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Commented out Pajek tests that relied on a remote server (which is do…
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…wn).

references #66
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@krivit
krivit committed Nov 18, 2024
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304 changes: 152 additions & 152 deletions tests/testthat/test-read.paj.R
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Expand Up @@ -154,158 +154,158 @@ expect_equal(fillIn%v%'shape',c('box','box','box','ellipse'))



# this file has character encoding issues
scotland<-tempfile('scotland',fileext='.zip')
download.file(
'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip',
scotland,
quiet = TRUE)
scotpaj<-tempfile('Scotland',fileext='.paj')
con <- unz(scotland,'Scotland.paj')
cat(
readLines(con, encoding = "UTF-8"),
sep='\n',
file = scotpaj
)
close(con)
scotproj<-read.paj(scotpaj)

# produces two element list, containing networks and partitions
expect_equal(names(scotproj),c("networks","partitions"))
expect_equal(network.size(scotproj[[1]][[1]]),244)
expect_equal(names(scotproj$partitions),c("Affiliation.partition.of.N1.[108,136]","Industrial_categories.clu"))


A95net<-read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd95/A95.net")
expect_equal(network.size(A95net),36)
expect_equal(network.vertex.names(A95net)[1:5],c("MUX","INSTRUCTION BUFFER (4 x 16)", "RCV","DRV","ROM REG"))

# test reading a .paj project file
bkfratProj<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/data/ucinet/bkfrat.paj')

# should have two networks
expect_equal(sapply(bkfratProj,class),c('network','network'),check.attributes=FALSE)
# .. with wierd names
expect_equal(names(bkfratProj),c('UciNet\\BKFRAT.DAT : BKFRAB','UciNet\\BKFRAT.DAT : BKFRAC'))
# and 58 vertices
expect_equal(sapply(bkfratProj,network.size),c(58,58),check.attributes=FALSE)
expect_equal(sapply(bkfratProj,network.edgecount),c(1934,3306),check.attributes=FALSE)

#check edge values and attribute naming
expect_equal((bkfratProj[[1]]%e%"UciNet\\BKFRAT.DAT : BKFRAB")[1900:1934],c(1, 1, 1, 5, 2, 4, 2, 1, 3, 1, 3, 1, 2, 5, 1, 1, 1, 2, 1, 2, 2, 1, 6, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 1, 1))

# check vert attrs
expect_equal(list.vertex.attributes(bkfratProj[[1]]),c('na','vertex.names','x','y','z'))

# check network attrs
expect_equal(bkfratProj[[1]]%n%'title',"UciNet\\BKFRAT.DAT : BKFRAB")
expect_equal(bkfratProj[[2]]%n%'title',"UciNet\\BKFRAT.DAT : BKFRAC")

# check loop flagging

tmptest<-tempfile()
cat("*Vertices 2
1 'A'
2 'B'
*Arcs
1 1 1
",file=tmptest)
loopTest<-read.paj(tmptest,verbose=FALSE)
expect_true(has.loops(loopTest))

# check edge.name argument

tmptest<-tempfile()
cat("*Vertices 2
1 'A'
2 'B'
*Arcs
1 1 1
",file=tmptest)
loopTest<-read.paj(tmptest,verbose=FALSE,edge.name='weight')
expect_equal(list.edge.attributes(loopTest),c('na','weight'))

# the rest of these will take longer, so including in opttest block so won't run on CRAN
require(statnet.common)
opttest(testvar = "ENABLE_statnet_TESTS",{


# ----- examples from http://vlado.fmf.uni-lj.si/pub/networks/doc/ECPR/08/ECPR01.pdf ---

GraphSet<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/GraphSet.net')
expect_true(is.directed(GraphSet))
expect_equal(network.edgecount(GraphSet),27)
# network contains some repeated edges
expect_true(is.multiplex(GraphSet))
expect_equal(network.vertex.names(GraphSet),letters[1:12])

Tina<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/TinaSet.net')

# arcslist
GraphList<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/GraphList.net')
# http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/TinaList.net # arcslist

# matrix
GraphMat <-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/GraphMat.net')
expect_equal(network.vertex.names(GraphMat),letters[1:12])
# check that edge attribute created and parsed correctly
expect_equal(as.matrix(GraphMat,attrname='GraphMat')[3,7],2)

# partition
TinaPaj<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Tina.paj')
expect_equal(class(TinaPaj$partitions),'data.frame')
expect_equal( TinaPaj$partitions[,1],c(2,1,2,2,2,2,2,2,3,3,3),use.names=FALSE)
expect_true(is.network(TinaPaj$networks$Tina))

# --- crude timing info --
# by default timing info should be added as attribute
timetest<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Time.net')
expect_equal(timetest%e%'pajekTiming',c("[7]","[6-8]"))
expect_equal(timetest%v%'pajekTiming',c("[5-10,12-14]", "[1-3,7]", "[4-*]"))
expect_true(setequal(list.vertex.attributes(timetest),c('na','pajekTiming','vertex.names'))) # no x or y
expect_true(setequal(list.edge.attributes(timetest),c('na','pajekTiming','Time')))

