UrbanAnalyst · mpadge · Aug 24, 2026 · Aug 24, 2026 · Aug 24, 2026 · Aug 24, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dodgr
 Title: Distances on Directed Graphs
-Version: 0.4.3.038
+Version: 0.4.3.042
 Authors@R: c(
     person("Mark", "Padgham", , "mark.padgham@email.com", role = c("aut", "cre")),
     person("Andreas", "Petutschnig", role = "aut"),
@@ -31,15 +31,15 @@ Depends:
     R (>= 3.5.0)
 Imports:
     callr,
-    digest,
     fs,
     geodist (>= 0.1.0),
     magrittr,
     memoise,
     methods,
     osmdata,
     Rcpp (>= 0.12.6),
-    RcppParallel
+    RcppParallel,
+    secretbase
 Suggests:
     bench,
     dplyr,
@@ -65,4 +65,4 @@ LazyData: true
 NeedsCompilation: yes
 Roxygen: list(markdown = TRUE)
 SystemRequirements: GNU make
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -63,10 +63,12 @@ importFrom(graphics,plot)
 importFrom(magrittr,"%>%")
 importFrom(memoise,memoise)
 importFrom(methods,is)
-importFrom(osmdata,add_osm_feature)
-importFrom(osmdata,getbb)
-importFrom(osmdata,opq)
-importFrom(osmdata,osm_poly2line)
-importFrom(osmdata,osmdata_sf)
-importFrom(osmdata,trim_osmdata)
+importFrom(osmdata,
+  add_osm_feature,
+  getbb,
+  opq,
+  osm_poly2line,
+  osmdata_sf,
+  trim_osmdata
+)
 useDynLib(dodgr, .registration = TRUE)
diff --git a/NEWS.md b/NEWS.md
@@ -10,6 +10,8 @@
 
 ## Minor changes
 
+- Replace `digest` dependency with `secretbase` for all internal graph hashing/caching
+- Graph hashes used for caching now also incorporate `d`, `d_weighted`, `time`, and `time_weighted` columns
 - Fix a few minor bugs with compound junction construction (#305, #316)
 - Add `pairwise` parameter to `dodgr_times()`; thanks to @leoniedu (#314)
 - Fix bug with categorical distances that neglected edges through compound junctions (#305)

diff --git a/R/cache.R b/R/cache.R
@@ -16,21 +16,32 @@ get_hash <- function (graph, verts = NULL, contracted = FALSE, force = FALSE) {
     if (contracted) {
         if (is.null (hash)) {
             gr_cols <- dodgr_graph_cols (graph)
-            hash <- digest::digest (list (
-                graph [[gr_cols$edge_id]], names (graph), verts
+            hash <- secretbase::siphash13 (list (
+                hash_cols (graph, gr_cols), names (graph), verts
             ))
         }
     } else {
         if (is.null (hash)) {
             gr_cols <- dodgr_graph_cols (graph)
-            hash <- digest::digest (list (
-                graph [[gr_cols$edge_id]], names (graph)
+            hash <- secretbase::siphash13 (list (
+                hash_cols (graph, gr_cols), names (graph)
             ))
         }
     }
     return (hash)
 }
 
+# Columns beyond `edge_id` whose values affect `dodgr` output, and which must
+# therefore also contribute to graph hashes, so that direct edits to weights
+# or distances (without also changing `edge_id`) invalidate caches rather
+# than silently serving stale results. See `?clear_dodgr_cache`.
+hash_cols <- function (graph, gr_cols) {
+    nms <- c ("edge_id", "d", "d_weighted", "time", "time_weighted")
+    idx <- do.call (c, gr_cols [nms])
+    idx <- idx [!is.na (idx)]
+    graph [, idx, drop = FALSE]
+}
+
 get_edge_map <- function (graph) {
 
     hashc <- get_hash (graph, contracted = TRUE)
@@ -61,11 +72,11 @@ get_edge_map <- function (graph) {
 #' re-loaded,
 #' and the uncontracted version returned.
 #' @noRd
-cache_graph <- function (graph, edge_col) {
+cache_graph <- function (graph, gr_cols) {
 
     td <- fs::path_temp ()
 
-    f <- function (graph, edge_col, td) {
+    f <- function (graph, gr_cols, td) {
 
         # the following line does not generate a coverage symbol because it is
         # cached, so # nocov:
@@ -81,12 +92,18 @@ cache_graph <- function (graph, edge_col) {
         fname <- fs::path (td, paste0 ("dodgr_graph_", hash, ".Rds"))
         saveRDS (graph, fname)
 
