Fix spurious toa coercion and Matrix deprecation warnings (1.25.1)

CITATION.cff

@@ -3,7 +3,7 @@ message: 'To cite package "netdiffuseR" in publications use:'
 type: software
 license: MIT
 title: 'netdiffuseR: Analysis of Diffusion and Contagion Processes on Networks'
-version: 1.25.0
+version: 1.25.1
 doi: 10.32614/CRAN.package.netdiffuseR
 abstract: 'Empirical statistical analysis, visualization and simulation of diffusion
   and contagion processes on networks. The package implements algorithms for calculating
@@ -69,6 +69,6 @@ references:
     given-names: Thomas
     orcid: https://orcid.org/0000-0002-8824-5816
   year: '2026'
-  notes: R package version 1.25.0
+  notes: R package version 1.25.1
   url: https://github.com/USCCANA/netdiffuseR
   doi: 10.32614/CRAN.package.netdiffuseR

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: netdiffuseR
 Title: Analysis of Diffusion and Contagion Processes on Networks
-Version: 1.25.0
+Version: 1.25.1
 Authors@R: c(
   person("George", "Vega Yon", email="g.vegayon@gmail.com", role=c("aut", "cre"),
     comment=c(ORCID = "0000-0002-3171-0844", what="Rewrite functions with Rcpp, plus new features")

NEWS.md

@@ -1,3 +1,17 @@
+# Changes in netdiffuseR version 1.25.1 (2026-10-21)
+
+## Bug fixes
+
+* Multi-behavior simulations with `rdiffnet()` no longer emit a spurious
+  "Coercing -toa- into integer." warning. `new_diffnet()` now checks the storage
+  mode of `toa` instead of its class, which failed for integer matrices (#86).
+
+* `exposure(..., alt.graph = "se")` no longer triggers the deprecated
+  `as(<dgeMatrix>, "dgCMatrix")` coercion from the **Matrix** package.
+  `as_dgCMatrix()` now uses the recommended `dMatrix` -> `generalMatrix` ->
+  `CsparseMatrix` coercion chain (#87).
+
+
 # Changes in netdiffuseR version 1.25.0 (2026-03-27)
 
 ## User-visible changes

R/diffnet-class.r

@@ -623,7 +623,7 @@ new_diffnet <- function(
   }
 
   # Step 2.1: Checking class of TOA and coercing if necessary
-  if (!inherits(toa, "integer")) {
+  if (!is.integer(toa)) {
 
     warning("Coercing -toa- into integer.")
     toa[] <- as.integer(toa)

R/misc.r

@@ -490,7 +490,10 @@ as_spmat <- as_dgCMatrix
 #' @rdname as_dgCMatrix
 as_dgCMatrix.default <- function(x, make.dimnames = TRUE, ...) {
 
-  ans <- methods::as(x, "dgCMatrix")
+  ans <- methods::as(
+    methods::as(methods::as(x, "dMatrix"), "generalMatrix"),
+    "CsparseMatrix"
+  )
 
   # Updating row and colnames if necesary
   if (make.dimnames)

tests/testthat/test-rdiffnet.R

@@ -210,3 +210,20 @@ test_that("Disadoption works", {
   expect_true(all(should_be_ones_or_zeros %in% c(0,1)))
 
 })
+
+# Multi-behavior simulations should not warn about -toa- coercion (#86)
+test_that("Multi-behavior rdiffnet does not coerce toa", {
+
+  set.seed(1231)
+  expect_silent(
+    ans <- suppressMessages(rdiffnet(
+      200, 10,
+      seed.p.adopt = list(0.1, 0.15),
+      seed.nodes   = list("random", "random"),
+      behavior     = list("Behavior 1", "Behavior 2")
+    ))
+  )
+
+  expect_true(is.integer(ans$toa))
+
+})

tests/testthat/test-struct_equiv.R

@@ -177,3 +177,17 @@ test_that("transformGraphBy", {
   expect_equivalent(ans1, ans2)
 
 })
+
+# SE exposure should not use deprecated Matrix coercions (#87)
+test_that("SE exposure avoids deprecated Matrix coercions", {
+
+  # Turning deprecated coercions into errors
+  old <- options(Matrix.warnDeprecatedCoerce = 2)
+  on.exit(options(old))
+
+  set.seed(1231)
+  diffnet <- rdiffnet(100, 5, seed.graph = "small-world")
+
+  expect_silent(exposure(diffnet, alt.graph = "se", valued = TRUE))
+
+})