Merge pull request #77 from SpatLyu/dev

draft r interface for dmi

Author: SpatLyu

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)

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).

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)
 }

R/dmi.R

@@ -0,0 +1,27 @@
+.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))
+}
+
+#' Delayed Mutual Information
+#'
+#' @inheritParams fnn
+#' @param base (optional) Logarithm base of the entropy.
+#' @param normalize (optional) Whether to normalize MI values.
+#'
+#' @return A vector.
+#' @export
+#' @name dmi
+#' @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"))
+#' pc::dmi(abun, 2)
+#'
+methods::setMethod("dmi", "data.frame", .dmi_ts)

_pkgdown.yml

@@ -27,8 +27,9 @@ reference:
 
 - title: Pattern Causality Analysis
 
-- subtitle: embedding dimension choice
+- subtitle: Phase Space Reconstruction
   contents:
+  - dmi
   - fnn
 
 - subtitle: optimal parameters search