynamic.only=TRUE)!="test.active"){
+   stop("list.network.attributes.active did not return expect results for vector attributes")
+ }
> 
> # check its ok if called with network 
> net <-network.initialize(2)
> expect_equal(list.network.attributes(net),list.network.attributes.active(net,onset=-Inf,terminus=Inf))
> 
> # should return regular 7 network attributes
> expect_equal(length(list.network.attributes.active(network.initialize(0),at=0)),7)
> 
> #deactivate.vertex.attribute
> ####################################################################################################################################################
> #testing if deactivating a spell with one value, leaving rest spell active
> ##########################################################################
> nd <- network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.vertex.attribute(nd,"letters","c",onset=2,terminus=3)
> deactivate.vertex.attribute(nd,prefix="letters",onset=1,terminus=2)
> 
> # was the expected structure created?
> if(!all(nd$val[[1]]$letters.active[[1]][[1]] == "a",
+         nd$val[[1]]$letters.active[[1]][[2]] == "c",
+         all(nd$val[[1]]$letters.active[[2]] == matrix(c(0,1, 2,3),ncol=2,byrow=TRUE)))){
+   stop("deactivate.vertex.attribute did not deactivate attribute with expected structure")
+ }
> 
> 
> 
> 
> nd <- network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.vertex.attribute(nd,"letters","c",onset=2,terminus=3)
> deactivate.vertex.attribute(nd,prefix="letters",onset=-Inf,terminus=Inf)
> 
> # was the expected structure created?
> if(!all(nd$val[[1]]$letters.active[[1]][[1]]=="NA",
+         nd$val[[1]]$letters.active[[2]]==matrix(c(Inf,Inf),ncol=2)
+ )){
+   stop("deactivate.vertex.attribute did not deactivate attribute with expected structure")
+ }
> 
> 
> 
> 
> 
> ##########################################################################
> #testing if the deactivating period across two spells
> ##########################################################################
> 
> nd <- network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=2)
> activate.vertex.attribute(nd,"letters","b",onset=3,terminus=5)
> activate.vertex.attribute(nd,"letters","c",onset=5,terminus=7)
> deactivate.vertex.attribute(nd,prefix="letters",onset=1,terminus=4)
> 
> # was the expected structure created?
> if(!all(nd$val[[1]]$letters.active[[1]][[1]] == "a",
+         nd$val[[1]]$letters.active[[1]][[2]] == "b",
+         nd$val[[1]]$letters.active[[1]][[3]] == "c",
+         all(nd$val[[1]]$letters.active[[2]] == matrix(c(0,1, 4,5, 5,7),ncol=2,byrow=TRUE)))){
+   stop("deactivate.vertex.attribute did not deactivate attribute with expected structure")
+ }
> 
> ##########################################################################
> #testing if the deactivating period within one spell, and keep the spell time order
> ##########################################################################
> 
> nd <- network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters","b",onset=2,terminus=5)
> activate.vertex.attribute(nd,"letters","c",onset=5,terminus=7)
> deactivate.vertex.attribute(nd,prefix="letters",onset=3,terminus=4)
> 
> # was the expected structure created?
> if(!all(nd$val[[1]]$letters.active[[1]][[1]] == "a",
+         nd$val[[1]]$letters.active[[1]][[2]] == "b",
+         nd$val[[1]]$letters.active[[1]][[3]] == "b",
+         nd$val[[1]]$letters.active[[1]][[4]] == "c",
+         all(nd$val[[1]]$letters.active[[2]] == matrix(c(0,1,2,3,4,5,5,7),ncol=2,byrow=TRUE)))){
+   stop("deactivate.vertex.attribute did not deactivate attribute with expected structure")
+ }
> 
> ##########################################################################
> #testing if the deactivating the non-activate period
> ##########################################################################
> 
> nd <- network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters","b",onset=4,terminus=5)
> activate.vertex.attribute(nd,"letters","c",onset=5,terminus=7)
> deactivate.vertex.attribute(nd,prefix="letters",onset=2,terminus=3)
> 
> # was the expected structure created?
> if(!all(nd$val[[1]]$letters.active[[1]][[1]] == "a",
+         nd$val[[1]]$letters.active[[1]][[2]] == "b",
+         nd$val[[1]]$letters.active[[1]][[3]] == "c",
+         all(nd$val[[1]]$letters.active[[2]] == matrix(c(0,1,4,5,5,7),ncol=2,byrow=TRUE)))){
+   stop("deactivate.vertex.attribute did not deactivate attribute with expected structure")
+ }
> 
> deactivate.vertex.attribute(network.initialize(0),'foo')
> 
> 
> ##########################################################################
> #04/01, testing if the deactivating the non-activate vertex
> ##########################################################################
> 
> #initialize network
> test<-network.initialize(5)
> #activate vertex attribute
> test<-activate.vertex.attribute(test,"letter","a",onset=0,terminus=3,v=1:4)
> 
> # #deactive vertex attribute
> # expect_warning(deactivate.vertex.attribute(test, "letter", onset=0, terminus=3),"intend to deactivate attribute on inactivate vertex")# need to fix this
> # 
> test <- deactivate.vertex.attribute(test, "letter", onset=0, terminus=3)
> 
> if(length(list.vertex.attributes.active(test, onset=0,terminus=3,dynamic.only=T))!=0)
+   stop("error with deactivating the non-activate vertex")
> 
> 
> ##########################################################################
> #04/04, testing if the deactivating single/two vertex attributes
> ##########################################################################
> 
> 
> nd <- network.initialize(5)
> activate.vertex.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.vertex.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.vertex.attribute(nd,"letters","c",onset=2,terminus=3)
> deactivate.vertex.attribute(nd,prefix="letters",onset=-Inf,terminus=Inf,v=c(5,2))
> 
> # get.vertex.attribute.active(nd,"letters",onset=0,terminus=3)
> # Warning message:
> #   In get.vertex.attribute.active(nd, "letters", onset = 0, terminus = 3) :
> #   Multiple attribute values matched query spell for attribute letters.active on some vertices. Only earliest value used
> 
> # was the expected structure created?
