Merge branch 'develop'

matrix-profile-foundation · Oct 16, 2018 · 8fea7ce · 8fea7ce
2 parents 080f764 + e4cc4cf
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,7 +1,7 @@
 CONTRIBUTING
 ================
 Francisco Bischoff
-\- 13 Oct 2018
+\- 16 Oct 2018
 
 <!-- CONTRIBUTING.md is generated from CONTRIBUTING.Rmd Please edit that file -->
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tsmp
 Type: Package
 Title: Time Series with Matrix Profile
-Version: 0.3.1.9028
+Version: 0.3.1.9031
 Authors@R: c(
     person("Francisco", "Bischoff", email = "[email protected]", role = c("aut", "cre"),
     comment = c(ORCID = "https://orcid.org/0000-0002-5301-8672")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -10,6 +10,7 @@ S3method(plot,Motif)
 S3method(plot,MultiMatrixProfile)
 S3method(plot,MultiMotif)
 S3method(plot,Salient)
+S3method(plot,SimpleMatrixProfile)
 S3method(print,ArcCount)
 S3method(print,Chain)
 S3method(print,Fluss)
@@ -18,6 +19,7 @@ S3method(print,Motif)
 S3method(print,MultiMatrixProfile)
 S3method(print,MultiMotif)
 S3method(print,Salient)
+S3method(print,SimpleMatrixProfile)
 export("%>%")
 export("%T>%")
 export(as.arccount)

diff --git a/NEWS b/NEWS
@@ -11,6 +11,8 @@ tsmp 0.3.1.9000
 -   Fixed SCRIMP and added PRE-SCRIMP, so this is the SCRIMP++. AB-join
     not yet implemented.
 -   Changed progress bar for a better one from `progress` package.
+-   Added Print and Plot to SiMPle. Issue \#24
+-   Added Print and Plot to Salient.
 
 tsmp 0.3.1
 ==========

diff --git a/NEWS.Rmd b/NEWS.Rmd
@@ -30,6 +30,8 @@ knitr::opts_chunk$set(
 * Changed verbose mode, added one more step to separate messages from progression bar.
 * Fixed SCRIMP and added PRE-SCRIMP, so this is the SCRIMP++. AB-join not yet implemented.
 * Changed progress bar for a better one from `progress` package.
+* Added Print and Plot to SiMPle. Issue #24
+* Added Print and Plot to Salient.
 
 # tsmp 0.3.1
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,7 @@
 NEWS
 ================
 Francisco Bischoff
-\- 13 Oct 2018
+\- 16 Oct 2018
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
@@ -16,6 +16,8 @@ Francisco Bischoff
   - Fixed SCRIMP and added PRE-SCRIMP, so this is the SCRIMP++. AB-join
     not yet implemented.
   - Changed progress bar for a better one from `progress` package.
+  - Added Print and Plot to SiMPle. Issue \#24
+  - Added Print and Plot to Salient.
 
 # tsmp 0.3.1
 

diff --git a/R/plot.R b/R/plot.R
@@ -256,6 +256,43 @@ plot.MultiMatrixProfile <- function(x, ylab = "distance", xlab = "index", main =
   graphics::par(def_par)
 }
 
+#' @export
+#' @keywords hplot
+#' @name plot
+#'
+plot.SimpleMatrixProfile <- function(x, ylab = "distance", xlab = "index", main = "SiMPle Matrix Profile", ...) {
+  def_par <- graphics::par(no.readonly = TRUE)
+  allmatrix <- FALSE
+  n_dim <- ncol(x$mp)
+
+  if (!is.null(x$lmp) && !all(x$lpi == -1)) {
+    allmatrix <- TRUE
+  }
+
+  if (allmatrix == TRUE) {
+    graphics::layout(matrix(seq_len(3 * n_dim), ncol = 3, byrow = TRUE))
+  }
+  graphics::par(
+    mar = c(4.1, 4.1, 2.1, 2.1),
+    oma = c(1, 1, 3, 0), cex.lab = 1.5
+  )
+  for (i in seq_len(n_dim)) {
+    graphics::plot(x$mp[, i], type = "l", main = paste0("Matrix Profile (w = ", x$w, "; ez = ", x$ez, ")"), ylab = ylab, xlab = xlab, ...)
+  }
+  graphics::mtext(text = main, font = 2, cex = 1.5, outer = TRUE)
+
+  if (allmatrix == TRUE) {
+    for (i in seq_len(n_dim)) {
+      graphics::plot(x$rmp[, i], type = "l", main = "Right Matrix Profile", ylab = ylab, xlab = xlab, ...)
+    }
+    for (i in seq_len(n_dim)) {
+      graphics::plot(x$lmp[, i], type = "l", main = "Left Matrix Profile", ylab = ylab, xlab = xlab, ...)
+    }
+  }
+
+  graphics::par(def_par)
+}
+
 #' @export
 #' @keywords hplot
 #' @name plot
@@ -560,7 +597,7 @@ plot.Salient <- function(x, data, main = "Salient Subsections", xlab = "index",
   y_max <- max(data)
 
   mds <- salient_mds(x, data)
-  idxs <- sort(x$salient$indexes[,1])
+  idxs <- sort(x$salient$indexes[, 1])
 
