R Under development (unstable) (2024-11-21 r87360 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
> ######################################################################
> # tests for the reconcile activity functions
> 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' 0.11.5 (2024-11-21), 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
> 
> # ---- reconcile.vertex.activity tests ------------
> # test when called with wrong object
> expect_error(reconcile.vertex.activity("net"), 'only be applied to networkDynamic objects')
> 
> # test with isolate and inactive edge
> nd<-network.initialize(6)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> nd2<-reconcile.vertex.activity(nd,mode='match')
> spls<-get.vertex.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(-Inf, 1,1,1,5,-Inf),info='test reconcile.vertex.activity w isolate and inactive')
> expect_equal(spls$terminus,c(Inf,3,3,3,7,Inf))
> expect_equal(spls$vertex.id,c(1,2,3,4,4,5))
> 
> # test modifiy in place
> nd<-network.initialize(6)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> reconcile.vertex.activity(nd,mode='match')
> spls<-get.vertex.activity(nd,as.spellList=TRUE)
> expect_equal(spls$onset,c(-Inf, 1,1,1,5,-Inf),info='reconcile.vertex.activity modify in place')
> expect_equal(spls$terminus,c(Inf,3,3,3,7,Inf),info='reconcile.vertex.activity modify in place')
> expect_equal(spls$vertex.id,c(1,2,3,4,4,5),info='reconcile.vertex.activity modify in place')
> 
> # test with edge active default FALSE
> nd<-network.initialize(6)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> nd2<-reconcile.vertex.activity(nd, mode='match',edge.active.default=FALSE)
> spls<-get.vertex.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(1, 5, 1, 1, 1, 5))
> expect_equal(spls$terminus,c(3, 7, 3, 3, 3, 7))
> expect_equal(spls$vertex.id,c(1, 1, 2, 3, 4, 4))
> 
> # test with bad mode
> expect_error(reconcile.vertex.activity(nd,mode='foobar'),"'arg' should be one of")
> 
> # ---- reconcile.vertex.activity tests (expand.to.edges mode) ------------
> 
> nd<-network.initialize(6)
> deactivate.vertices(nd, onset=-Inf, terminus=Inf)
> activate.vertices(nd, v=2, onset=2, terminus=5)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> nd2<-reconcile.vertex.activity(nd, mode='expand.to.edges')
> spls<-get.vertex.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(-Inf, 1,1,1,5,-Inf))
> expect_equal(spls$terminus,c(Inf,5,3,3,7,Inf))
> expect_equal(spls$vertex.id,c(1,2,3,4,4,5))
> 
> nd<-network.initialize(6)
> deactivate.vertices(nd, onset=-Inf, terminus=Inf)
> activate.vertices(nd, v=2, onset=5, terminus=7)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> nd2<-reconcile.vertex.activity(nd, mode='expand.to.edges')
> spls<-get.vertex.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(-Inf, 1,5,1,1,5,-Inf))
> expect_equal(spls$terminus,c(Inf,3,7,3,3,7,Inf))
> expect_equal(spls$vertex.id,c(1,2,2,3,4,4,5))
> 
> # test active default
> 
> nd<-network.initialize(3,directed=FALSE)
> activate.vertices(nd,at=0)
> nd[,]<-1
> reconcile.vertex.activity(nd,mode='expand',edge.active.default=TRUE)
> spls<-get.vertex.activity(nd,as.spellList=TRUE)
> expect_equal(spls$onset,c(-Inf,-Inf,-Inf))
> expect_equal(spls$terminus,c(Inf,Inf,Inf))
> 
> nd<-network.initialize(3,directed=FALSE)
> activate.vertices(nd,at=0)
> nd[,]<-1
> reconcile.vertex.activity(nd,mode='expand',edge.active.default=FALSE)
> spls<-get.vertex.activity(nd,as.spellList=TRUE)
> expect_equal(spls$onset,c(0,0,0))
> expect_equal(spls$terminus,c(0,0,0))
> 
> 
> # ---- reconcile.vertex.activity tests (encompass.edges mode) ------------
> 
> nd<-network.initialize(3)
> activate.vertices(nd,v=1,onset=0,terminus=2)
> activate.vertices(nd,v=1,onset=3,terminus=4)
> add.edges.active(nd,tail=1,head=2,onset=-1,terminus=5)
> reconcile.vertex.activity(nd, mode='encompass.edges')
> 
> 
> nd<-network.initialize(6)
> deactivate.vertices(nd, onset=-Inf, terminus=Inf)
> activate.vertices(nd, v=2, onset=2, terminus=5)
> activate.vertices(nd, v=2, onset=8, terminus=10)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> nd2<-reconcile.vertex.activity(nd, mode='encompass.edges')
> spls<-get.vertex.activity(nd2,as.spellList=TRUE)
> # combines the spells for vertex 4
> expect_equal(spls$onset,c(-Inf, 1,1,1,-Inf))
> expect_equal(spls$terminus,c(Inf,3,3,7,Inf))
> expect_equal(spls$vertex.id,c(1,2,3,4,5))
> 
> # testing 0-duration spells
> nd<-network.initialize(6)
> deactivate.vertices(nd, onset=-Inf, terminus=Inf)
> activate.vertices(nd, v=2, onset=2, terminus=5)
