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matrix-profile-foundation · Jun 3, 2019 · 5e7e30b · 5e7e30b
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -7,6 +7,7 @@
 ^cran-comments\.md$
 ^packrat/
 ^docs/
+^dev/
 ^\.Rprofile$
 ^\.travis\.yml$
 ^.*\.Rproj$

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tsmp
 Type: Package
 Title: Time Series with Matrix Profile
-Version: 0.3.5.9001
+Version: 0.3.5.9000
 Authors@R: c(
     person("Francisco", "Bischoff", email = "fbischoff@med.up.pt", role = c("aut", "cre"),
     comment = c(ORCID = "https://orcid.org/0000-0002-5301-8672")),
@@ -29,11 +29,12 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 6.1.1.9000
 NeedsCompilation: no
-Suggests: 
+Suggests:
     spelling,
     testthat,
     knitr,
     rmarkdown,
     gdtools,
-    vdiffr
+    vdiffr,
+    animation
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("[",AnnotationVector)
+S3method("[",ArcCount)
+S3method("[",Chain)
+S3method("[",Discord)
+S3method("[",Floss)
+S3method("[",Fluss)
+S3method("[",MatrixProfile)
+S3method("[",Motif)
+S3method("[",MultiMatrixProfile)
+S3method("[",MultiMotif)
+S3method("[",Salient)
+S3method("[",SimpleMatrixProfile)
 S3method(find_discord,MatrixProfile)
 S3method(find_motif,MatrixProfile)
 S3method(find_motif,MultiMatrixProfile)

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,7 @@
 NEWS
 ================
 Francisco Bischoff
-\- 01 Jun 2019
+\- 03 Jun 2019
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 

diff --git a/R/dist_profile.R b/R/dist_profile.R
@@ -61,9 +61,11 @@
 #' # weighted
 #' weight <- c(rep(1, w / 3), rep(0.5, w / 3), rep(0.8, w / 3)) # just an example
 #'
-#' nn <- dist_profile(ref_data, ref_data, window_size = w, index = 1, method = "weighted", weight = weight)
+#' nn <- dist_profile(ref_data, ref_data, window_size = w, index = 1, method = "weighted",
+#'  weight = weight)
 #' distance_profile <- Re(sqrt(nn$distance_profile))
-dist_profile <- function(data, query, ..., window_size = NULL, method = "v3", index = 1, k = NULL, weight = NULL, paa = 1) {
+dist_profile <- function(data, query, ..., window_size = NULL, method = "v3", index = 1, k = NULL,
+                         weight = NULL, paa = 1) {
 
   ## ---- Verify if method exists ----
   # set as v3 if no method is entered

diff --git a/R/fluss.R b/R/fluss.R
@@ -82,7 +82,7 @@ floss <- function(.mp, new_data, data_window, threshold = 1, exclusion_zone = NU
       .mp$cac_final <- NULL
       return(.mp)
     } else {
-      .mp <- stompi_update(.mp, head(new_data, data_window - data_size))
+      .mp <- stompi_update(.mp, utils::head(new_data, data_window - data_size))
       new_data <- new_data[(data_window - data_size + 1):new_data_size]
     }
   }
@@ -103,7 +103,7 @@ floss <- function(.mp, new_data, data_window, threshold = 1, exclusion_zone = NU
 
     .mp$cac_final <- c(
       rep(NA, chunk_size + mp_offset - chunk_size),
-      head(.mp$cac, -(round(data_window * (1 - vars()$kmode) - (1 - vars()$kmode) * .mp$w) - 0.5 * chunk_size + ifelse(mp_offset > 0, 1, 2)))
+      utils::head(.mp$cac, -(round(data_window * (1 - vars()$kmode) - (1 - vars()$kmode) * .mp$w) - 0.5 * chunk_size + ifelse(mp_offset > 0, 1, 2)))
     )
 
     na_head <- round(vars()$kmode * data_window + (0.5 * chunk_size - vars()$kmode * .mp$w)) + mp_offset
@@ -130,7 +130,7 @@ floss <- function(.mp, new_data, data_window, threshold = 1, exclusion_zone = NU
   res <- floss_extract(.mp, threshold)
 
   if (!keep_cac) {
-    res$cac_final <- tail(res$cac_final, -length(new_data))
+    res$cac_final <- utils::tail(res$cac_final, -length(new_data))
   }
 