> if(!all(nd$val[[2]]$letters.active[[1]][[1]]=="NA",
+         nd$val[[2]]$letters.active[[2]]==matrix(c(Inf,Inf),ncol=2)
+ )){
+   stop("deactivate.vertex.attribute did not deactivate attribute with expected structure")
+ }
> 
> 
> if(!all(nd$val[[5]]$letters.active[[1]][[1]]=="NA",
+         nd$val[[5]]$letters.active[[2]]==matrix(c(Inf,Inf),ncol=2)
+ )){
+   stop("deactivate.vertex.attribute did not deactivate attribute with expected structure")
+ }
> 
> 
> 
> 
> 
> ##########################################################################
> ##########################################################################
> # ------ deactivate.edge.attribute
> ##########################################################################
> #testing if deactivating a spell with one value, leaving rest spell active
> ##########################################################################
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.edge.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.edge.attribute(nd,"letters","c",onset=2,terminus=3)
> 
> deactivate.edge.attribute(x=nd, prefix="letters", onset=1, terminus=2)
> 
> if(!all(nd$mel[[1]]$atl$letters.active[[1]][[1]] == "a",
+         nd$mel[[1]]$atl$letters.active[[1]][[2]] == "c",
+         all(nd$mel[[1]]$atl$letters.active[[2]] == matrix(c(0,1,2,3),ncol=2,byrow=TRUE)))){
+   stop("deactivate.vertex.attribute did not deactivate attribute with expected structure")
+ }
> 
> 
> ##########################################################################
> #testing if deactivating all spells. 
> ##########################################################################
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.edge.attribute(nd,"letters","b",onset=1,terminus=2)
> activate.edge.attribute(nd,"letters","c",onset=2,terminus=3)
> 
> deactivate.edge.attribute(x=nd, prefix="letters", onset=-Inf, terminus=Inf)
> 
> if(!all(nd$mel[[1]]$atl$letters.active[[1]][[1]]=="NA",
+         nd$mel[[1]]$atl$letters.active[[2]]==matrix(c(Inf,Inf),ncol=2)
+         
+ )){
+   stop("deactivate.edge.attribute did not deactivate attribute with expected structure")
+ }
> 
> 
> ##########################################################################
> #testing if the deactivating period across two spells
> ##########################################################################
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=2)
> activate.edge.attribute(nd,"letters","b",onset=2,terminus=4)
> activate.edge.attribute(nd,"letters","c",onset=5,terminus=6)
> 
> deactivate.edge.attribute(x=nd, prefix="letters", onset=1, terminus=3)
> 
> if(!all(nd$mel[[1]]$atl$letters.active[[1]][[1]] == "a",
+         nd$mel[[1]]$atl$letters.active[[1]][[2]] == "b",
+         nd$mel[[1]]$atl$letters.active[[1]][[3]] == "c",
+         all(nd$mel[[1]]$atl$letters.active[[2]] == matrix(c(0,1,3,4,5,6),ncol=2,byrow=TRUE)))){
+   stop("deactivate.edge.attribute did not deactivate attribute with expected structure")
+ }
> ##########################################################################
> 
> 
> ##########################################################################
> #testing if the deactivating period within one spell
> ##########################################################################
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.edge.attribute(nd,"letters","b",onset=1,terminus=4)
> activate.edge.attribute(nd,"letters","c",onset=5,terminus=6)
> 
> deactivate.edge.attribute(x=nd, prefix="letters", onset=2, terminus=3)
> 
> if(!all(nd$mel[[1]]$atl$letters.active[[1]][[1]] == "a",
+         nd$mel[[1]]$atl$letters.active[[1]][[2]] == "b",
+         nd$mel[[1]]$atl$letters.active[[1]][[3]] == "b",
+         nd$mel[[1]]$atl$letters.active[[1]][[4]] == "c",
+         all(nd$mel[[1]]$atl$letters.active[[2]] == matrix(c(0,1,1,2,3,4,5,6),ncol=2,byrow=TRUE)))){
+   stop("deactivate.edge.attribute did not deactivate attribute with expected structure")
+ }
> ##########################################################################
> 
> 
> 
> ##########################################################################
> #4/4 testing if the deactivating one or two edges
> ##########################################################################
