Register TWDTW as a distance measure of the proxy package

NAMESPACE

@@ -95,6 +95,7 @@ importFrom(mgcv,gam)
 importFrom(mgcv,predict.gam)
 importFrom(plyr,alply)
 importFrom(proxy,dist)
+importFrom(proxy,pr_DB)
 importFrom(reshape2,melt)
 importFrom(scales,date_format)
 importFrom(scales,percent)

R/twdtwDist.R

@@ -1,12 +1,27 @@
 
-
-.twdtwDist = function (object, ...) {
-  d = lapply(seq_along(object), function (i) { 
-    x = subset(object,  i)
-    y = subset(object, -i)
-    res = twdtwApply(x, y, n=1)
-    res[]
-  })
-  d
+.twdtwDist = function (x, y, ...) {
+  d = do.call("rbind", lapply(x, function (xx) {
+      sapply(y, function (yy) {
+          res = twdtwApply(twdtwTimeSeries(xx), twdtwTimeSeries(yy), n=1, ...)
+          res[[1]]$distance[1]
+      })
+  }))
+  as.matrix(d)
 }
 
+# library(dtwSat)
+# library(dtw)
+# library(dtwclust)
+# log_fun = logisticWeight(-0.1, 100)
+# phi = proxy::dist(x=MOD13Q1.patterns.list, y=MOD13Q1.patterns.list[1:2], method="TWDTW", weight.fun=log_fun)
+# phi
+# a=twdtwApply(twdtwTimeSeries(MOD13Q1.patterns.list), twdtwTimeSeries(MOD13Q1.patterns.list), n=1, weight.fun=log_fun)
+# a[[3]]
+# 
+# aux = c(MOD13Q1.patterns.list, MOD13Q1.patterns.list, MOD13Q1.patterns.list)
+# a1 = tsclust(series = aux, distance = "DTW", trace = TRUE, type = "hierarchical", k = 3)
+# log_fun = logisticWeight(-0.1, 100)
+# a2 = tsclust(series = aux, distance = "TWDTW", trace = TRUE, type = "hierarchical", k = 3, weight.fun=log_fun, span = 300)
+# a1
+# a2
+

R/zzz.R

@@ -16,14 +16,23 @@
   packageStartupMessage(
     sprintf("Loaded dtwSat v%s. See ?dtwSat for help, citation(\"dtwSat\") for use in publication.\n",
             utils::packageDescription("dtwSat")$Version) )
+
+  ## Register TWDTW as a distance function into package proxy
+  pr_DB$set_entry(FUN   = .twdtwDist,
+                  names = c("TWDTW","twdtw"),
+                  loop  = FALSE,
+                  type  = "metric",
+                  description = "Time-Weighted Dynamic Time Warping",
+                  reference   = "Maus V, Camara G, Cartaxo R, Sanchez A, Ramos FM, de Queiroz GR (2016). A Time-Weighted Dynamic Time Warping method for land use and land cover mapping. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 9 (8), pp. 3729--3739. <doi: 10.1109/JSTARS.2016.2517118>."
+  );
 }
 
 #' @import zoo 
 #' @import raster
 #' @import ggplot2
 #' @import methods
 #' @import rgdal 
-#' @importFrom proxy dist
+#' @importFrom proxy dist pr_DB
 #' @importFrom reshape2 melt
 #' @importFrom scales pretty_breaks date_format percent
 #' @importFrom grDevices terrain.colors gray.colors