From cecf205cdc27cc1dd1367a153a9e2d661fe1191f Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Tue, 11 Aug 2026 00:00:01 +0800
Subject: [PATCH 01/14] draft r interface for dmi

---
 R/dmi.R | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 R/dmi.R

diff --git a/R/dmi.R b/R/dmi.R
new file mode 100644
index 0000000..e69de29

From 694e35ffac1f2502cdd45e880c0c4d7aab3cc2e5 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Tue, 11 Aug 2026 00:00:01 +0800
Subject: [PATCH 02/14] draft r interface for dmi

---
 R/Agenerics.R |  2 +-
 R/dmi.R       | 39 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/R/Agenerics.R b/R/Agenerics.R
index ccd1766..7945f0a 100644
--- a/R/Agenerics.R
+++ b/R/Agenerics.R
@@ -7,6 +7,6 @@ register_generic = \(name, def = NULL) {
   }
 }
 
-for (gen in c("pc", "ops", "fnn")) {
+for (gen in c("pc", "ops", "fnn", "dmi")) {
   register_generic(gen)
 }
diff --git a/R/dmi.R b/R/dmi.R
index e69de29..919917e 100644
--- a/R/dmi.R
+++ b/R/dmi.R
@@ -0,0 +1,39 @@
+.dmi_ts = \(data, target, tau = 1:10, pred = NULL, k = 3,
+            base = exp(1), normalize = FALSE, threads = 1) {
+  tv = .validate_var(data, target)[[1]]
+  if (is.null(pred)) pred = which(!is.na(tv))
+  return(RcppFNN(tv, rt, eps, lib, pred, E, tau, style, dist.metric,
+                 k, threads, higher.parallel, NULL, NULL))
+}
+
+#' False Nearest Neighbors
+#'
+#' @param data Observation data.
+#' @param target Integer of column indice for the target variable.
+#' @param E (optional) Embedding dimensions.
+#' @param k (optional) Number of nearest neighbors used for evaluation.
+#' @param tau (optional) Step of lag.
+#' @param style (optional) Embedding style (`0` includes current state, `1` excludes it).
+#' @param lib (optional) Libraries indices.
+#' @param pred (optional) Predictions indices.
+#' @param dist.metric (optional) Distance measure to be used.
+#' @param rt (optional) Relative distance threshold.
+#' @param eps (optional) Absolute distance threshold.
+#' @param threads (optional) Number of threads used.
+#' @param higher.parallel (optional) Whether to use a higher level of parallelism.
+#' @param detrend (optional) Whether to remove the linear trend.
+#' @param nb (optional) Neighbours list.
+#' @param ... Additional arguments to absorb unused inputs in method dispatch.
+#'
+#' @return A vector.
+#' @export
+#' @name fnn
+#' @aliases fnn,data.frame-method
+#' @references
+#' Kennel, M.B., Brown, R., Abarbanel, H.D.I., 1992. Determining embedding dimension for phase-space reconstruction using a geometrical construction. Physical Review A 45, 3403–3411.
+#'
+#' @examples
+#' crash = sf::read_sf(system.file("case/crash.gpkg", package = "pc"))
+#' pc::fnn(crash, 1, threads = 1)
+#'
+methods::setMethod("dmi", "data.frame", .dmi_ts)

From 4090797955e91bc2ac6632a7fb97275376dcb325 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Tue, 11 Aug 2026 00:00:01 +0800
Subject: [PATCH 03/14] draft r interface for dmi

---
 R/dmi.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/dmi.R b/R/dmi.R
index 919917e..afafee8 100644
--- a/R/dmi.R
+++ b/R/dmi.R
@@ -6,7 +6,7 @@
                  k, threads, higher.parallel, NULL, NULL))
 }
 
