R/TRACDS.R

In rEMM: Extensible Markov Model for Modelling Temporal Relationships Between Clusters

#######################################################################
# rEMM - Extensible Markov Model (EMM) for Data Stream Clustering in R
# Copyright (C) 2011 Michael Hahsler
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

## creator for TRACDS
TRACDS <- function(lambda = 0) {
  new("TRACDS", lambda = lambda)
}

## show
setMethod("show", signature(object = "TRACDS"),
  function(object) {
    cat("tNN with", nstates(object), "states.\n")
    invisible(NULL)
  })

setMethod("copy", signature(x = "TRACDS"),
  function(x) {
    r <- new("TRACDS")

    ## copy environment
    r@tracds_d <- as.environment(as.list(x@tracds_d))

    r
  })


setMethod("nstates", signature(x = "TRACDS"),
  function(x)
    smc_size(x@tracds_d$mm))

setMethod("states", signature(x = "TRACDS"),
  function(x)
    smc_states(x@tracds_d$mm))

setMethod("current_state", signature(x = "TRACDS"),
  function(x)
    x@tracds_d$current_state)

setMethod("ntransitions", signature(x = "TRACDS"),
  function(x, threshold = NA) {
    if (is.na(threshold))
      sum(smc_countMatrix(x@tracds_d$mm) > 0)
    else
      sum(smc_countMatrix(x@tracds_d$mm) >= threshold)
  })

setMethod("transitions", signature(x = "TRACDS"),
  function(x) {
    m <- smc_countMatrix(x@tracds_d$mm)

    ### check for no transition
    if (sum(m) < 1)
      edges <- matrix(as.character(NA), nrow = 0, ncol = 2)
    else
      edges <- apply(
        which(m > 0, arr.ind = T),
        MARGIN = 2,
        FUN = function(x)
          colnames(m)[x]
      )

    colnames(edges) <- c("from", "to")
    edges
  })

setMethod("rare_transitions", signature(x = "TRACDS"),
  function(x, count_threshold) {
    ts <- transitions(x)
    ts[transition(x, ts, type = "counts", prior = FALSE) <= count_threshold, ]
  })