Bug fixes in new code

Author: baddstats

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: spatstat.sparse
-Version: 3.1-0.010
+Version: 3.1-0.011
 Date: 2026-04-27
 Title: Sparse Three-Dimensional Arrays and Linear Algebra Utilities
 Authors@R: c(person("Adrian", "Baddeley", 

NAMESPACE

@@ -42,6 +42,7 @@ export("evalSparse3Dentrywise")
 export("expandSparse")
 export("gridadjacencymatrix")
 export("inside3Darray")
+export("isComplex")
 export("length.sparse3Darray")
 export("mapSparseEntries")
 export("marginSumsSparse")

NEWS

@@ -1,5 +1,5 @@
 
-        CHANGES IN spatstat.sparse VERSION 3.1-0.010
+        CHANGES IN spatstat.sparse VERSION 3.1-0.011
 
 OVERVIEW
 

R/linalg.R

@@ -6,7 +6,7 @@
 #'  Copyright (c) Adrian Baddeley, Ege Rubak and Rolf Turner 2016-2020
 #'  GNU Public Licence >= 2.0
 #'
-#' $Revision: 1.39 $ $Date: 2026/04/24 05:57:32 $
+#' $Revision: 1.40 $ $Date: 2026/04/27 07:36:07 $
 #'
 
 sumouter <- function(x, w=NULL, y=x) {
@@ -243,13 +243,13 @@ sumsymouter <- function(x, w=NULL, distinct=TRUE) {
   ## w is a matrix or sparse matrix
   ## Computes the sum of outer(x[,i,j], x[,j,i]) * w[i,j] over all pairs i != j
   ## handle complex values
-  if(is.complex(w)) {
+  if(isComplex(w)) {
     a <- sumsymouter(x, Re(w), distinct=distinct)
     b <- sumsymouter(x, Im(w), distinct=distinct)
     result <- a + b * 1i
     return(result)
   }
-  if(is.complex(x)) {
+  if(isComplex(x)) {
     a <- sumsymouter(Re(x), w=w, distinct=distinct)
     b <- sumsymouter(Im(x), w=w, distinct=distinct)
     d <- sumsymouter(Re(x)+Im(x), w=w, distinct=distinct)

R/sparse3Darray.R

@@ -6,7 +6,7 @@
 #' Copyright (c) Adrian Baddeley, Ege Rubak and Rolf Turner 2016-2020
 #' GNU Public Licence >= 2.0
 #'
-#' $Revision: 1.47 $  $Date: 2026/04/27 02:38:37 $
+#' $Revision: 1.49 $  $Date: 2026/04/27 07:47:02 $
 #'
 
 sparse3Darray <- function(i=integer(0), j=integer(0), k=integer(0),
@@ -864,6 +864,25 @@ Summary.sparse3Darray <- function(..., na.rm=FALSE) {
 }
 
 
+isComplex <- function(x) {
+  if(is.null(x)) return(FALSE)
+  if(is.vector(x) || is.matrix(x) || is.array(x)) 
+    return(is.complex(x))
+  nd <- length(dim(x))
+  if(nd == 0 || nd == 1) {
+    x <- as(x, "sparseVector")
+    return(is.complex(x@x))
+  } else if(nd == 2) {
+    x <- as(x, "TsparseMatrix")
+    return(is.complex(x@x)) ## currently not supported by Matrix package
+  } else if(nd == 3) {
+    x <- as.sparse3Darray(x)
+    return(is.complex(x$x))
+  } else 
+    stop("Arrays of more than 3 dimensions are not supported", call.=FALSE)    
+}
+
+
 SparseIndices <- function(x) {
   #' extract indices of entries of sparse vector/matrix/array
   nd <- length(dim(x))

R/sparselinalg.R

@@ -202,7 +202,7 @@ sumsymouterSparse <- function(x, w=NULL, distinct=TRUE, dbg=FALSE) {
   ##  result <- a + b * 1i
   ##  return(result)
   ## }
-  if(is.complex(x)) {
+  if(isComplex(x)) {
     a <- sumsymouter(Re(x), w=w, distinct=distinct)
     b <- sumsymouter(Im(x), w=w, distinct=distinct)
     d <- sumsymouter(Re(x)+Im(x), w=w, distinct=distinct)

inst/doc/packagesizes.txt

@@ -19,4 +19,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2023-03-12" "3.0-1" 15 48 0 2092 740
 "2023-10-24" "3.0-3" 15 48 0 2092 740
 "2024-06-21" "3.1-0" 15 48 0 2092 740
-"2026-04-27" "3.1-0.010" 18 53 0 2325 943
+"2026-04-27" "3.1-0.011" 18 54 0 2344 943

inst/info/packagesizes.txt

@@ -19,4 +19,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2023-03-12" "3.0-1" 15 48 0 2092 740
 "2023-10-24" "3.0-3" 15 48 0 2092 740
 "2024-06-21" "3.1-0" 15 48 0 2092 740
-"2026-04-27" "3.1-0.010" 18 53 0 2325 943
+"2026-04-27" "3.1-0.011" 18 54 0 2344 943