-#' False Nearest Neighbors
+#' Delayed Mutual Information
 #'
 #' @param data Observation data.
 #' @param target Integer of column indice for the target variable.
@@ -27,13 +27,13 @@
 #'
 #' @return A vector.
 #' @export
-#' @name fnn
-#' @aliases fnn,data.frame-method
+#' @name dmi
+#' @aliases dmi,data.frame-method
 #' @references
 #' Kennel, M.B., Brown, R., Abarbanel, H.D.I., 1992. Determining embedding dimension for phase-space reconstruction using a geometrical construction. Physical Review A 45, 3403–3411.
 #'
 #' @examples
-#' crash = sf::read_sf(system.file("case/crash.gpkg", package = "pc"))
-#' pc::fnn(crash, 1, threads = 1)
+#' abun = readr::read_csv(system.file("case/abundance.csv", package = "pc"))
+#' pc::dmi(abun, 2)
 #'
 methods::setMethod("dmi", "data.frame", .dmi_ts)

From 1f5af16b1c8acf18c34ac17cbfa14097a314468d Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Tue, 11 Aug 2026 00:00:01 +0800
Subject: [PATCH 04/14] register dmi generic

---
 _pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 95ed274..62d94db 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -30,6 +30,7 @@ reference:
 - subtitle: embedding dimension choice
   contents:
   - fnn
+  - dmi
 
 - subtitle: optimal parameters search
   contents:

From 97746d9f1207d4ebc202af23b071b647a363b0ea Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Tue, 11 Aug 2026 00:00:01 +0800
Subject: [PATCH 05/14] register dmi generic

---
 _pkgdown.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 62d94db..737f41f 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -29,8 +29,8 @@ reference:
 
 - subtitle: embedding dimension choice
   contents:
-  - fnn
   - dmi
+  - fnn
 
 - subtitle: optimal parameters search
   contents:

From e2f8b9c6aa55f0116f56cd0fa532df49eb8cd7a4 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Tue, 11 Aug 2026 00:00:01 +0800
Subject: [PATCH 06/14] polish title

---
 _pkgdown.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 737f41f..9613b7c 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -27,7 +27,7 @@ reference:
 
 - title: Pattern Causality Analysis
 
-- subtitle: embedding dimension choice
+- subtitle: Phase Space Reconstruction
   contents:
   - dmi
   - fnn

From 956a7e172d271b58731f81c4f725eba289ce0fd6 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Tue, 11 Aug 2026 00:00:01 +0800
Subject: [PATCH 07/14] draft r interface for dmi

---
 R/dmi.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/dmi.R b/R/dmi.R
index afafee8..306d601 100644
--- a/R/dmi.R
+++ b/R/dmi.R
@@ -1,9 +1,8 @@
 .dmi_ts = \(data, target, tau = 1:10, pred = NULL, k = 3,
-            base = exp(1), normalize = FALSE, threads = 1) {
+            base = exp(1), normalize = FALSE, threads = length(tau), ...) {
   tv = .validate_var(data, target)[[1]]
   if (is.null(pred)) pred = which(!is.na(tv))
-  return(RcppFNN(tv, rt, eps, lib, pred, E, tau, style, dist.metric,
-                 k, threads, higher.parallel, NULL, NULL))
+  return(RcppDMI(tv, tau, pred, k, 0, base, normalize, threads))
 }
 
 #' Delayed Mutual Information

From e2151906e8921d14d62f0b717e759efb098d45bf Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Tue, 11 Aug 2026 00:00:01 +0800
Subject: [PATCH 08/14] draft r interface for dmi

---
 R/dmi.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/dmi.R b/R/dmi.R
index 306d601..aed4363 100644
--- a/R/dmi.R
+++ b/R/dmi.R
@@ -29,7 +29,7 @@
 #' @name dmi
 #' @aliases dmi,data.frame-method
 #' @references
-#' Kennel, M.B., Brown, R., Abarbanel, H.D.I., 1992. Determining embedding dimension for phase-space reconstruction using a geometrical construction. Physical Review A 45, 3403–3411.
+#' Fraser, A.M., Swinney, H.L., 1986. Independent coordinates for strange attractors from mutual information. Physical Review A 33, 1134–1140.
 #'
 #' @examples
 #' abun = readr::read_csv(system.file("case/abundance.csv", package = "pc"))