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1)
> activate.edge.attribute(nd,"letters","b",onset=1,terminus=4)
> activate.edge.attribute(nd,"letters","c",onset=5,terminus=6)
> 
> deactivate.edge.attribute(x=nd, prefix="letters", onset=2, terminus=3, e=c(2,1))
> 
> if(!all(nd$mel[[1]]$atl$letters.active[[1]][[1]] == "a",
+         nd$mel[[1]]$atl$letters.active[[1]][[2]] == "b",
+         nd$mel[[1]]$atl$letters.active[[1]][[3]] == "b",
+         nd$mel[[1]]$atl$letters.active[[1]][[4]] == "c",
+         all(nd$mel[[1]]$atl$letters.active[[2]] == matrix(c(0,1,1,2,3,4,5,6),ncol=2,byrow=TRUE)))){
+   stop("deactivate.edge.attribute did not deactivate attribute with expected structure")
+ }
> 
> 
> if(!all(nd$mel[[3]]$atl$letters.active[[1]][[1]] == "a",
+         nd$mel[[3]]$atl$letters.active[[1]][[2]] == "b",
+         nd$mel[[3]]$atl$letters.active[[1]][[3]] == "c",
+         all(nd$mel[[3]]$atl$letters.active[[2]] == matrix(c(0,1,1,4,5,6),ncol=2,byrow=TRUE)))){
+   stop("deactivate.edge.attribute did not deactivate attribute with expected structure")
+ }
> 
> ##########################################################################
> 
> 
> expect_warning(deactivate.edge.attribute(network.initialize(0),'foo'), 'does not contain any edges')
> 
> 
> ##########################################################################
> #04/01, testing if the deactivating inacitivate edge attribute
> ##########################################################################
> nd <- network.initialize(5)
> add.edge(nd,1,2)
> add.edge(nd,2,3)
> add.edge(nd,3,4)
> activate.edge.attribute(nd,"letters","a",onset=0,terminus=1,e=1:2)
> 
> # expect_warning(deactivate.edge.attribute(nd,"letters", onset=0,terminus=1),"intend to deactivate attribute on inactivate edge")
> test <- deactivate.edge.attribute(nd,"letters", onset=0,terminus=1)
> if(!length(list.edge.attributes.active(test, onset=0,terminus=3,dynamic.only=T))==0)
+   stop("error in deactivating inacitivate edge attribute")
> 
> 
> ##########################################################################
> ##########################################################################
> # ----------------- deactivate.network.attribute
> ##########################################################################
> 
> nd <-network.initialize(5)
> activate.network.attribute(nd,"test","a",onset=1,terminus=3)
> activate.network.attribute(nd,"test","b",onset=4,terminus=5)
> activate.network.attribute(nd,"test","c",onset=6,terminus=10)
> 
> deactivate.network.attribute(nd,"test",onset=2,terminus=7)
> 
> if(!all(nd$gal$test.active[[1]][[1]] == "a",
+         nd$gal$test.active[[1]][[2]] == "c",
+         all(nd$gal$test.active[[2]] == matrix(c(1,2,7,10),ncol=2,byrow=TRUE)))){
+   stop("deactivate.network.attribute did not deactivate activity attribute with expected structure")
+ }
> 
> 
> # ---- test 'earliest' and 'latest' attribute aggregation rules ----
> test<-network.initialize(1)
> activate.vertex.attribute(test,'letter',"a",onset=0,terminus=1)
> activate.vertex.attribute(test,'letter',"b",onset=1,terminus=2)
> activate.vertex.attribute(test,'letter',"c",onset=2,terminus=3)
> expect_equal(get.vertex.attribute.active(test,'letter',onset=0,terminus=4,rule='earliest'),'a')
> expect_equal(get.vertex.attribute.active(test,'letter',onset=0,terminus=4,rule='latest'),'c')
> 
> test<-network.initialize(2)
> test[1,2]<-1
> activate.edge.attribute(test,'letter',"a",onset=0,terminus=1)
> activate.edge.attribute(test,'letter',"b",onset=1,terminus=2)
> activate.edge.attribute(test,'letter',"c",onset=2,terminus=3)
> expect_equal(get.edge.attribute.active(test,'letter',onset=0,terminus=4,rule='earliest'),'a')
> expect_equal(get.edge.attribute.active(test,'letter',onset=0,terminus=4,rule='latest'),'c')
> 
> 
> test<-network.initialize(1)
> activate.network.attribute(test,'letter',"a",onset=0,terminus=1)
> activate.network.attribute(test,'letter',"b",onset=1,terminus=2)
> activate.network.attribute(test,'letter',"c",onset=2,terminus=3)
> expect_equal(get.network.attribute.active(test,'letter',onset=0,terminus=4,rule='earliest'),'a')
> expect_equal(get.network.attribute.active(test,'letter',onset=0,terminus=4,rule='latest'),'c')
> 
> 
> proc.time()
   user  system elapsed 
   2.09    0.18    2.21