   return(res)
@@ -179,9 +179,9 @@ floss_extract <- function(.mpac, threshold = 1, exclusion_zone = NULL) {
   new_data <- ifelse(is.null(attr(.mpac, "new_data")), 0, attr(.mpac, "new_data"))
 
   if (offset == 0 || cac_fin_len == floor((mp_len * vars()$kmode + new_data * 1.5))) {
-    cac <- tail(.mpac$cac_final, -new_data)
+    cac <- utils::tail(.mpac$cac_final, -new_data)
   } else {
-    cac <- tail(.mpac$cac_final, -offset)
+    cac <- utils::tail(.mpac$cac_final, -offset)
   }
 
   cac[cac > threshold] <- NA

diff --git a/R/mass-pre-w.R b/R/mass-pre-w.R
@@ -20,7 +20,8 @@
 #' w <- mp_toy_data$sub_len
 #' ref_data <- mp_toy_data$data[, 1]
 #' query_data <- mp_toy_data$data[, 1]
-#' weight <- c(rep(1, mp_toy_data$sub_len / 3), rep(0.5, mp_toy_data$sub_len / 3), rep(1, mp_toy_data$sub_len / 3))
+#' weight <- c(rep(1, mp_toy_data$sub_len / 3), rep(0.5, mp_toy_data$sub_len / 3),
+#' rep(1, mp_toy_data$sub_len / 3))
 #'
 #' pre <- tsmp:::mass_pre_w(ref_data, query_data, w, weight)
 #'

diff --git a/R/mass.R b/R/mass.R
@@ -22,7 +22,8 @@
 #' @references Website: <https://www.cs.unm.edu/~mueen/FastestSimilaritySearch.html>
 
 #' @name mass-deprecated
-#' @usage mass(data_fft, query_window, data_size, window_size, data_mean, data_sd, query_mean, query_sd)
+#' @usage mass(data_fft, query_window, data_size, window_size, data_mean, data_sd,
+#'  query_mean, query_sd)
 #' @seealso \code{\link{tsmp-deprecated}}
 #' @keywords internal
 NULL
@@ -33,7 +34,8 @@ NULL
 #'
 #' @export
 
-mass <- function(data_fft, query_window, data_size, window_size, data_mean, data_sd, query_mean, query_sd) {
+mass <- function(data_fft, query_window, data_size, window_size, data_mean, data_sd,
+                 query_mean, query_sd) {
   .Deprecated("dist_profile")
   # pre-process query for fft
   query_window <- rev(query_window)

diff --git a/R/mass_weighted.R b/R/mass_weighted.R
@@ -28,7 +28,8 @@
 #' w <- mp_toy_data$sub_len
 #' ref_data <- mp_toy_data$data[, 1]
 #' query_data <- mp_toy_data$data[, 1]
-#' weight <- c(rep(1, mp_toy_data$sub_len / 3), rep(0.5, mp_toy_data$sub_len / 3), rep(1, mp_toy_data$sub_len / 3))
+#' weight <- c(rep(1, mp_toy_data$sub_len / 3), rep(0.5, mp_toy_data$sub_len / 3),
+#'  rep(1, mp_toy_data$sub_len / 3))
 #'
 #' pre <- tsmp:::mass_pre_w(ref_data, query_data, w, weight)
 #'
@@ -39,7 +40,8 @@
 #'     pre$data_mean, pre$data_sd, pre$data_pre, pre$weight
 #'   )
 #' }
-mass_weighted <- function(query_window, window_size, data_fft, data_size, data_mean, data_sd, data_pre, weight, ...) {
+mass_weighted <- function(query_window, window_size, data_fft, data_size, data_mean, data_sd,
+                          data_pre, weight, ...) {
   if (length(weight) != window_size) {
     stop("'weight' must have the same length as the 'window_size'.")
   }

