R Under development (unstable) (2023-11-05 r85474 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 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.

> ## These are tests related to the centralization (since r~3454) of various
> ## methods for symmetrizing the (possibly asymmetric) 'Dimnames' of symmetric
> ## matrices.
> 
> library(Matrix)
> 
> if (interactive()) {
+     options(Matrix.verbose = TRUE, warn = 1, error = recover)
+ } else {
+     options(Matrix.verbose = TRUE, warn = 1)
+ }
> 
> ## For getting and setting '[dD]imnames' on '[mM]atrix'
> DN <- function(x) {
+     if (is(x, "Matrix")) {
+         x@Dimnames
+     } else {
+         dimnames(x)
+     }
+ }
> `DN<-` <- function(x, value) {
+     if (is(x, "Matrix")) {
+         x@Dimnames <- value
+     } else {
+         dimnames(x) <- value
+     }
+     x
+ }
> 
> ## SDN1(dn) is documented to behave as SDN2(dn, NULL)
> SDN1 <- Matrix:::symDN
> SDN2 <- function(dn, uplo = NULL) {
+     J <-
+         if (is.null(uplo)) {
+             if (!is.null(dn[[1L]]) && is.null(dn[[2L]])) 1L else 2L
+         } else {
+             if (uplo == "U") 2L else 1L
+         }
+     rep(dn[J], 2L)
+ }
> 
> ## isSDN1(dn) is documented to behave as isSDN2(dn)
> isSDN1 <- Matrix:::isSymmetricDN
> isSDN2 <- function(dn) {
+     (is.null(ndn <- names(dn)) || !all(nzchar(ndn)) || ndn[1L] == ndn[2L]) &&
+         (is.null(rn <- dn[[1L]]) || is.null(cn <- dn[[2L]]) ||
+          isTRUE(all(rn == cn | (is.na(rn) & is.na(cn)))))
+ }
> 
> ## Various possible (a)symmetries of 'Dimnames'
> n <- 4L
> rn <- letters[seq_len(n)]
> cn <- LETTERS[seq_len(n)]
> ldn <- list(list(rn, rn),
+             list(rn, cn),
+             list(rn, NULL),
+             list(NULL, cn),
+             list(NULL, NULL),
+             list(x = rn, rn),
+             list(x = rn, cn),
+             list(x = rn, NULL),
+             list(x = NULL, cn),
+             list(x = NULL, NULL),
+             list(rn, y = rn),
+             list(rn, y = cn),
+             list(rn, y = NULL),
+             list(NULL, y = cn),
+             list(NULL, y = NULL),
+             list(x = rn, y = rn),
+             list(x = rn, y = cn),
+             list(x = rn, y = NULL),
+             list(x = NULL, y = cn),
+             list(x = NULL, y = NULL))
> 
> ## 'matrix' and _most_ 'd..Matrix' ...
> ## zero matrices are fine for the purpose of testing handling of 'Dimnames'
> lM <- c(list(matrix(0, n, n),
+              new("ddiMatrix", x = double(n), Dim = c(n, n)),
+              new("dgeMatrix", x = double(n * n), Dim = c(n, n))),
+         .mapply(new,
+                 expand.grid(Class = c("dsyMatrix", "dtrMatrix"),
+                             uplo = c("U", "L"),
+                             stringsAsFactors = FALSE),
+                 list(x = double(n * n), Dim = c(n, n))),
+         .mapply(new,
+                 expand.grid(Class = c("dspMatrix", "dtpMatrix"),
+                             uplo = c("U", "L"),
+                             stringsAsFactors = FALSE),
+                 list(x = double((n * (n + 1L)) %/% 2L), Dim = c(n, n))),
+         list(new("dgCMatrix", x = double(0L), Dim = c(n, n),
+                  i = integer(0L), p = rep.int(0L, n + 1L))),
+         .mapply(new,
+                 expand.grid(Class = c("dsCMatrix", "dtCMatrix"),
+                             uplo = c("U", "L"),
+                             stringsAsFactors = FALSE),
+                 list(x = double(0L), Dim = c(n, n),
+                      i = integer(0L), p = rep.int(0L, n + 1L))))
> 
> ## A few dense symmetric matrices, which are _not_ symmetricMatrix
> ## and whose symmetry (in the sense of 'isSymmetric') should depend
> ## only on their 'Dimnames' slot
> .d <- diag(n)
> .lM <- list(new("dgeMatrix",
+                 x = as.vector(.d), Dim = c(n, n)),
+             new("ltrMatrix",
+                 x = as.vector(.d != 0), Dim = c(n, n), uplo = "U"),
+             new("ntpMatrix",
+                 x = .d[upper.tri(.d, TRUE)] != 0, Dim = c(n, n), uplo = "U"))
> .iS <- function(M, dn) {
+     M@Dimnames <- dn
+     isSymmetric(M, tol = 0, checkDN = TRUE)
+ }
> 
> for (dn in ldn) {
+     stopifnot(identical(sdn <- SDN1(dn), SDN2(dn)),
+               (isdn <- isSDN1(dn)) == isSDN2(dn),
+               vapply(.lM, .iS, NA, dn = dn) == isdn)
+ 
+     for (M in lM) {
+         DN(M) <- dn
+         if (is.s <- is(M, "symmetricMatrix")) {
+             ## 'dimnames' should symmetrize
+             stopifnot(identical(dimnames(M), sdn))
+         }
+ 
+         if (is.s && !identical(dn[1L], dn[2L])) {
+             ## Methods for 'symmetricMatrix' assume symmetric 'Dimnames'
+             ## for efficiency ... should they?
