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authorGertjan van den Burg <gertjanvandenburg@gmail.com>2020-03-12 14:33:57 +0000
committerGertjan van den Burg <gertjanvandenburg@gmail.com>2020-03-12 14:33:57 +0000
commit7ef8f6e58990fc069cccc71ed6564e8c639ea4fc (patch)
tree9e7662a34b7d0c1f1c5d9faf6d7d6ea8672f6410 /execs/R/cpdbench_changepointnp.R
downloadTCPDBench-7ef8f6e58990fc069cccc71ed6564e8c639ea4fc.tar.gz
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+#' ---
+#' title: Wrapper for changepoint.np package in TCPDBench
+#' author: G.J.J. van den Burg
+#' date: 2019-09-30
+#' license: See LICENSE file.
+#' copyright: 2019, The Alan Turing Institute
+#' ---
+
+library(argparse)
+library(changepoint.np)
+
+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 changepoint.np 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$add_argument('-p',
+ '--penalty',
+ choices=c(
+ 'None',
+ 'SIC',
+ 'BIC',
+ 'MBIC',
+ 'AIC',
+ 'Hannan-Quinn',
+ 'Asymptotic'
+ ),
+ help='Choice of penalty in the cpt function',
+ default='MBIC'
+ )
+ parser$add_argument('-q',
+ '--nquantiles',
+ type='integer',
+ help='Number of quantiles to use',
+ default=10
+ )
+ return(parser$parse_args())
+}
+
+main <- function() {
+ args <- parse.args()
+
+ # load the data
+ data <- load.dataset(args$input)
+
+ # get the parameter list
+ defaults <- list(method='PELT',
+ test.stat='empirical_distribution',
+ minseglen=1)
+ params <- make.param.list(args, defaults)
+
+ if (data$origina$n_dim > 1) {
+ # changepoint.np package can't handle multidimensional data
+ exit.error.multidim(data$original, args, params)
+ }
+
+ vec <- as.vector(data$mat)
+ start.time <- Sys.time()
+
+ result <- tryCatch({
+ locs <- cpt.np(vec,
+ penalty=params$penalty,
+ method=params$method,
+ test.stat=params$test.stat,
+ minseglen=params$minseglen,
+ nquantiles=params$nquantiles,
+ class=FALSE
+ )
+ list(locations=locs, error=NULL)
+ }, error=function(e) {
+ return(list(locations=NULL, error=e$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$error)
+ }
+
+ # convert indices to 0-based indices
+ locations <- as.list(result$locations - 1)
+
+ exit.success(data$original, args, params, locations, runtime)
+}
+
+load.utils()
+main()