Merge pull request #45 from SpatLyu/dev

export surd generic

Author: SpatLyu

DESCRIPTION

@@ -19,6 +19,7 @@ LinkingTo:
     Rcpp,
     RcppThread,
 Imports: 
+    methods,
     sdsfun,
     sf,
     terra
@@ -27,4 +28,6 @@ Suggests:
     NlinTS,
     Rcpp,
     RcppThread,
-    readr
+    readr,
+    spEDM,
+    tEDM

NAMESPACE

@@ -7,4 +7,5 @@ export(entropy)
 export(je)
 export(mi)
 export(te)
+exportMethods(surd)
 useDynLib(infoxtr, .registration = TRUE)

R/Agenerics.R

@@ -0,0 +1,12 @@
+register_generic = \(name, def = NULL) {
+  if (!methods::isGeneric(name)){
+    if (is.null(def)) {
+      def = eval(bquote(function(data, ...) standardGeneric(.(name))))
+    }
+    methods::setGeneric(name, def)
+  }
+}
+
+for (gen in c("surd")) {
+  register_generic(gen)
+}

R/surd.R

@@ -0,0 +1,62 @@
+.surd_ts = \(data, target, agent, lag = 1, bin = 5, method = "equal",
+             max.combs = 3, threads = 1, base = 2.0, normalize = TRUE) {
+  mat = .convert2mat(data)
+  return(RcppSURD(mat, target, agent, lag, bin, max.combs, 
+                  threads, base, normalize, method))
+}
+
+.surd_lattice = \(data, target, agent, lag = 1, bin = 5, method = "equal", 
+                  max.combs = 3, threads = 1, base = 2.0, normalize = TRUE, nb = NULL) {
+  if (is.null(nb)) nb = sdsfun::spdep_nb(data)
+  mat = .convert2mat(data)
+  return(RcppSURD(mat, target, agent, lag, bin, max.combs, 
+                  threads, base, normalize, method, nb))
+}
+
+.surd_grid = \(data, target, agent, lag = 1, bin = 5, method = "equal",
+               max.combs = 3, threads = 1, base = 2.0, normalize = TRUE) {
+  mat = .convert2mat(data)
+  return(RcppSURD(mat, target, agent, lag, bin, max.combs, 
+                  threads, base, normalize, method, NULL, terra::nrow(data[[1]])))
+}
+
+#' SURD
+#' 
+#' Synergistic-Unique-Redundant Decomposition of causality
+#' 
+#' @note SURD only support numeric data.
+#'
+#' @inheritParams te
+#' @param lag (optional) Lag of the agent variables.
+#' @param bin (optional) Number of discretization bins.
+#' @param method (optional) Discretization method. One of
+#'   `"sd"`, `"equal"`, `"geometric"`, `"quantile"`,
+#'   `"natural("jenks")"`, or `"headtail"("headtails")`.
+#' @param max.combs (optional) Maximum combination order.
+#' @param threads (optional) Number of threads used.
+#' @param nb (optional) Neighbours list.
+#'
+#' @return A list.
+#' \describe{
+#'   \item{vars}{Character vector indicating the variable combination associated with each information component.}
+#'   \item{types}{Character vector indicating the information type of each component.}
+#'   \item{values}{Numeric vector giving the magnitude of each information component.}
+#' }
+#'
+#' @export
+#' @name surd
+#' @aliases surd,data.frame-method
+#' @references
+#' Martinez-Sanchez, A., Arranz, G. & Lozano-Duran, A. Decomposing causality into its synergistic, unique, and redundant components. Nat Commun 15, 9296 (2024).
+#'
+#' @examples
+#' columbus = sf::read_sf(system.file("case/columbus.gpkg", package="spEDM"))
+#' infoxtr::surd(columbus, 1, 2:3)
+#'
+methods::setMethod("surd", "data.frame", .surd_ts)
+
+#' @rdname surd
+methods::setMethod("surd", "sf", .surd_lattice)
+
+#' @rdname surd
+methods::setMethod("surd", "SpatRaster", .surd_grid)

_pkgdown.yml

@@ -32,6 +32,7 @@ reference:
 - subtitle: Information flow
   contents:
   - te
+  - surd
 
 - title: Miscellaneous Utility Functions
   contents:

man/surd.Rd

@@ -71,11 +71,9 @@ Rcpp::List RcppSURD(const Rcpp::NumericMatrix& mat,
     );
     for (size_t j = 0; j < ag.size(); ++j)
     {   
-        size_t col_id = ag[j];
-
         for (size_t r = 0; r < n_obs; ++r)
         {
-            cppMat[r][col_id] = mat(r, col_id);
+            cppMat[r][j] = mat(r, ag[j]);
         }
     }