Finish v0.3.2

matrix-profile-foundation · Oct 23, 2018 · dca9924 · dca9924
2 parents 8fea7ce + a60bead
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diff --git a/API-v0.3.2 b/API-v0.3.2
@@ -0,0 +1,77 @@
+# API for tsmp package
+
+## Exported functions
+
+as.arccount(.mp)
+as.chain(.mp)
+as.fluss(.mp)
+as.matrixprofile(.mp)
+as.motif(.mp)
+as.multimatrixprofile(.mp)
+as.multimotif(.mp)
+as.salient(.mp)
+av_apply(.mp)
+av_complexity(.mp, data, dilution_factor = 0, apply = FALSE)
+av_hardlimit_artifact(.mp, data, apply = FALSE)
+av_motion_artifact(.mp, data, apply = FALSE)
+av_stop_word(.mp, data, stop_word_loc, exclusion_zone = NULL, threshold = 0.1, apply = FALSE)
+av_zerocrossing(.mp, data, apply = FALSE)
+fast_movavg(data, window_size)
+fast_movsd(data, window_size)
+find_chains(.mp)
+find_motif(.mp, ...)
+fluss(.mp, num_segments, exclusion_zone = NULL)
+fluss_cac(.mp, exclusion_zone = NULL)
+fluss_extract(.mpac, num_segments, exclusion_zone = NULL)
+fluss_score(gtruth, extracted, data_size)
+get_data(.mp)
+mass(data_fft, query_window, data_size, window_size, data_mean, data_sd, query_mean, query_sd)
+mass_pre(data, data_size, query = NULL, query_size = NULL, window_size)
+mstomp(data, window_size, exclusion_zone = 1/2, verbose = 2, must_dim = NULL, exc_dim = NULL)
+mstomp_par(data, window_size, exclusion_zone = 1/2, verbose = 2, must_dim = NULL, exc_dim = NULL, n_workers = 2)
+plot_arcs(pairs, alpha = NULL, quality = 30, lwd = 15, col = c("blue", "orange"), main = "Arc Plot", ylab, xlab = "Profile Index", ...)
+salient_mds(.mp, data, bit_idx = 1)
+salient_score(.mp, gtruth)
+salient_subsequences(.mp, data, n_bits = 8, n_cand = 10, exclusion_zone = NULL, verbose = 2)
+scrimp(..., window_size, exclusion_zone = 1/2, verbose = 2, s_size = Inf, pre_scrimp = 1/4)
+sdts_predict(model, data, window_size)
+sdts_score(pred, gtruth, beta = 1)
+sdts_train(data, label, window_size, beta = 1, pat_max = Inf, parallel = TRUE, verbose = 2)
+set_data(.mp, data)
+simple_fast(..., window_size, exclusion_zone = 1/2, verbose = 2)
+stamp(..., window_size, exclusion_zone = 1/2, verbose = 2, s_size = Inf)
+stamp_par(..., window_size, exclusion_zone = 1/2, verbose = 2, s_size = Inf, n_workers = 2)
+stomp(..., window_size, exclusion_zone = 1/2, verbose = 2)
+stomp_par(..., window_size, exclusion_zone = 1/2, verbose = 2, n_workers = 2)
+tsmp(..., window_size, exclusion_zone = 1/2, mode = c("stomp", "stamp", "simple", "mstomp", "scrimp"), verbose = 2, s_size = Inf, must_dim = NULL, exc_dim = NULL, n_workers = 1, .keep_data = TRUE)
+
+## Own S3 methods
+
+find_motif.MatrixProfile(.mp, data, n_motifs = 3, n_neighbors = 10, radius = 3, exclusion_zone = NULL, ...)
+find_motif.MultiMatrixProfile(.mp, data, n_motifs = 3, mode = c("guided", "unconstrained"), n_bit = 4, exclusion_zone = NULL, n_dim = NULL, ...)
+
+## Foreign S3 methods
+
+plot.ArcCount(x, data, type = c("data", "matrix"), exclusion_zone = NULL, edge_limit = NULL, threshold = stats::quantile(x$cac, 0.1), main = "Arcs Discover", xlab = "index", ylab, ...)
+plot.Chain(x, data, type = c("data", "matrix"), main = "Chain Discover", xlab = "index", ylab, ...)
+plot.Fluss(x, data, type = c("data", "matrix"), main = "Fast Low-cost Unipotent Semantic Segmentation", xlab = "index", ylab, ...)
+plot.MatrixProfile(x, ylab = "distance", xlab = "index", main = "Unidimensional Matrix Profile", ...)
+plot.Motif(x, data, type = c("data", "matrix"), ncol = 3, main = "MOTIF Discover", xlab = "index", ylab, ...)
+plot.MultiMatrixProfile(x, ylab = "distance", xlab = "index", main = "Multidimensional Matrix Profile", ...)
+plot.MultiMotif(x, data, type = c("data", "matrix"), ncol = 3, main = "Multidimensional MOTIF Discover", xlab = "index", ylab, ...)
+plot.Salient(x, data, main = "Salient Subsections", xlab = "index", ylab, ...)
+plot.SimpleMatrixProfile(x, ylab = "distance", xlab = "index", main = "SiMPle Matrix Profile", ...)
+print.ArcCount(x, ...)
+print.Chain(x, ...)
+print.Fluss(x, ...)
+print.MatrixProfile(x, ...)
+print.Motif(x, ...)
+print.MultiMatrixProfile(x, ...)
+print.MultiMotif(x, ...)
+print.Salient(x, ...)
+print.SimpleMatrixProfile(x, ...)
+
+## Reexported objects
+
+::%>%
+::%T>%
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,7 +1,7 @@
 CONTRIBUTING
 ================
 Francisco Bischoff
-\- 16 Oct 2018
+\- 23 Oct 2018
 