-        # The hash for the contracted graph is generated from the edge IDs of
-        # the full graph plus default NULL vertices. Internal functions can not
-        # be called here, so code copied directly from `get_hash`:
+        # The hash for the contracted graph is generated from the edge IDs
+        # and weight/distance columns of the full graph plus default NULL
+        # vertices. Internal functions can not be called here, so code
+        # copied directly from `get_hash` and `hash_cols`:
         # hashc <-
         #     get_hash (graph, verts = NULL, contracted = TRUE, force = TRUE)
-        hashc <- digest::digest (list (graph [[edge_col]], names (graph), NULL))
+        hash_nms <- c ("edge_id", "d", "d_weighted", "time", "time_weighted")
+        hash_idx <- do.call (c, gr_cols [hash_nms])
+        hash_idx <- hash_idx [!is.na (hash_idx)]
+        hashc <- secretbase::siphash13 (list (
+            graph [, hash_idx, drop = FALSE], names (graph), NULL
+        ))
 
         graphc <- dodgr::dodgr_contract_graph (graph)
         fname_c <- fs::path (td, paste0 ("dodgr_graphc_", hashc, ".Rds"))
@@ -119,7 +136,7 @@ cache_graph <- function (graph, edge_col) {
     }
 
     sink (file = fs::path (fs::path_temp (), "Rout.txt"))
-    res <- callr::r_bg (f, list (graph, edge_col, td))
+    res <- callr::r_bg (f, list (graph, gr_cols, td))
     sink ()
 
     return (res) # R6 processx object
@@ -128,11 +145,14 @@ cache_graph <- function (graph, edge_col) {
 #' Remove cached versions of `dodgr` graphs.
 #'
 #' This function should generally \emph{not} be needed, except if graph
-#' structure has been directly modified other than through `dodgr` functions;
-#' for example by modifying edge weights or distances. Graphs are cached based
-#' on the vector of edge IDs, so manual changes to any other attributes will not
-#' necessarily be translated into changes in `dodgr` output unless the cached
-#' versions are cleared using this function. See
+#' structure has been directly modified other than through `dodgr` functions.
+#' Graphs are cached based on a hash of the `edge_id`, `d`, `d_weighted`,
+#' `time`, and `time_weighted` columns, so manual changes to any of those will
+#' be detected automatically. Manual changes to any other column or
+#' attribute (for example, `from`/`to` vertex identifiers) will not be
+#' reflected in the hash, and so will not necessarily be translated into
+#' changes in `dodgr` output unless the cached versions are cleared using this
+#' function. See
 #' \url{https://github.com/UrbanAnalyst/dodgr/wiki/Caching-of-streetnets-and-contracted-graphs} # nolint
 #' for details of caching process.
 #'

diff --git a/R/centrality.R b/R/centrality.R
@@ -207,7 +207,7 @@ dodgr_centrality <- function (graph,
 
     if (is_dodgr_cache_on () && edges) {
         # re-cache graph with centrality measure:
-        attr (res, "px") <- cache_graph (res, gr_cols$edge_id)
+        attr (res, "px") <- cache_graph (res, gr_cols)
     }
 
     return (res)

diff --git a/R/fund-cycles.R b/R/fund-cycles.R
@@ -100,7 +100,7 @@ dodgr_fundamental_cycles <- function (graph,
         # each element of res is a list, so flatten these:
         res <- flatten_list (res)
         # These hash each and remove any duplicated ones:
-        dig <- unlist (lapply (res, digest::digest))
+        dig <- unlist (lapply (res, secretbase::siphash13))
         res <- res [which (!duplicated (dig))]
     }
 

diff --git a/R/graph-contraction.R b/R/graph-contraction.R
@@ -76,7 +76,9 @@ dodgr_contract_graph <- function (graph, verts = NULL, nocache = FALSE) {
         graph_contracted <- dodgr_contract_graph_internal (graph, v, verts)
 
         gr_cols <- dodgr_graph_cols (graph_contracted$graph)
-        hashe <- digest::digest (graph_contracted$graph [[gr_cols$edge_id]])
+        hashe <- secretbase::siphash13 (
+            hash_cols (graph_contracted$graph, gr_cols)
+        )
         attr (graph_contracted$graph, "hash") <- hash
         attr (graph_contracted$graph, "hashc") <- hashc
         attr (graph_contracted$graph, "hashe") <- hashe
@@ -308,7 +310,7 @@ dodgr_uncontract_graph <- function (graph) {
 
