R Under development (unstable) (2024-07-02 r86866 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #  part of the Statnet suite
> #  of packages for network analysis, http://statnet.org .
> #
> #  This software is distributed under the GPL-3 license.  It is free,
> #  open source, and has the attribution requirements (GPL Section 7) at
> #  http://statnet.org/attribution
> #
> #  Copyright 2012-2014 Statnet Commons
> #######################################################################
> 
> # tests for the network animation layout functions
> require(ndtv)
Loading required package: ndtv
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

Loading required package: networkDynamic

'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

Loading required package: animation
Loading required package: sna
Loading required package: statnet.common

Attaching package: 'statnet.common'

The following objects are masked from 'package:base':

    attr, order

sna: Tools for Social Network Analysis
Version 2.7-2 created on 2023-12-05.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.


'ndtv' 0.13.4 (2024-06-30), part of the Statnet Project
* 'news(package="ndtv")' for changes since last version
* 'citation("ndtv")' for citation information
* 'https://statnet.org' for help, support, and other information

> require(testthat)
Loading required package: testthat
> # ---- test using a dynamic attribute for layout positions ----
> 
> # check what happens if coords not defined
> nd <-as.networkDynamic(network.initialize(3))
> expect_error(compute.animation(nd,animation.mode='useAttribute'), 'unable to find vertex attribute x containing x')
No slice.par found, using
slice parameters:
  start:0
  end:0
  interval:1
  aggregate.dur:1
  rule:latest

Calculating layout for network slice from time  0 to 1
Warning message:
In guessSlicePar(net) :
  network does not appear to have any dynamic information. Using start=0 end=1
> 
> #check when coordinates specified
> nd <-network.initialize(3)
> activate.vertex.attribute(nd,'x',c(1,2,3),at=0)
> activate.vertex.attribute(nd,'y',c(0,0,0),at=0)
> activate.vertex.attribute(nd,'x',c(2,3,4),at=1)
> activate.vertex.attribute(nd,'y',c(1,1,1),at=1)
> activate.vertex.attribute(nd,'x',c(3,4,5),at=2)
> activate.vertex.attribute(nd,'y',c(2,2,2),at=2)
> 
> compute.animation(nd,animation.mode='useAttribute',layout.par=list(x='x',y='y'))
No slice.par found, using
slice parameters:
  start:0
  end:2
  interval:1
  aggregate.dur:1
  rule:latest

Calculating layout for network slice from time  0 to 1
Calculating layout for network slice from time  1 to 2
Calculating layout for network slice from time  2 to 3
> expect_equal(unlist(get.vertex.attribute(nd,'x.active',unlist=FALSE)[[1]][[1]]),1:3)
> 
> 
> # check what happens if coords missing for time period
> nd <-network.initialize(3)
> activate.vertex.attribute(nd,'x',c(1,2,3),at=0)
> activate.vertex.attribute(nd,'y',c(0,0,0),at=0)
> activate.vertex.attribute(nd,'x',c(2,3,4),at=3)
> activate.vertex.attribute(nd,'y',c(1,1,1),at=3)
> activate.vertex.attribute(nd,'x',c(3,4,5),at=4)
> activate.vertex.attribute(nd,'y',c(2,2,2),at=4)
> expect_error(compute.animation(nd,animation.mode='useAttribute',layout.par=list(x='x',y='y')),'coordinates must be numeric')
No slice.par found, using
slice parameters:
  start:0
  end:4
  interval:1
  aggregate.dur:1
  rule:latest