+             next
+         }
+         stopifnot(identical(DN(forceSymmetric(M)), sdn),
+                   identical(DN(symmpart(M)),       sdn),
+                   identical(DN(skewpart(M)),       sdn))
+         ## others?
+     }
+ }
> 
> ## r3459: allowing initialization with typeof(Dimnames[[i]]) != "character"
> ## ... nothing to do with symmetry, but here for now ...
> stopifnot(identical(new("dgeMatrix", x = as.double(1:4), Dim = c(2L, 2L),
+                         Dimnames = list(1:2, as.factor(3:4))),
+                     new("dgeMatrix", x = as.double(1:4), Dim = c(2L, 2L),
+                         Dimnames = list(c("1", "2"), c("3", "4")))))
> 
> stopifnot(vapply(ldn, isSDN1, NA) == vapply(ldn, isSDN2, NA))
> 
> 
> ## cov2cor(),  dimScale()  etc -- matrix-Bugs [#6783]  2022-10-23 by Ben  Bolker
> "https://r-forge.r-project.org/tracker/?func=detail&atid=294&aid=6783&group_id=61"
[1] "https://r-forge.r-project.org/tracker/?func=detail&atid=294&aid=6783&group_id=61"
> 
> ## base R vs Matrix cov2cor()
> m <- diag(1:3)
> dimnames(m) <- adn <- list(LETTERS[1:3], letters[1:3]) # MM: *a*symmetric dimnames ..
> Md <- as(m, "denseMatrix")
> Ms <- as(m, "sparseMatrix")
> stopifnot(exprs = {
+     identical(adn, dimnames(cov2cor(m)))
+     identical((dn2 <- rep(adn[2], 2)), dimnames(ms <- forceSymmetric(m))) # a b c for *both* rows & cols
+     identical( dn2, dimnames(cMd <- cov2cor(Md)))
+     identical( dn2, dimnames(cMs <- cov2cor(Ms))) # gave error in Matrix <= 1.5-1
+     all.equal(as(cMd, "sparseMatrix"), cMs, tolerance=1e-15) # see even tol=0
+ })
> 
> dns <- rep(list(letters[1:3]), 2)
> m <- matrix(1:9, 3, dimnames = dns); m <- (m+t(m))/2 + 2*diag(3) # to be pos.def.
> m
  a b  c
a 3 3  5
b 3 7  7
c 5 7 11
> (cm <- cov2cor(m))
          a         b         c
a 1.0000000 0.6546537 0.8703883
b 0.6546537 1.0000000 0.7977240
c 0.8703883 0.7977240 1.0000000
> (cM <- cov2cor(M <- as(m, "denseMatrix")))
3 x 3 Matrix of class "corMatrix"
          a         b         c
a 1.0000000 0.6546537 0.8703883
b 0.6546537 1.0000000 0.7977240
c 0.8703883 0.7977240 1.0000000
> stopifnot(exprs = {
+     identical(dns, dimnames(cm))
+     inherits(cM, "dpoMatrix")
+     identical(dns, dimnames(cM))
+     inherits((cS <- cov2cor(S <- as(m, "sparseMatrix"))), "dsCMatrix")
+     identical(dns, dimnames(cS))
+     all.equal(cS, dimScale(S))
+     all.equal(as(cM, "sparseMatrix"), cS,
+               tolerance=2e-15) # see even tol=0
+     all.equal(as(cM, "dpoMatrix"), as(dimScale(M), "dpoMatrix"),
+               tolerance=2e-15) # seen 1.665e-16
+ })
> 
> 
> 
> cat("Time elapsed:", proc.time(), "\n") # "stats"
Time elapsed: 1.54 0.14 1.67 NA NA 
> 
> proc.time()
   user  system elapsed 
   1.54    0.14    1.67