man/spatstat.sparse-internal.Rd

@@ -9,6 +9,7 @@
 %% sparse 3D arrays
 \alias{unionOfSparseIndices}
 \alias{inside3Darray}
+\alias{isComplex}
 \alias{SparseEntries}
 \alias{SparseIndices}
 \alias{SparseMatrixEntries}
@@ -35,6 +36,7 @@ check.mat.mul(A, B, Acols, Brows, fatal)
 %% sparse 3D arrays
 unionOfSparseIndices(A,B)
 inside3Darray(d, i, j, k)
+isComplex(x)
 SparseEntries(x)
 SparseIndices(x)
 SparseMatrixEntries(x, base)

tests/sparse3Darrays.R

@@ -5,12 +5,12 @@ require(spatstat.sparse)
 ALWAYS <- FULLTEST <- TRUE
 #'    tests/sparse3Darrays.R
 #'  Basic tests of code in sparse3Darray.R and sparsecommon.R
-#'  $Revision: 1.32 $ $Date: 2023/06/23 02:34:57 $
+#'  $Revision: 1.33 $ $Date: 2026/04/27 06:49:58 $
 
 if(!exists("ALWAYS")) ALWAYS <- TRUE
 if(!exists("FULLTEST")) FULLTEST <- ALWAYS
 
-if(ALWAYS) { # fundamental, C code
+if(ALWAYS) { # fundamental R and/or C code
 local({
   #' forming arrays
 
@@ -106,7 +106,18 @@ local({
       stop("Incorrect answer from marginSumsSparse")
     }
 
-  }
+    #' check strategy for avoiding compressed representation of symmetric matrix
+    A <- matrix(c(10,  0,  0, 1,
+                   0, 20,  2, 7,
+                   0,  2, 30, 0,
+                   1,  7,  0, 40),
+                4,4)
+    As <- as(A, "sparseMatrix")
+    dfA <- SparseEntries(As)
+    if(nrow(dfA) != sum(A != 0))
+      stop(paste("SparseEntries() does not correctly handle",
+                 "the compressed representation of a symmetric matrix"))
+  } 
 })
 
 
@@ -325,19 +336,35 @@ local({
     Mmap3 <- mapSparseEntries(Mempty, 1, matrix(1:10, 5, 2), across=3)
 
     #'  -------------- sparselinalg.R -------------------------
-    U <- aperm(M,c(3,1,2))  # 2 x 5 x 5
-    UU <- sumsymouterSparse(U, dbg=TRUE)
-    w <- matrix(0, 5, 5)
-    w[cbind(1:3,2:4)] <- 0.5
-    w <- as(w, "sparseMatrix")
-    UU <- sumsymouterSparse(U, w, dbg=TRUE)
-    Uempty <- sparse3Darray(dims=c(2,5,5))
-    UU <- sumsymouterSparse(Uempty, w, dbg=TRUE)
+    Us <- aperm(M,c(3,1,2))  # 2 x 5 x 5, sparse3Darray
+    Um <- as.array(Us)
+    wm <- matrix(0, 5, 5)
+    wm[cbind(1:3,2:4)] <- 0.5
+    ws <- as(wm, "sparseMatrix")
+    bm <- wm + t(wm)
+    bs <- as(as(bm, "symmetricMatrix"), "sparseMatrix")
+    ## run different cases
+    UUm <- sumsymouter(Um)
+    UUs <- sumsymouterSparse(Us, dbg=TRUE)
+    UUwm <- sumsymouter(Um, wm)
+    UUws <- sumsymouterSparse(Us, ws, dbg=TRUE)
+    UUbm <- sumsymouter(Um, bm)
+    UUbs <- sumsymouterSparse(Us, bs)
+    Vempty <- sparse3Darray(dims=c(2,5,5))
+    VVws <- sumsymouterSparse(Vempty, ws)
+    VVwm <- sumsymouter(as.array(Vempty), wm)
     #' complex
-    Ucom <- U + U * 1i
-    UU <- sumsymouterSparse(Ucom)
-    UU <- sumsymouterSparse(Ucom, w)
-    #' 
+    Ucom <- Us + Us * 1i
+    UUc <- sumsymouter(Ucom)
+    UUcw <- sumsymouter(Ucom, wm)
+    ## check validity
+    if(!all(UUs == UUm))
+      stop("sumsymouter(x): sparse and non-sparse algorithms disagree")
+    if(!all(UUws == UUwm))
+      stop("sumsymouter(x, w): sparse and non-sparse algorithms disagree")
+    if(!all(UUbs == UUbm))
+      stop(paste("sumsymouter(x, w): sparse and non-sparse algorithms disagree",
+                 "when w is symmetric"))
   }
 
   ## 1 x 1 x 1 arrays