From 04a7ead66ab226c92cceba78a4a70bb1ed6e26d3 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Wed, 12 Aug 2026 00:00:01 +0800
Subject: [PATCH 09/14] draft r interface for dmi

---
 R/dmi.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/dmi.R b/R/dmi.R
index aed4363..2ec1f35 100644
--- a/R/dmi.R
+++ b/R/dmi.R
@@ -30,6 +30,7 @@
 #' @aliases dmi,data.frame-method
 #' @references
 #' Fraser, A.M., Swinney, H.L., 1986. Independent coordinates for strange attractors from mutual information. Physical Review A 33, 1134–1140.
+#' Kraskov, A., Stogbauer, H., Grassberger, P., 2004. Estimating mutual information. Physical Review E 69, 066138.
 #'
 #' @examples
 #' abun = readr::read_csv(system.file("case/abundance.csv", package = "pc"))

From 25fac3fa11e95f259a6bd34550eb3f58506a5c1b Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Wed, 12 Aug 2026 00:00:01 +0800
Subject: [PATCH 10/14] draft r interface for dmi

---
 R/dmi.R | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/R/dmi.R b/R/dmi.R
index 2ec1f35..269c463 100644
--- a/R/dmi.R
+++ b/R/dmi.R
@@ -1,5 +1,5 @@
-.dmi_ts = \(data, target, tau = 1:10, pred = NULL, k = 3,
-            base = exp(1), normalize = FALSE, threads = length(tau), ...) {
+.dmi_ts = \(data, target, tau = 1:10, pred = NULL, k = 3, base = exp(1), 
+            normalize = FALSE, threads = length(tau), ...) {
   tv = .validate_var(data, target)[[1]]
   if (is.null(pred)) pred = which(!is.na(tv))
   return(RcppDMI(tv, tau, pred, k, 0, base, normalize, threads))
@@ -19,9 +19,6 @@
 #' @param rt (optional) Relative distance threshold.
 #' @param eps (optional) Absolute distance threshold.
 #' @param threads (optional) Number of threads used.
-#' @param higher.parallel (optional) Whether to use a higher level of parallelism.
-#' @param detrend (optional) Whether to remove the linear trend.
-#' @param nb (optional) Neighbours list.
 #' @param ... Additional arguments to absorb unused inputs in method dispatch.
 #'
 #' @return A vector.

From 1c0371b477897bc3ce87bc52ac459c3eb78957e1 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Wed, 12 Aug 2026 00:00:01 +0800
Subject: [PATCH 11/14] draft r interface for dmi

---
 R/dmi.R | 16 +++-------------
 1 file changed, 3 insertions(+), 13 deletions(-)

diff --git a/R/dmi.R b/R/dmi.R
index 269c463..b3a04cb 100644
--- a/R/dmi.R
+++ b/R/dmi.R
@@ -7,19 +7,9 @@
 
 #' Delayed Mutual Information
 #'
-#' @param data Observation data.
-#' @param target Integer of column indice for the target variable.
-#' @param E (optional) Embedding dimensions.
-#' @param k (optional) Number of nearest neighbors used for evaluation.
-#' @param tau (optional) Step of lag.
-#' @param style (optional) Embedding style (`0` includes current state, `1` excludes it).
-#' @param lib (optional) Libraries indices.
-#' @param pred (optional) Predictions indices.
-#' @param dist.metric (optional) Distance measure to be used.
-#' @param rt (optional) Relative distance threshold.
-#' @param eps (optional) Absolute distance threshold.
-#' @param threads (optional) Number of threads used.
-#' @param ... Additional arguments to absorb unused inputs in method dispatch.
+#' @inheritParams fnn
+#' @param base (optional) Logarithm base of the entropy.
+#' @param normalize (optional) Whether to normalize MI values.
 #'
 #' @return A vector.
 #' @export

From 2106f1cf2018e58b2de8e679b7a3057d670a1647 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Wed, 12 Aug 2026 00:00:01 +0800
Subject: [PATCH 12/14] export r interface for dmi

