tso.R

##NOTE 
# with tsmethod = "stsm", the element "xreg" could be defined in the 
# object "stsm" instead of using argument "xreg" in "tso0". However, 
# it is more convenient to let the function "stsm::stsmFit" handle this element;
# in this way, the same arguments are passed to "stats::arima" and "stsmFit" 
# and the code is simplified here avoiding "if" statements depending on "tsmethod"

tso <- function(y, xreg = NULL, cval = NULL, delta = 0.7, n.start = 50,
  types = c("AO", "LS", "TC"), # c("IO", "AO", "LS", "TC", "SLS")
  maxit = 1, maxit.iloop = 4, maxit.oloop = 4, cval.reduce = 0.14286, 
  discard.method = c("en-masse", "bottom-up"), discard.cval = NULL, 
  remove.method, remove.cval, 
  tsmethod = c("auto.arima", "arima", "stsm"), 
  args.tsmethod = NULL, args.tsmodel = NULL, logfile = NULL)
{
  if (!missing(remove.method))
  {
    discard.method <- remove.method
    warning("argument \'remove.method\' is deprecated and will be ignored in future versions, ",
    "\'discard.method\' should be used instead")
  }

  if (!missing(remove.cval))
  {
    discard.cval <- remove.cval
    warning("argument \'remove.cval\' is deprecated and will be ignored in future versions, ",
    "\'discard.cval\' should be used instead")
  }

  tsmethod <- match.arg(tsmethod)
  discard.method <- match.arg(discard.method)
  attr.y <- attributes(y)
  n <- length(y)
  yname <- deparse(substitute(y))
  #stopifnot(is.ts(y))

  if (!is.null(args.tsmethod$xreg))
  {
    if (is.null(xreg))
    {
      # check if external regressors were defined through "args.tsmethod" 
      # instead of using argument "xreg"
      xreg <- args.tsmethod$xreg
      args.tsmethod$xreg <- NULL # this removes element "xreg" from the list
    } else {
      # check if external regressors were defined both 
      # in "xreg" and "args.tsmethod$xreg" but with different values
      if (!identical(xreg, args.tsmethod$xreg))
      {
        warning(paste("non-null \'args.tsmethod$xreg\' was ignored;", 
        "argument \'xreg\' was used instead"))
      } # else # "xreg" was defined twice with the same values (no warning)
      args.tsmethod$xreg <- NULL # this removes element "xreg" from the list
    }
  }

  if (is.null(dim(xreg))) {
    xreg <- cbind(xreg=xreg)
  } else
  if (is.null(colnames(xreg)))
    colnames(xreg) <- paste0("xreg", seq_len(ncol(xreg)))

  if (tsmethod == "stsm")
  {
    if (is.null(args.tsmodel$model))
      args.tsmodel$model <- ifelse(frequency(y) == 1, "local-level", "BSM")   

##FIXME these defaults only if stsm.method = "maxlik.fd.scoring"

    if (is.null(args.tsmodel$ssd))
      args.tsmodel$ssd <- TRUE
    if (is.null(args.tsmodel$sgfc))
      args.tsmodel$sgfc <- TRUE
    # let "stsm::stsmFit" handle "xreg", not here
    y <- do.call("stsm.model", args = c(list(y = y), args.tsmodel))
    #ylist <- list(m = m)
  } #else
    #ylist <- list(x = y) # m <- y

  # if "ylist" or "m <- y" were used, then the "if" statement below where "fit" is 
  # created could be avoided using "do.call(tsmethod, args = c(x = m, list())"
  # but this involves storing two identical objects ("y" and "m" or "ylist")

  # default arguments

  if (is.null(args.tsmethod))
  {
    args.tsmethod <- switch(tsmethod,
      "auto.arima" = list(allowdrift = FALSE, ic = "bic"),
      "arima" = list(order = c(0, 1, 1), seasonal = list(order = c(0, 1, 1))),
      "stsm" = list(stsm.method = "maxlik.td.optim", method = "L-BFGS-B",
        KF.version = "KFKSDS", KF.args = list(P0cov = TRUE), gr = "numerical")) #hessian = TRUE
      #list(stsm.method = "maxlik.fd.scoring", step = NULL, information = "expected"))
  }