# test converting to networkDynamic format
timetestNd<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Time.net',time.format='networkDynamic')
expect_equal(class(timetestNd),c('networkDynamic','network'))
# check that activiy matrices are built as expected
expect_equal(get.vertex.attribute(timetestNd,'active',unlist=FALSE),list(structure(c(5, 12, 11, 15), .Dim = c(2L, 2L)), structure(c(1, 7, 4, 8), .Dim = c(2L, 2L)), structure(c(4, Inf), .Dim = 1:2)))
expect_equal(get.edge.attribute(timetestNd,'active',unlist=FALSE),list(structure(c(7, 8), .Dim = 1:2), structure(c(6, 9), .Dim = 1:2)))

# read a *big* one http://vlado.fmf.uni-lj.si/pub/networks/data/CRA/Days.zip
# 1.3 Mb, 13k vertices, 256K lines.
# days<-tempfile('days',fileext='.zip')
# download.file('http://vlado.fmf.uni-lj.si/pub/networks/data/CRA/Days.zip',days)
# terrorTerms<-read.paj(unz(days,'Days.net'),verbose=TRUE,time.format='networkDynamic',edge.name='count')



# multiple networks
sampson<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/pajek/data/Sampson.net')
lapply(sampson,class) # for some reason it is a formula?
expect_equal(names(sampson$networks),c("SAMPLK1", "SAMPLK2", "SAMPLK3", "SAMPDLK", "SAMPES","SAMPDES","SAMPIN","SAMPNIN","SAMPPR","SAMNPR"))

# multiple networks in arcslist format
# sampsonL<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/pajek/data/SampsonL.net')

# two-mode
sandi<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/data/2mode/sandi/sandi.net')
expect_true(is.bipartite(sandi))
expect_equal(sandi%n%'bipartite',314)
Davis<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Davis.paj') # two-mode
expect_equal(Davis$networks[[1]]%n%'bipartite',18)

# lots of edge and vertex attributes
A96<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd96/A96.net')
expect_equal(network.size(A96),1096)
expect_equal(list.vertex.attributes(A96),c("bw","fos","na","shape","vertex.names", "x","x_fact","y","y_fact")) # note no z attribute
expect_equal(head(A96%v%'shape'),c("box","ellipse", "ellipse", "ellipse", "ellipse", "ellipse"))
# check edge attribute parsing
expect_equal(list.edge.attributes(A96),c("A96", "fos", "l" , "lr", "na", "s", "w" ))
# l is the only one with unique values
expect_equal(head(A96%e%'l'),c("a", "s","n","r","s","t"))

}) # end of non-cran tests
## # this file has character encoding issues
## scotland<-tempfile('scotland',fileext='.zip')
## download.file(
## 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip',
## scotland,
## quiet = TRUE)
## scotpaj<-tempfile('Scotland',fileext='.paj')
## con <- unz(scotland,'Scotland.paj')
## cat(
## readLines(con, encoding = "UTF-8"),
## sep='\n',
## file = scotpaj
## )
## close(con)
## scotproj<-read.paj(scotpaj)

## # produces two element list, containing networks and partitions
## expect_equal(names(scotproj),c("networks","partitions"))
## expect_equal(network.size(scotproj[[1]][[1]]),244)
## expect_equal(names(scotproj$partitions),c("Affiliation.partition.of.N1.[108,136]","Industrial_categories.clu"))


## A95net<-read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd95/A95.net")
## expect_equal(network.size(A95net),36)
## expect_equal(network.vertex.names(A95net)[1:5],c("MUX","INSTRUCTION BUFFER (4 x 16)", "RCV","DRV","ROM REG"))

## # test reading a .paj project file
## bkfratProj<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/data/ucinet/bkfrat.paj')

## # should have two networks
## expect_equal(sapply(bkfratProj,class),c('network','network'),check.attributes=FALSE)
## # .. with wierd names
## expect_equal(names(bkfratProj),c('UciNet\\BKFRAT.DAT : BKFRAB','UciNet\\BKFRAT.DAT : BKFRAC'))
## # and 58 vertices
## expect_equal(sapply(bkfratProj,network.size),c(58,58),check.attributes=FALSE)
## expect_equal(sapply(bkfratProj,network.edgecount),c(1934,3306),check.attributes=FALSE)

## #check edge values and attribute naming
## expect_equal((bkfratProj[[1]]%e%"UciNet\\BKFRAT.DAT : BKFRAB")[1900:1934],c(1, 1, 1, 5, 2, 4, 2, 1, 3, 1, 3, 1, 2, 5, 1, 1, 1, 2, 1, 2, 2, 1, 6, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 1, 1))

## # check vert attrs
## expect_equal(list.vertex.attributes(bkfratProj[[1]]),c('na','vertex.names','x','y','z'))

## # check network attrs
## expect_equal(bkfratProj[[1]]%n%'title',"UciNet\\BKFRAT.DAT : BKFRAB")
## expect_equal(bkfratProj[[2]]%n%'title',"UciNet\\BKFRAT.DAT : BKFRAC")