Calculating layout for network slice from time  0 to 1
Calculating layout for network slice from time  1 to 2
> 
> # ------ test layout.distance function ----
> test<-network.initialize(4)
> add.edges(test,tail=1:2,head=2:3)
> expect_equal(layout.distance(test),matrix(c(0,1,2,2,1,0,1,2,2,1,0,2,2,2,2,0),ncol=4,byrow=TRUE), info='test layout distance')
> expect_equal(layout.distance(test,.5),matrix(c(0,1,2,.5, 1,0,1,.5, 2,1,0,.5, .5,.5,.5,0),ncol=4,byrow=TRUE),info='test inf replace value for layout distance')
> 
> set.edge.attribute(test,'weight',c(3,6))
> expect_equal(layout.distance(test,weight.attr='weight'),matrix(c(0, 6, 9, 2, 6, 0, 3, 2, 9, 3, 0, 2, 2, 2, 2, 0),ncol=4,byro=TRUE),info='test layout distance with weights')
> 
> expect_equal(layout.distance(test,weight.attr='weight',weight.dist=TRUE),matrix(c(0, 3, 9, 2, 3, 0, 6, 2, 9, 6, 0, 2, 2, 2, 2, 0),ncol=4,byro=TRUE),info='test layout distance with weights with weights as distance')
> 
> # test symetrization
> test_that("symetrization of directed network according to weight.dist",{
+   test<-network.initialize(2,directed=TRUE)
+   test[1,2]<-1
+   test[2,1]<-1
+   set.edge.attribute(test,'count',value=c(1,2))
+   expect_equal(as.vector(layout.distance(test,weight.attr='count',weight.dist=TRUE)),c(0,1,1,0))
+   expect_equal(as.vector(layout.distance(test,weight.attr='count',weight.dist=FALSE)),c(0,2,2,0))
+ })
Test passed 🥳
> 
> # ----- test layout centering ----
> 
> pos<-matrix(c(1:5,1:5),ncol=2,byrow=FALSE)
> 
> # center on 0,0
> expect_equal(layout.center(pos,xlim=c(0,0),ylim=c(0,0)),pos-3)
> 
> # center in 100 px square
> expect_equal(layout.center(pos,xlim=c(0,100),ylim=c(0,100)),matrix(c(48, 49, 50, 51, 52, 48, 49, 50, 51, 52),ncol=2))
> 
> 
> # ----- test layout zooming ------
> 
> pos<-matrix(c(1:5,1:5),ncol=2,byrow=FALSE)
> 
> # factor 0 does nothing
> expect_equal(ndtv:::layout.zoomfactor(pos,0),pos)
> 
> # factor 10 (scale at origin)
> expect_equal(ndtv:::layout.zoomfactor(pos,10),pos*10)
> 
> # factor 10, scale at 1,1
> expect_equal(ndtv:::layout.zoomfactor(pos,10,center=c(1,1)),(pos*10)-9)
> 
> # zoom on set of vertices
> expect_equal(ndtv:::layout.zoomfactor(pos,2,v=2:3),matrix(c(-0.5, 1.5, 3.5, 5.5, 7.5, -0.5, 1.5, 3.5, 5.5, 7.5),ncol=2))
> 
> # ----- graphviz tests -----
> 
> # graphviz layout test
> # set up a basic tree structure
> tree<-network.initialize(21)
> add.edges.active(tree,head=1,tail=2,onset=0,terminus=5)
> add.edges.active(tree,head=c(2,2),tail=c(3,4),onset=1,terminus=5)
> add.edges.active(tree,head=c(3,3,3,4,4),tail=5:9,onset=2,terminus=5)
> add.edges.active(tree,head=c(6,6,8,9,9),tail=10:14,onset=3,terminus=5)
> add.edges.active(tree,head=c(10,10,12,12,12,14,14),tail=15:21,onset=4,terminus=5)
> 
> # the tests below are contional on graphviz being installed on the system
> if (ndtv:::check.graphviz()){
+ #plot.network(tree,coord=network.layout.animate.Graphviz(tree))
+ coords<-network.layout.animate.Graphviz(tree)
+ expect_equal(nrow(coords),21)
+ expect_equal(ncol(coords),2)
+ 
+ # check verbose
+ network.layout.animate.Graphviz(tree,verbose=FALSE)
+ 
+ # check using layout par to set differnet engines
+ network.layout.animate.Graphviz(tree,layout.par=list(gv.engine='dot'))
+ 
+ # check passing in gv.args
+ network.layout.animate.Graphviz(tree,layout.par=list(gv.engine='dot',gv.args='-Grankdir=LR'))
+ 
+ # check passing bad gv.args