  # default critical value
  # the same is done in functions "locate.outliers.oloop" and "discard.outliers"
  # "cval" is passed as a non-null value from tso() to those functions
  # but keep there this block so that default value is used when those functions 
  # are called outside tso()

  if (is.null(cval))
  {
    #n <- length(y)
    if (n <= 50) {
      cval <- 3
    } else 
    if (n >= 450) {
      cval <- 4
    } else
      cval <- round(3 + 0.0025 * (n - 50), 2)
  }

  cval0 <- cval
  if (is.null(discard.cval))
    discard.cval <- cval

  # "res0" is used below to generate the output, 
  # "res" is overwritten until no more outliers are found 
  # "res0" is also used if maxit = 1

  res0 <- res <- tso0(x = y, xreg = xreg, cval = cval, 
    delta = delta, n.start = n.start,
    types = types, maxit.iloop = maxit.iloop, maxit.oloop = maxit.oloop,
    discard.method = discard.method, discard.cval = discard.cval,
    tsmethod = tsmethod, args.tsmethod = args.tsmethod, 
    logfile = logfile)

  fit.wo.outliers <- res$fit0 # model without outliers (if maxit>1 res0 may change)
  moall <- res$outliers
  outtimes <- res$times

  iter <- 1
  cval <- round(cval * (1 - cval.reduce), 2)

  if (nrow(moall) > 1)
  while (iter < maxit)
  {
##FIXME see move res0 <- res after if(...) break

if (tsmethod == "stsm")
{
##FIXME TODO create stsm object based on res$yadj as done above
  warning("currently ", sQuote("maxit"), " > 1 is not allowed for ", sQuote("tsmethod=\"stsm\""))
  break
}
    # save "res" to have a copy of the last fitted model, res$fit;
    # if in the current run no outliers are found then 
    # tso0() does not return the fitted model

    res0 <- res

    res <- tso0(x = res$yadj, xreg = xreg, cval = cval, 
      delta = delta, n.start = n.start,
      types = types, maxit.iloop = maxit.iloop, 
      discard.method = discard.method, discard.cval = discard.cval, 
      tsmethod = tsmethod, args.tsmethod = args.tsmethod, 
      logfile = logfile)

##FIXME check
    #discard (remove) duplicates and outliers at consecutive type points (if any)
    #
    #do not discard according to abs(t-stat) because the detection of outliers 
    #are based on res$yadj (not the original series); discarding an outlier 
    #from a previous iteration would require changing the current res$yadj
    #
    #discard outliers at an observation where an outlier (of the same or other type)
    #was detected in a previous iteration
    id <- which(res$outliers[,"ind"] %in% res0$outliers[,"ind"])
    if (length(id) > 0)
      res$outliers <- res$outliers[id,]
    #discard consecutive outliers of any type, keep the outlier from previous iterations
    id <- which(apply(outer(res$outliers[,"ind"], res0$outliers[,"ind"], "-"), MARGIN=1, 
      FUN = function(x) any(x == 1)))
    if (length(id) > 0)
      res$outliers <- res$outliers[id,]

    if (nrow(res$outliers) == 0)
      break

    moall <- rbind(moall, res$outliers)
    outtimes <- c(outtimes, res$times)
    
    iter <- iter + 1
  }

  # final model given the detected outliers

  if (nrow(moall) > 0)
  {
    #NOTE 'pars' is relevant only for innovational outliers, 
    #when 'maxit'>1, see if it would be better to use 'res' instead of 'res0',
    #preferably it should be based on 'pars' from a model for the original data 
    #rather than the series adjusted for outliers

    pars <- switch(tsmethod, 
      "auto.arima" = , "arima" = coefs2poly(res0$fit),
      #"stsm" = stsm::char2numeric(res0$fit$model)) #Hari is trying to undock stsm package
      "stsm" = char2numeric(res0$fit$model))

    # 'xreg': input regressor variables such as calendar effects (if any)
    # 'xreg.outl': outliers regressor variables detected above (if any)
    # 'xregall': all regressors ('xreg' and 'xreg.outl')

    xreg.outl <- outliers.effects(mo = moall, n = n, weights = FALSE, delta = delta, 
      pars = pars, n.start = n.start, freq = frequency(y))
    xregall <- cbind(xreg, xreg.outl)
    nms.outl <- colnames(xreg.outl)
    colnames(xregall) <- c(colnames(xreg), nms.outl)

    ##NOTE
    # rerunning "auto.arima" (model selection) may not be necessary at this point

    if (tsmethod == "stsm") {
      fit <- do.call("stsmFit", args = c(list(x = y, xreg = xregall), args.tsmethod))
    } else {
      fit <- do.call(tsmethod, args = c(list(x = y, xreg = xregall), args.tsmethod))
      # this is for proper printing of results from "auto.arima" and "arima"
      fit$series <- yname
    }

    id <- colnames(xreg.outl)
    if (tsmethod == "stsm")
    {
##FIXME TODO 
#if xregall!=xreg.outl (i.e. argument xreg is not NULL)
#       xregcoefs <- fit$xreg$coef
#       stde <- fit$xreg$stde
#       if (is.null(stde))
#         stde <- sqrt(diag(vcov(fit, type = "optimHessian")))
      xregcoefs <- fit$pars[id]
      tstats <- xregcoefs / fit$std.errors[id]
    } else { # method "auto.arima", "arima"
      xregcoefs <- coef(fit)[id]
      tstats <- xregcoefs / sqrt(diag(fit$var.coef)[id])
    }