> add.edges.active(nd,tail=1:2,head=2:3,onset=1,terminus=3)
> 
> add.edges.active(nd,tail=4,head=1,onset=9,terminus=9)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> activate.edges(nd, e=2, at=3)
> #get.edge.activity(nd, as.spell=T)
> #get.vertex.activity(nd, as.spell=T)
> nd2<-reconcile.vertex.activity(nd, mode='encompass.edges')
> spls<-get.vertex.activity(nd2,as.spellList=TRUE)
> # combines the spells for vertex 4
> expect_equal(spls$onset,c(-Inf, 1,1,9,-Inf))
> expect_equal(spls$terminus,c(Inf,4,4,9,Inf))
> expect_equal(spls$vertex.id,c(1,2,3,4,5))
> 
> 
> # ---- reconcile.edge.activity tests (reduce.to.vertices mode) ------------
> nd<- network.initialize(6)
> activate.vertices(nd, onset=1, terminus=2)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> #get.edge.activity(nd, as.spell=T)
> #get.vertex.activity(nd, as.spell=T)
> nd2<-reconcile.edge.activity(nd, mode='reduce.to.vertices')
> spls<-get.edge.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(1,1,1,1))
> expect_equal(spls$terminus,c(2,2,2,2))
> expect_equal(spls$edge.id,c(1,2,3,6))
> 
> # censored spells
> nd<- network.initialize(6)
> activate.vertices(nd, onset=2, terminus=Inf)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> #get.edge.activity(nd, as.spell=T)
> #get.vertex.activity(nd, as.spell=T)
> nd2<-reconcile.edge.activity(nd, mode='reduce.to.vertices')
> spls<-get.edge.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(2,2,2,5,2))
> expect_equal(spls$terminus,c(3,3,3,7,Inf))
> expect_equal(spls$edge.id,c(1,2,3,4,6))
> 
> # 0-duration spells
> nd<- network.initialize(6)
> activate.vertices(nd, onset=1, terminus=2)
> activate.vertices(nd, at=6)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> #get.edge.activity(nd, as.spell=T)
> #get.vertex.activity(nd, as.spell=T)
> nd2<-reconcile.edge.activity(nd, mode='reduce.to.vertices')
> spls<-get.edge.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(1,1,1,6,1,6))
> expect_equal(spls$terminus,c(2,2,2,6,2,6))
> expect_equal(spls$edge.id,c(1,2,3,4,6,6))
> 
> 
> # ---- reconcile.edge.activity tests (match.to.vertices mode) ------------
> nd<- network.initialize(6)
> activate.vertices(nd, onset=1, terminus=2)
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> deactivate.edges(nd, onset=-Inf, terminus=Inf, e=get.edgeIDs(nd, v=1, alter=6))
> add.edge(nd,tail=1, head=5)  # default activated
> get.edge.activity(nd, as.spell=T)
  onset terminus tail head onset.censored terminus.censored duration edge.id
1     1        3    1    2          FALSE             FALSE        2       1
2     1        3    2    3          FALSE             FALSE        2       2
3     1        3    3    4          FALSE             FALSE        2       3
4     5        7    4    1          FALSE             FALSE        2       4
5  -Inf      Inf    1    5           TRUE              TRUE      Inf       6
> get.vertex.activity(nd, as.spell=T)
  onset terminus vertex.id onset.censored terminus.censored duration
1     1        2         1          FALSE             FALSE        1
2     1        2         2          FALSE             FALSE        1
3     1        2         3          FALSE             FALSE        1
4     1        2         4          FALSE             FALSE        1
5     1        2         5          FALSE             FALSE        1
6     1        2         6          FALSE             FALSE        1
> nd2<-reconcile.edge.activity(nd, mode='match.to.vertices')
> spls<-get.edge.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(1,1,1,1,1,1))
> expect_equal(spls$terminus,c(2,2,2,2,2,2))
> expect_equal(spls$edge.id,c(1,2,3,4,5,6))
> 
> # 0-duration spells
> nd<- network.initialize(6)
> activate.vertices(nd, onset=1, terminus=2, v=c(1,2,3))
> deactivate.vertices(nd, v=4, onset=-Inf, terminus=Inf)
> activate.vertices(nd, at=6, v=c(1,6))
> add.edges.active(nd,tail=1:3,head=2:4,onset=1,terminus=3)
> add.edges.active(nd,tail=4,head=1,onset=5,terminus=7)
> add.edge(nd,tail=1,head=6)
> add.edge(nd,tail=1, head=5)  # default activated
> #get.edge.activity(nd, as.spell=T)
> #get.vertex.activity(nd, as.spell=T)
> nd2<-reconcile.edge.activity(nd, mode='match.to.vertices')
> spls<-get.edge.activity(nd2,as.spellList=TRUE)
> expect_equal(spls$onset,c(1,1,6,1,6))
> expect_equal(spls$terminus,c(2,2,6,2,6))
> expect_equal(spls$edge.id,c(1,2,5,6,6))
> 
> # test error from bad mode
> expect_error(nd2<-reconcile.edge.activity(nd, mode='destroy.everything!'),"'arg' should be one of")
> 
> proc.time()
   user  system elapsed 
   4.10    0.56    4.65