---
 NAMESPACE  |  1 +
 man/dmi.Rd | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 man/dmi.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 69178c8..1147e9d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,6 +5,7 @@ S3method(plot,pc_single)
 S3method(print,pc_boot)
 S3method(print,pc_ops)
 S3method(print,pc_single)
+exportMethods(dmi)
 exportMethods(fnn)
 exportMethods(ops)
 exportMethods(pc)
diff --git a/man/dmi.Rd b/man/dmi.Rd
new file mode 100644
index 0000000..9612921
--- /dev/null
+++ b/man/dmi.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dmi.R
+\name{dmi}
+\alias{dmi}
+\alias{dmi,data.frame-method}
+\title{Delayed Mutual Information}
+\usage{
+\S4method{dmi}{data.frame}(
+  data,
+  target,
+  tau = 1:10,
+  pred = NULL,
+  k = 3,
+  base = exp(1),
+  normalize = FALSE,
+  threads = length(tau),
+  ...
+)
+}
+\arguments{
+\item{data}{Observation data.}
+
+\item{target}{Integer of column indice for the target variable.}
+
+\item{tau}{(optional) Step of lag.}
+
+\item{pred}{(optional) Predictions indices.}
+
+\item{k}{(optional) Number of nearest neighbors used for evaluation.}
+
+\item{base}{(optional) Logarithm base of the entropy.}
+
+\item{normalize}{(optional) Whether to normalize MI values.}
+
+\item{threads}{(optional) Number of threads used.}
+
+\item{...}{Additional arguments to absorb unused inputs in method dispatch.}
+}
+\value{
+A vector.
+}
+\description{
+Delayed Mutual Information
+}
+\examples{
+abun = readr::read_csv(system.file("case/abundance.csv", package = "pc"))
+pc::dmi(abun, 2)
+
+}
+\references{
+Fraser, A.M., Swinney, H.L., 1986. Independent coordinates for strange attractors from mutual information. Physical Review A 33, 1134–1140.
+Kraskov, A., Stogbauer, H., Grassberger, P., 2004. Estimating mutual information. Physical Review E 69, 066138.
+}

From 7556447d61a317e4fef84c5d2463ae6da91d9096 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Wed, 12 Aug 2026 00:00:01 +0800
Subject: [PATCH 13/14] document dmi in news

---
 NEWS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index d434908..26fc1d0 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,9 @@
 # pc 0.3
 
+## new
+
+* Provide `dmi` generic for *delayed mutual information* method (#77).
+
 ### enhancements
 
 * Clarify output indexing and boundary handling in `fnn` generic (#69).

From 4694093885a9bfd9a23acff3da2009221f4534e8 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Wed, 12 Aug 2026 00:00:01 +0800
Subject: [PATCH 14/14] update docs for dmi

---
 R/dmi.R    | 1 +
 man/dmi.Rd | 1 +
 2 files changed, 2 insertions(+)

diff --git a/R/dmi.R b/R/dmi.R
index b3a04cb..7112008 100644
--- a/R/dmi.R
+++ b/R/dmi.R
@@ -17,6 +17,7 @@
 #' @aliases dmi,data.frame-method
 #' @references
 #' Fraser, A.M., Swinney, H.L., 1986. Independent coordinates for strange attractors from mutual information. Physical Review A 33, 1134–1140.
+#' 
 #' Kraskov, A., Stogbauer, H., Grassberger, P., 2004. Estimating mutual information. Physical Review E 69, 066138.
 #'
 #' @examples
diff --git a/man/dmi.Rd b/man/dmi.Rd
index 9612921..bb3bdd4 100644
--- a/man/dmi.Rd
+++ b/man/dmi.Rd
@@ -49,5 +49,6 @@ pc::dmi(abun, 2)
 }
 \references{
 Fraser, A.M., Swinney, H.L., 1986. Independent coordinates for strange attractors from mutual information. Physical Review A 33, 1134–1140.
+
 Kraskov, A., Stogbauer, H., Grassberger, P., 2004. Estimating mutual information. Physical Review E 69, 066138.
 }