+ expect_error(network.layout.animate.Graphviz(tree,layout.par=list(gv.args='-Xhelloworld'),verbose=FALSE),regexp = 'Unable to parse coordinates')
+ 
+ # test passing a weighted network into neato
+ wtest<-network.initialize(5)
+ add.edges.active(wtest,tail = 1,head=2,onset=0,terminus=10)
+ add.edges.active(wtest,tail = 2,head=3,onset=1,terminus=10)
+ add.edges.active(wtest,tail = 3,head=4,onset=2,terminus=10)
+ activate.edge.attribute(wtest,'len',0.5,onset=0,terminus=5,e = 1)
+ activate.edge.attribute(wtest,'len',2.5,onset=5,terminus=10,e=1)
+ activate.edge.attribute(wtest,'len',2,onset=1,terminus=5,e = 2)
+ activate.edge.attribute(wtest,'len',1,onset=5,terminus=10,e=2)
+ activate.edge.attribute(wtest,'len',5,onset=2,terminus=5,e = 3)
+ activate.edge.attribute(wtest,'len',0.1,onset=5,terminus=10,e=3)
+ 
+ # test rendering using the gv 'len' attrigute
+ compute.animation(wtest,animation.mode = 'Graphviz',layout.par=list(gv.len.mode='gv.edge.len',gv.edge.attrs='len'))
+ #render.animation(wtest,edge.lwd='len')
+ 
+ # test passing in matrix of distances
+ compute.animation(wtest,animation.mode = 'Graphviz',weight.attr='len',layout.par=list(gv.engine='neato',gv.len.mode='ndtv.distance.matrix'))
+ 
+ # test using default dist to generate a matrix
+ compute.animation(wtest,animation.mode = 'Graphviz',default.dist=5)
+ 
+ # test bad weight mode
+ expect_error(compute.animation(wtest,animation.mode = 'Graphviz',layout.par=list(gv.len.mode='bla')))
+ 
+ }  else {
+ # graphivz not installed, so check fallback to kk
+ warning("graphviz layout tests skipped because graphviz not installed on system")
+ expect_warning(coords<-network.layout.animate.Graphviz(tree),'KamadaKawai')
+ expect_equal(nrow(coords),21)
+ expect_equal(ncol(coords),2)
+ 
+ }
Warning messages:
1: In ndtv:::check.graphviz() :
  The Graphviz neato utility does not appear to be installed on this system. See ?install.graphviz for more information
2: graphviz layout tests skipped because graphviz not installed on system 
> 
> # ------------- MDSJ tests -------
> # COMMENTING BECAUSE SKIP_ON_CRAN_STOPPED_WORKING
> # test_that("MDSJ algorithms",{
> # these need to be optionally enabled because they won't run if java and mdsj library not installed
> # skip_on_cran()
> # if (!is.null(ndtv:::check.mdsj()) ){
> #   wtest<-network.initialize(5)
> #   add.edges.active(wtest,tail = 1,head=2,onset=0,terminus=10)
> #   add.edges.active(wtest,tail = 2,head=3,onset=1,terminus=10)
> #   add.edges.active(wtest,tail = 3,head=4,onset=2,terminus=10)
> #   activate.edge.attribute(wtest,'len',0.5,onset=0,terminus=5,e = 1)
> #   activate.edge.attribute(wtest,'len',2.5,onset=5,terminus=10,e=1)
> #   activate.edge.attribute(wtest,'len',2,onset=1,terminus=5,e = 2)
> #   activate.edge.attribute(wtest,'len',1,onset=5,terminus=10,e=2)
> #   activate.edge.attribute(wtest,'len',5,onset=2,terminus=5,e = 3)
> #   activate.edge.attribute(wtest,'len',0.1,onset=5,terminus=10,e=3)
> #   
> #   compute.animation(wtest,animation.mode = 'MDSJ',weight.attr='len')
> # 
> #  # dests for changing dimensions of MDSJ layout
> # test<-network.initialize(10)
> # dim2mat<-network.layout.animate.MDSJ(test,layout.par=list(dimensions=2))
> # expect_equal(dim(dim2mat),c(10,2))
> # dim1mat<-network.layout.animate.MDSJ(test,layout.par=list(dimensions=1))
> # expect_equal(dim(dim1mat),c(10,1))
> # }
> # })
> 
> 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
   1.53    0.26    1.78