# tests/other-pkgs.R In Matrix: Sparse and Dense Matrix Classes and Methods

```####--------- Test interfaces to other non-standard Packages ---------------

library(Matrix)

source(system.file("test-tools.R", package = "Matrix"))# identical3() etc

MatrixRversion <- pkgRversion("Matrix")

###-- 1)  'graph' (from Bioconductor) ---------------------------
###-- ==  =======                     ---------------------------
## do not run the test "usually" for now [Solaris problem after detach() ..]:
if((Sys.getenv("USER") == "maechler" || doExtras) &&
isTRUE(try(require(graph)))) { # may be there and fail (with R-devel)

if(packageDescription("graph")\$Version <= "1.10.2") {
## graph 1.10.x for x <= 2 had too many problems  as(<graph>, "matrix")
cat("Version of 'graph' is too old --- no tests done here!\n")

} else if(pkgRversion("graph") != MatrixRversion) {

cat(sprintf("The R version (%s) of 'graph' installation differs from the Matrix one (%s)\n",
pkgRversion("graph"), MatrixRversion))

} else { ## do things

if(find("which")[[1L]] != "package:Matrix")
## *and* kills the correct working of Matrix::which(.)
## ___ why on earth ?!??!?!! ___
which <- Matrix::which

if(doPdf <- !dev.interactive(orNone = TRUE))
pdf("other-pkg-graph.pdf")

## 0) Simplest non-trivial graph: has no weights:
g0 <- graphNEL(paste(1:2), edgeL=list("1"="2"), "directed")
m0 <- as(g0, "Matrix")
stopifnot(is(m0,"ngCMatrix"), dim(m0) == c(2,2), Matrix::which(m0) == 3)
g. <- as(m0, "graph") ## failed in Matrix <= 1.1-0
m. <- as(g., "Matrix")
stopifnot( identical(m., m0) ) ## but (g0, g.) differ: the latter has '1' weights

## 1) undirected

V <- LETTERS[1:4]
edL <- vector("list", length=4)
names(edL) <- V
## 1a) unweighted
for(i in 1:4)
edL[[i]] <- list(edges = 5-i)
gR <- new("graphNEL", nodes=V, edgeL=edL)
str(edges(gR))
sm.g <- as(gR, "sparseMatrix")
str(sm.g) ## dgC: TODO: want 'ds.' (symmetric)
validObject(sm.g)
show( sm.g )## (incl colnames !)

## 1b) weighted
set.seed(123)
for(i in 1:4)
edL[[i]] <- list(edges = 5-i, weights=runif(1))
gRw <- new("graphNEL", nodes=V, edgeL=edL)
str(edgeWeights(gRw))
sm.gw <- as(gRw, "sparseMatrix")
str(sm.gw) ## *numeric* dgCMatrix
validObject(sm.gw)
show( sm.gw )## U[0,1] numbers in anti-diagonal

## 2) directed
gU <- gR; edgemode(gU) <- "directed"
sgU <- as(gU, "sparseMatrix")
str(sgU) ## 'dgC'
validObject(sgU)
show( sgU )

## Reverse :  sparseMatrix -> graph
sm.g[1,2] <- TRUE
gmg  <-  as(sm.g, "graph")
validObject(gmg2 <-  as(sm.g, "graphNEL"))
gmgw <-  as(sm.gw, "graph")
validObject(gmgw2 <- as(sm.gw, "graphNEL"))
gmgU <-  as(sgU, "graph")
validObject(gmgU2 <- as(sgU, "graphNEL"))
stopifnot(identical(gmg, gmg2),
identical(gmgw, gmgw2),
identical(gmgU, gmgU2))

data(CAex)
cc <- crossprod(CAex)
## work around bug in 'graph': diagonal must be empty:
diag(cc) <- 0; cc <- drop0(cc)
image(cc)
gg <- as(cc, "graph")

.r <- require# cheat checks - do *not* want it in DESCRIPTION:
if(.r("Rgraphviz")) {
plot(gg, "circo")
}
stopifnot(all.equal(edgeMatrix(gg),
rbind(from = c(rep(1:24, each=2), 25:48),
to   = c(rbind(25:48,49:72), 49:72))))

if(doPdf) dev.off()

} # {else}

} ## end{graph}

###-- 2)  'SparseM' ---------------------------------------------
###-- ==  ========  ---------------------------------------------

if(isTRUE(try(require(SparseM)))) { # may be there and fail

if(pkgRversion("SparseM") != MatrixRversion) {

cat(sprintf("The R version (%s) of 'SparseM' installation differs from the Matrix one (%s)\n",
pkgRversion("SparseM"), MatrixRversion))

} else { ## do things

set.seed(1)
a <- round(rnorm(5*4), 2)
a[abs(a) < 0.7] <- 0
A <- matrix(a,5,4)
print(M <- Matrix(A))
stopifnot(
validObject(A.csr <- as.matrix.csr(A)),
validObject(At.csr <- as.matrix.csr(t(A))),
validObject(A.csc <- as.matrix.csc(A)),
identical(At.csr, t(A.csr)),
identical(A, as.matrix(A.csr)),
identical(A.csr, as(M, "matrix.csr")),
identical(A.csc, as(M, "matrix.csc")),
identical3(M, as(A.csr, "CsparseMatrix"), as(A.csr, "dgCMatrix")),
identical(t(M), as(At.csr, "CsparseMatrix"))
)

## More tests, notably for triplets
A.coo <- as.matrix.coo(A)
str(T  <- as(M, "TsparseMatrix")) # has 'j' sorted
str(T. <- as(A.coo, "TsparseMatrix")) # has 'i' sorted

T3 <- as(as(T, "matrix.coo"), "Matrix") # dgT
M3 <- as(A.csr,               "Matrix") # dgC
M4 <- as(A.csc,               "Matrix") # dgC
M5 <- as(as(M, "matrix.coo"), "Matrix") # dgT
uniqT <- uniqTsparse
stopifnot(identical4(uniqT(T), uniqT(T.), uniqT(T3), uniqT(M5)),
identical3(M, M3, M4))