   # layout: matrix profile on top, motifs below.
   graphics::layout(matrix(c(1, 1, 1, 0, 2, 0), ncol = 3, byrow = TRUE))
@@ -569,8 +606,10 @@ plot.Salient <- function(x, data, main = "Salient Subsections", xlab = "index",
   graphics::plot(plot_data, type = "l", main = plot_subtitle, xlab = xlab, ylab = ylab)
   graphics::mtext(text = main, font = 2, cex = 1.5, outer = TRUE)
 
-  graphics::rect(idxs, y_min, xright = idxs + x$w, y_max, border = NA,
-                 col = grDevices::adjustcolor("blue", alpha.f = 0.1))
+  graphics::rect(idxs, y_min,
+    xright = idxs + x$w, y_max, border = NA,
+    col = grDevices::adjustcolor("blue", alpha.f = 0.1)
+  )
 
   graphics::plot(mds, main = "MDS")
 

diff --git a/R/print.R b/R/print.R
@@ -56,6 +56,34 @@ print.MultiMatrixProfile <- function(x, ...) {
   }
 }
 
+#' Prints a SiMPle Matrix Profile
+#'
+#' @param x a TSMP object of class `SimpleMatrixProfile`.
+#' @param ... additional arguments ignored.
+#' @export
+#' @keywords internal
+#' @noRd
+
+print.SimpleMatrixProfile <- function(x, ...) {
+  cat("SiMPle Matrix Profile\n")
+  cat("---------------------\n")
+
+  cat("Profile size =", nrow(x$mp), "\n")
+  cat("Dimensions =", x$n_dim, "\n")
+  cat("Window size =", x$w, "\n")
+  cat("Exclusion zone =", round(x$w * x$ez + vars()$eps), "\n")
+
+  if (!is.null(x$data)) {
+    set <- length(x$data)
+    obs <- nrow(x$data[[1]])
+    dim <- ncol(x$data[[1]])
+    cat(
+      "Contains", set, ifelse(set > 1, "sets", "set"), "of data with", obs, "observations and", dim,
+      ifelse(dim > 1, "dimensions", "dimension"), "\n"
+    )
+  }
+}
+
 #' Prints a CAC profile
 #'
 #' @param x a TSMP object of class `ArcCount`.

diff --git a/R/salient.R b/R/salient.R
@@ -430,7 +430,7 @@ salient_score <- function(.mp, gtruth) {
       }
     }
 
-    cutoff <- which(diff(.mp$salient$idx_bit_size[,b]) > 0)[1] - 1
+    cutoff <- which(diff(.mp$salient$idx_bit_size[, b]) > 0)[1] - 1
 
     if (!is.na(cutoff) && cutoff > 0) {
       hit_miss <- hit_miss[1:cutoff]

diff --git a/R/scrimp.R b/R/scrimp.R
@@ -271,7 +271,7 @@ scrimp <- function(..., window_size, exclusion_zone = 1 / 2, verbose = 2, s_size
     curdistance[i:num_queries] <-
       sqrt(abs(2 * (window_size -
         (curlastz[i:num_queries] - # x_term
-           window_size * pre$query_mean[i:num_queries] * pre$data_mean[1:(num_queries - i + 1)]) /
+          window_size * pre$query_mean[i:num_queries] * pre$data_mean[1:(num_queries - i + 1)]) /
           (pre$query_sd[i:num_queries] * pre$data_sd[1:(num_queries - i + 1)])
       )))
 

diff --git a/R/simple.R b/R/simple.R
@@ -12,7 +12,7 @@
 #' @param verbose an `int`. See details. (Default is `2`).
 #'
 #' @return Returns a `SimpleMatrixProfile` object, a `list` with the matrix profile `mp`, profile index `pi`,
-#' window size `w` and exclusion zone `ez`.
+#' number of dimensions `n_dim`, window size `w` and exclusion zone `ez`.
 #'
 #' @export
 #' @references * Silva D, Yeh C, Batista G, Keogh E. Simple: Assessing Music Similarity Using
@@ -220,6 +220,7 @@ simple_fast <- function(..., window_size, exclusion_zone = 1 / 2, verbose = 2) {
     mp = as.matrix(matrix_profile), pi = as.matrix(profile_index),
     rmp = NULL, rpi = NULL,
     lmp = NULL, lpi = NULL,
+    n_dim = n_dim,
     w = window_size,
     ez = ez
   )

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 README
 ================
 Francisco Bischoff
-\- 13 Oct 2018
+\- 16 Oct 2018
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 

diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/press.html b/docs/articles/press.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/as.matrixprofile.html b/docs/reference/as.matrixprofile.html
diff --git a/docs/reference/av_apply.html b/docs/reference/av_apply.html
diff --git a/docs/reference/av_complexity.html b/docs/reference/av_complexity.html
diff --git a/docs/reference/av_hardlimit_artifact.html b/docs/reference/av_hardlimit_artifact.html
diff --git a/docs/reference/av_motion_artifact.html b/docs/reference/av_motion_artifact.html
diff --git a/docs/reference/av_stop_word.html b/docs/reference/av_stop_word.html
diff --git a/docs/reference/av_zerocrossing.html b/docs/reference/av_zerocrossing.html
diff --git a/docs/reference/fast_movavg.html b/docs/reference/fast_movavg.html