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+#' ---
+#' title: Wrapper for ecp package in TCPDBench
+#' author: G.J.J. van den Burg
+#' date: 2019-09-29
+#' license: See LICENSE file.
+#' copyright: 2019, The Alan Turing Institute
+#' ---
+
+library(argparse)
+library(ecp)
+
+load.utils <- function() {
+ # get the name of the current script so we can load utils.R (yay, R!)
+ cmd.args <- commandArgs(trailingOnly=F)
+ file.arg <- "--file="
+ this.script <- sub(file.arg, "", cmd.args[grep(file.arg, cmd.args)])
+ this.dir <- dirname(this.script)
+ utils.script <- file.path(this.dir, 'utils.R')
+ source(utils.script)
+}
+
+parse.args <- function() {
+ parser <- ArgumentParser(description='Wrapper for ecp package')
+ parser$add_argument('-i',
+ '--input',
+ help='path to the input data file',
+ required=TRUE
+ )
+ parser$add_argument('-o',
+ '--output',
+ help='path to the output file'
+ )
+ parser$add_argument('-a',
+ '--algorithm',
+ help='algorithm to use',
+ choices=c('e.agglo', 'e.divisive', 'kcpa'),
+ required=TRUE
+ )
+ parser$add_argument('--alpha',
+ type='double',
+ help='alpha parameter for agglo and divisive')
+ parser$add_argument('--minsize',
+ help='minsize argument for e.divisive',
+ type='integer', default=30)
+ parser$add_argument('-R', '--runs',
+ help='number of random permutations to use',
+ type='integer', default=199)
+ parser$add_argument('--siglvl',
+ type='double',
+ help='Significance level to use for tests')
+ # No examples are provided in the ecp package documentation about
+ # reasonable values for C, so we use 1 as default.
+ parser$add_argument('-C', '--cost',
+ type='double',
+ help='cost to use in the kcpa algorithm',
+ default=1)
+ parser$add_argument('-L', '--maxcp',
+ help='maximum number of cps in kcpa algorithm',
+ choices=c('max', 'default')
+ )
+ return(parser$parse_args())
+}
+
+main <- function() {
+ args <- parse.args()
+
+ # load the dataset
+ data <- load.dataset(args$input)
+
+ # copy defaults from the ecp package
+ defaults <- list()
+ if (args$algorithm == 'e.divisive') {
+ defaults$k <- 'null'
+ }
+ if (args$algorithm == 'kcpa') {
+ # Again, we don't want to limit the number of change points a priori,
+ # so set the maximum to the length of the series.
+ if (args$maxcp == 'max')
+ defaults$L <- data$original$n_obs
+ else
+ defaults$L <- 5 # following binseg and segneigh default
+ }
+ params <- make.param.list(args, defaults)
+
+ start.time <- Sys.time()
+ result <- tryCatch({
+ if (args$algorithm == 'e.agglo') {
+ out <- e.agglo(data$mat, alpha=params$alpha)
+ locs <- out$estimates
+ } else if (args$algorithm == 'e.divisive') {
+ out <- e.divisive(data$mat, sig.lvl=params$siglvl, R=params$runs,
+ min.size=params$minsize, alpha=params$alpha)
+ locs <- out$estimates
+ } else {
+ # kcpa
+ out <- kcpa(data$mat, params$L, params$cost)
+ locs <- out
+ }
+ list(locations=locs, error=NULL)
+ }, error=function(e) {
+ return(list(locations=NULL, error=e$message))
+ })
+
+ stop.time <- Sys.time()
+ runtime <- difftime(stop.time, start.time, units='secs')
+
+ if (!is.null(result$error))
+ exit.with.error(data$original, args, params, result$error)
+
+ # convert to 0-based indices
+ locations <- as.list(result$locations - 1)
+
+ exit.success(data$original, args, params, locations, runtime)
+}
+
+load.utils()
+main()