     gr_cols <- dodgr_graph_cols (graph)
     hashe_ref <- attr (graph, "hashe")
-    hashe <- digest::digest (graph [[gr_cols$edge_id]])
+    hashe <- secretbase::siphash13 (hash_cols (graph, gr_cols))
 
     hash <- attr (graph, "hash")
     fname <- fs::path (fs::path_temp (), paste0 ("dodgr_graph_", hash, ".Rds"))

diff --git a/R/graph-functions.R b/R/graph-functions.R
@@ -208,14 +208,14 @@ dodgr_vertices <- function (graph) {
     hash <- attr (graph, hash)
     # make sure rows of graph have not been changed
     gr_cols <- dodgr_graph_cols (graph)
-    hashe <- digest::digest (graph [[gr_cols$edge_id]])
+    hashe <- secretbase::siphash13 (hash_cols (graph, gr_cols))
     if (!identical (hashe, hash)) {
         hash <- NULL
     }
     if (!is.null (hash)) {
         hashe_ref <- attr (graph, "hashe")
         hashe_ref <- ifelse (is.null (hashe_ref), "", hashe_ref)
-        hashe <- digest::digest (graph [[gr_cols$edge_id]])
+        hashe <- secretbase::siphash13 (hash_cols (graph, gr_cols))
         if (hashe != hashe_ref) {
             hash <- hashe
         }

diff --git a/R/weight-streetnet.R b/R/weight-streetnet.R
@@ -408,7 +408,7 @@ weight_streetnet.sf <- function (x,
     hash <- get_hash (graph, contracted = FALSE, force = TRUE)
     attr (graph, "hash") <- hash
     if (is_dodgr_cache_on ()) {
-        attr (graph, "px") <- cache_graph (graph, gr_cols$edge_id)
+        attr (graph, "px") <- cache_graph (graph, gr_cols)
     }
 
     return (graph)
@@ -772,7 +772,7 @@ weight_streetnet.sc <- function (x,
         get_hash (graph, contracted = FALSE, force = TRUE)
 
     if (is_dodgr_cache_on ()) {
-        attr (graph, "px") <- cache_graph (graph, gr_cols$edge_id)
+        attr (graph, "px") <- cache_graph (graph, gr_cols)
     }
 
     return (graph)

diff --git a/codemeta.json b/codemeta.json
@@ -11,7 +11,7 @@
   "codeRepository": "https://github.com/UrbanAnalyst/dodgr",
   "issueTracker": "https://github.com/UrbanAnalyst/dodgr/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.4.3.038",
+  "version": "0.4.3.042",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -270,18 +270,6 @@
       "sameAs": "https://CRAN.R-project.org/package=callr"
     },
     "3": {
-      "@type": "SoftwareApplication",
-      "identifier": "digest",
-      "name": "digest",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=digest"
-    },
-    "4": {
       "@type": "SoftwareApplication",
       "identifier": "fs",
       "name": "fs",
@@ -293,7 +281,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=fs"
     },
-    "5": {
+    "4": {
       "@type": "SoftwareApplication",
       "identifier": "geodist",
       "name": "geodist",
@@ -306,7 +294,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=geodist"
     },
-    "6": {
+    "5": {
       "@type": "SoftwareApplication",
       "identifier": "magrittr",
       "name": "magrittr",
@@ -318,7 +306,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=magrittr"
     },
-    "7": {
+    "6": {
       "@type": "SoftwareApplication",
       "identifier": "memoise",
       "name": "memoise",
@@ -330,12 +318,12 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=memoise"
     },
-    "8": {
+    "7": {
       "@type": "SoftwareApplication",
       "identifier": "methods",
       "name": "methods"
     },
-    "9": {
+    "8": {
       "@type": "SoftwareApplication",
       "identifier": "osmdata",
       "name": "osmdata",
@@ -347,7 +335,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=osmdata"
     },
-    "10": {
+    "9": {
       "@type": "SoftwareApplication",
       "identifier": "Rcpp",
       "name": "Rcpp",
@@ -360,7 +348,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=Rcpp"
     },
-    "11": {
+    "10": {
       "@type": "SoftwareApplication",
       "identifier": "RcppParallel",
       "name": "RcppParallel",
@@ -372,9 +360,21 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=RcppParallel"
     },
+    "11": {
+      "@type": "SoftwareApplication",
+      "identifier": "secretbase",
+      "name": "secretbase",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=secretbase"
+    },
     "SystemRequirements": "GNU make"
   },
-  "fileSize": "36594.088KB",
+  "fileSize": "36598.339KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/man/clear_dodgr_cache.Rd b/man/clear_dodgr_cache.Rd