 <!-- CONTRIBUTING.md is generated from CONTRIBUTING.Rmd Please edit that file -->
 

diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2018-09-10.
-Once it is accepted, delete this file and tag the release (commit 4801b48199).
+This package was submitted to CRAN on 2018-10-23.
+Once it is accepted, delete this file and tag the release (commit 0e7131cff8).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tsmp
 Type: Package
 Title: Time Series with Matrix Profile
-Version: 0.3.1.9031
+Version: 0.3.2
 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")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,7 @@
 NEWS
 ================
 Francisco Bischoff
-\- 16 Oct 2018
+\- 23 Oct 2018
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 

diff --git a/R/sdts-train.R b/R/sdts-train.R
@@ -92,12 +92,17 @@ sdts_train <- function(data, label, window_size, beta = 1, pat_max = Inf, parall
   }
 
   pos <- unlist(pos)
-  pos_alt_st <- which(is.infinite(pos)) + 1
+  pos_alt_st <- list()
+  for (i in 1:n_window_size) {
+    pos_alt_st[[i]] <- which(is.infinite(pos)) + 1
+    max_pos_idx <- pos_alt_st[[i]] > (length(pos) - window_size[i] + 1)
+    pos_alt_st[[i]][max_pos_idx] <- (length(pos) - window_size[i] + 1)
+  }
+
   pos_alt_ed <- which(is.infinite(pos)) - 1
   pos_alt_ed <- c(pos_alt_ed[-1], length(pos))
 
-  max_pos_idx <- pos_alt_st > (length(pos) - max(window_size) + 1)
-  pos_alt_st[max_pos_idx] <- (length(pos) - max(window_size) + 1)
+
 
   # run matrix profile on concatenated positive segment ----
   if (verbose > 0) {
@@ -125,15 +130,15 @@ sdts_train <- function(data, label, window_size, beta = 1, pat_max = Inf, parall
     candi_dist <- rep(0, n_pos)
 
     for (j in 1:n_pos) {
-      temp <- mat_pro[[i]][pos_alt_st[j]:max(pos_alt_st[j], (pos_alt_ed[j] - window_size[i] + 1), na.rm = TRUE)]
+      temp <- mat_pro[[i]][pos_alt_st[[i]][j]:max(pos_alt_st[[i]][j], (pos_alt_ed[j] - window_size[i] + 1), na.rm = TRUE)]
       rlt_idx <- which.min(temp)
       if (length(temp[rlt_idx]) == 0) {
         print("Zero")
       }
 
       candi_dist[j] <- temp[rlt_idx]
 
-      alt_idx <- pos_alt_st[j] + rlt_idx - 1
+      alt_idx <- pos_alt_st[[i]][j] + rlt_idx - 1
       candi[[i]][[j]] <- pos[alt_idx:(alt_idx + window_size[i] - 1)]
       candi_idx[[i]][j] <- pos_st[j] + rlt_idx - 1
     }

diff --git a/README.Rmd b/README.Rmd
@@ -113,7 +113,6 @@ devtools::install_github("franzbischoff/tsmp")
 
 ## Roadmap
 
-* MOTIFs under Uniform Scaling
 * Exact Detection of Variable Length Motifs
 * Profile-Based Shapelet Discovery
 * GPU-STOMP

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 README
 ================
 Francisco Bischoff
-\- 16 Oct 2018
+\- 23 Oct 2018
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
@@ -109,7 +109,6 @@ devtools::install_github("franzbischoff/tsmp")
 
 ## Roadmap
 
-  - MOTIFs under Uniform Scaling
   - Exact Detection of Variable Length Motifs
   - Profile-Based Shapelet Discovery
   - GPU-STOMP

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
diff --git a/docs/reference/fast_movsd.html b/docs/reference/fast_movsd.html
diff --git a/docs/reference/find_chains.html b/docs/reference/find_chains.html
diff --git a/docs/reference/find_motif.html b/docs/reference/find_motif.html
diff --git a/docs/reference/fluss.html b/docs/reference/fluss.html
diff --git a/docs/reference/fluss_cac.html b/docs/reference/fluss_cac.html
diff --git a/docs/reference/fluss_extract.html b/docs/reference/fluss_extract.html