diff --git a/R/plot.R b/R/plot.R
@@ -29,6 +29,8 @@
 #' @param ylab a `string`. (Default is `""`). Y label.
 #' @param xlab a `string`. (Default is `"Profile Index"`). X label.
 #' @param ... further arguments to be passed to [plot()]. See [par()].
+#' @param xmin an `int`. (Default is `NULL`). Set the minimum value of x axis.
+#' @param xmax an `int`. (Default is `NULL`). Set the maximum value of x axis.
 #'
 #' @return None
 #' @keywords hplot
@@ -164,8 +166,8 @@ plot.ArcCount <- function(x, data, type = c("data", "matrix"), exclusion_zone =
   if (cac_size < nrow(profile_index)) {
     warning("cac_size < profile_index")
     cac_offset <- nrow(profile_index) - cac_size
-    plot_data <- as.matrix(tail(plot_data, cac_size))
-    profile_index <- as.matrix(tail(profile_index, cac_size) - cac_offset)
+    plot_data <- as.matrix(utils::tail(plot_data, cac_size))
+    profile_index <- as.matrix(utils::tail(profile_index, cac_size) - cac_offset)
   }
 
   xnum <- seq_len(nrow(x$mp) + min(x$w) - 1)
@@ -390,7 +392,7 @@ plot.SimpleMatrixProfile <- function(x, ylab = "distance", xlab = "index", main
 
     if (n_dim > 1) {
       for (i in 2:n_dim) {
-        lines(xnum, x$data[[1]][, i], main = paste0("Data"), ylab = "", xlab = xlab, col = i, ...)
+        graphics::lines(xnum, x$data[[1]][, i], main = paste0("Data"), ylab = "", xlab = xlab, col = i, ...)
       }
     }
 
@@ -402,7 +404,7 @@ plot.SimpleMatrixProfile <- function(x, ylab = "distance", xlab = "index", main
 
       if (n_dim > 1) {
         for (i in 2:n_dim) {
-          lines(xnum, x$data[[2]][, i], main = paste0("Data"), ylab = "", xlab = xlab, col = i, ...)
+          graphics::lines(xnum, x$data[[2]][, i], main = paste0("Data"), ylab = "", xlab = xlab, col = i, ...)
         }
       }
     }
@@ -540,7 +542,7 @@ plot.Floss <- function(x, data, type = c("data", "matrix"),
   if (cac_fin_len == floor((mp_len * vars()$kmode + new_data / 2))) {
     cac <- x$cac_final
   } else {
-    cac <- tail(x$cac_final, -offset)
+    cac <- utils::tail(x$cac_final, -offset)
   }
   cac_size <- length(cac)
   cac <- c(cac, rep(NA, nrow(x$mp) + min(x$w) - 1 - cac_size))

diff --git a/R/stompi.R b/R/stompi.R
@@ -95,24 +95,24 @@ stompi_update <- function(.mp, new_data, history_size = FALSE) {
   }
 
   if (history_size && (data_upd_size > history_size)) {
-    data_upd <- tail(data_upd, history_size)
+    data_upd <- utils::tail(data_upd, history_size)
     mp_new_size <- history_size - .mp$w + 1
     offset <- data_upd_size - history_size
 
-    mp_new <- tail(mp_new, mp_new_size)
-    pi_new <- tail(pi_new - offset, mp_new_size)
-    lmp_new <- tail(lmp_new, mp_new_size)
-    lpi_new <- tail(lpi_new - offset, mp_new_size)
-    rmp_new <- tail(rmp_new, mp_new_size)
-    rpi_new <- tail(rpi_new - offset, mp_new_size)
+    mp_new <- utils::tail(mp_new, mp_new_size)
+    pi_new <- utils::tail(pi_new - offset, mp_new_size)
+    lmp_new <- utils::tail(lmp_new, mp_new_size)
+    lpi_new <- utils::tail(lpi_new - offset, mp_new_size)
+    rmp_new <- utils::tail(rmp_new, mp_new_size)
+    rpi_new <- utils::tail(rpi_new - offset, mp_new_size)
 
     if (is.null(attr(.mp, "offset"))) {
       attr(.mp, "offset") <- offset
     } else {
       attr(.mp, "offset") <- attr(.mp, "offset") + offset
     }
 
-    # pi_new <- tail(pi_new - attr(.mp, "offset"), mp_new_size)
+    # pi_new <- utils::tail(pi_new - attr(.mp, "offset"), mp_new_size)
   }
 
   .mp$mp <- as.matrix(mp_new)
@@ -126,7 +126,7 @@ stompi_update <- function(.mp, new_data, history_size = FALSE) {
 
   # TODO: with tail or not (tail will recompute some things)
   #  if (history_size && (data_upd_size > history_size)) {
-  #    return(tail(.mp, history_size))
+  #    return(utils::tail(.mp, history_size))
   #  } else {
   return(.mp)
   #  }