## # check loop flagging

## tmptest<-tempfile()
## cat("*Vertices 2
## 1 'A'
## 2 'B'
## *Arcs
## 1 1 1
## ",file=tmptest)
## loopTest<-read.paj(tmptest,verbose=FALSE)
## expect_true(has.loops(loopTest))

## # check edge.name argument

## tmptest<-tempfile()
## cat("*Vertices 2
## 1 'A'
## 2 'B'
## *Arcs
## 1 1 1
## ",file=tmptest)
## loopTest<-read.paj(tmptest,verbose=FALSE,edge.name='weight')
## expect_equal(list.edge.attributes(loopTest),c('na','weight'))

## # the rest of these will take longer, so including in opttest block so won't run on CRAN
## require(statnet.common)
## opttest(testvar = "ENABLE_statnet_TESTS",{


## # ----- examples from http://vlado.fmf.uni-lj.si/pub/networks/doc/ECPR/08/ECPR01.pdf ---

## GraphSet<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/GraphSet.net')
## expect_true(is.directed(GraphSet))
## expect_equal(network.edgecount(GraphSet),27)
## # network contains some repeated edges
## expect_true(is.multiplex(GraphSet))
## expect_equal(network.vertex.names(GraphSet),letters[1:12])

## Tina<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/TinaSet.net')

## # arcslist
## GraphList<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/GraphList.net')
## # http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/TinaList.net # arcslist

## # matrix
## GraphMat <-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/GraphMat.net')
## expect_equal(network.vertex.names(GraphMat),letters[1:12])
## # check that edge attribute created and parsed correctly
## expect_equal(as.matrix(GraphMat,attrname='GraphMat')[3,7],2)

## # partition
## TinaPaj<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Tina.paj')
## expect_equal(class(TinaPaj$partitions),'data.frame')
## expect_equal( TinaPaj$partitions[,1],c(2,1,2,2,2,2,2,2,3,3,3),use.names=FALSE)
## expect_true(is.network(TinaPaj$networks$Tina))

## # --- crude timing info --
## # by default timing info should be added as attribute
## timetest<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Time.net')
## expect_equal(timetest%e%'pajekTiming',c("[7]","[6-8]"))
## expect_equal(timetest%v%'pajekTiming',c("[5-10,12-14]", "[1-3,7]", "[4-*]"))
## expect_true(setequal(list.vertex.attributes(timetest),c('na','pajekTiming','vertex.names'))) # no x or y
## expect_true(setequal(list.edge.attributes(timetest),c('na','pajekTiming','Time')))

## # test converting to networkDynamic format
## timetestNd<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Time.net',time.format='networkDynamic')
## expect_equal(class(timetestNd),c('networkDynamic','network'))
## # check that activiy matrices are built as expected
## expect_equal(get.vertex.attribute(timetestNd,'active',unlist=FALSE),list(structure(c(5, 12, 11, 15), .Dim = c(2L, 2L)), structure(c(1, 7, 4, 8), .Dim = c(2L, 2L)), structure(c(4, Inf), .Dim = 1:2)))
## expect_equal(get.edge.attribute(timetestNd,'active',unlist=FALSE),list(structure(c(7, 8), .Dim = 1:2), structure(c(6, 9), .Dim = 1:2)))

## # read a *big* one http://vlado.fmf.uni-lj.si/pub/networks/data/CRA/Days.zip
## # 1.3 Mb, 13k vertices, 256K lines.
## # days<-tempfile('days',fileext='.zip')
## # download.file('http://vlado.fmf.uni-lj.si/pub/networks/data/CRA/Days.zip',days)
## # terrorTerms<-read.paj(unz(days,'Days.net'),verbose=TRUE,time.format='networkDynamic',edge.name='count')



## # multiple networks
## sampson<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/pajek/data/Sampson.net')
## lapply(sampson,class) # for some reason it is a formula?
## expect_equal(names(sampson$networks),c("SAMPLK1", "SAMPLK2", "SAMPLK3", "SAMPDLK", "SAMPES","SAMPDES","SAMPIN","SAMPNIN","SAMPPR","SAMNPR"))

## # multiple networks in arcslist format
## # sampsonL<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/pajek/data/SampsonL.net')

## # two-mode
## sandi<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/data/2mode/sandi/sandi.net')
## expect_true(is.bipartite(sandi))
## expect_equal(sandi%n%'bipartite',314)
## Davis<-read.paj('http://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Davis.paj') # two-mode
## expect_equal(Davis$networks[[1]]%n%'bipartite',18)

## # lots of edge and vertex attributes
## A96<-read.paj('http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd96/A96.net')
## expect_equal(network.size(A96),1096)
## expect_equal(list.vertex.attributes(A96),c("bw","fos","na","shape","vertex.names", "x","x_fact","y","y_fact")) # note no z attribute
## expect_equal(head(A96%v%'shape'),c("box","ellipse", "ellipse", "ellipse", "ellipse", "ellipse"))
## # check edge attribute parsing
## expect_equal(list.edge.attributes(A96),c("A96", "fos", "l" , "lr", "na", "s", "w" ))
## # l is the only one with unique values
## expect_equal(head(A96%e%'l'),c("a", "s","n","r","s","t"))

## }) # end of non-cran tests



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