    moall[,"coefhat"] <- xregcoefs
    moall[,"tstat"] <- tstats

    oeff <- xreg.outl %*% cbind(xregcoefs)
    attributes(oeff) <- attr.y #attributes(y)

    yadj <- if(is.ts(y)) y - oeff else y@y - oeff

  } else { # no outliers detected
    fit <- fit.wo.outliers
    oeff <- NULL
    yadj <- if(is.ts(y)) y else y@y
  }

  structure(list(outliers = moall, y = if(is.ts(y)) y else y@y, yadj = yadj, 
    cval = cval0, fit = fit, effects = oeff, times = outtimes), 
    class = "tsoutliers")
}

tso0 <- function(x, xreg = NULL, cval = 3.5, delta = 0.7, n.start = 50,
  types = c("AO", "LS", "TC"), maxit.iloop = 4, maxit.oloop = 4, 
  discard.method = c("en-masse", "bottom-up"), discard.cval = NULL, 
  tsmethod = c("auto.arima", "arima", "stsm"), args.tsmethod = NULL,
  args.tsmodel = NULL, logfile = NULL)
{
  # "x" can be either a "ts" object or a "stsm" object;
  # if !inherits(x, "stsm") then two identical objects are stored ("x" and "y")

  y <- if(is.ts(x)) { x } else x@y

  #discard.method <- match.arg(discard.method)
  #tsmethod <- match.arg(tsmethod)
  #discard.method <- match.arg(discard.method)
  fitmethod <- gsub("stsm", "stsmFit", tsmethod)

  if (is.null(discard.cval))
    discard.cval <- cval

  # fit time series model

  fit.wo.outliers <- 
  fit <- do.call(fitmethod, args = c(list(x = x, xreg = xreg), args.tsmethod))
  #fit$series <- deparse(substitute(y))

  if (!is.null(logfile))
  {
    cat(paste("model selection:\n"), file = logfile, append = FALSE)
    capture.output(fit, file = logfile, append = TRUE)
  }

  # identify and locate prospective outliers by type
  # given a fitted time series model

  stage1 <- locate.outliers.oloop(y = y, fit = fit, types = types, cval = cval, 
    maxit.iloop = maxit.iloop, maxit.oloop = maxit.oloop, 
    delta = delta, n.start = n.start, logfile = logfile)

  # choose and fit the model including the outlier regressors detected so far
  # (the weights of the outliers is fine tuned, to see it 
  # compare 'moall[,"coefhat"]' with 'coef(fit)["oeffi"]') then
  # remove the outliers detected so far if they are not significant in the new model/fit

  if (nrow(stage1$outliers) > 0)
  {
    stage2 <- discard.outliers(x = stage1, y = y, cval = discard.cval, 
      method = discard.method, delta = delta, n.start = n.start, 
      tsmethod.call = fit$call, fdiff = NULL, logfile = logfile)

#moall <- stage2$outliers
stopifnot(ncol(stage2$xreg) == length(stage2$xregcoefs))
  } else 
    stage2 <- list(xreg = NULL, fit = stage1$fit)

  # final outliers and
  # original series adjusted for the outlier effects

  if (!is.null(stage2$xreg))
  {
    # stage2$fit$xreg is not returned by arima()
    moall <- stage2$outliers
    ##NOTE changed 2016Nov12 after changes in discard.outliers(), "moall" is updated there
    #moall[,"coefhat"] <- stage2$xregcoefs
    #moall[,"tstat"] <- stage2$xregtstats

    oeff <- stage2$xreg %*% cbind(stage2$xregcoefs)
    attributes(oeff) <- attributes(y)
    yadj <- y - oeff

    moall <- moall[,c("type", "ind", "coefhat", "tstat")]
    outtimes <- time(y)[moall[,"ind"]]
    if (frequency(y) > 1) 
      outseason <- formatC(as.vector(cycle(y)[moall[,"ind"]]), 
        width = 2, flag="0")

    moall <- cbind(moall[,c("type", "ind")], 
      "time" = if (frequency(y) > 1) paste(floor(outtimes), 
        outseason, sep = ":") else outtimes,
      moall[,c("coefhat","tstat")])

    oind <- order(moall[,"ind"])
    moall <- moall[oind,]
    outtimes <- outtimes[oind]
    rownames(moall) <- NULL

  } else { # no outliers detected
    oeff <- NULL
    yadj <- y
    moall <- data.frame(array(dim = c(0, 4)))
    colnames(moall) <- c("type", "ind", "coefhat", "tstat")
    outtimes <- NULL
  }

  if (!is.null(logfile))
  {
    msg <- paste("\nfinal outliers\n")
    cat(msg, file = logfile, append = TRUE)
    capture.output(moall, file = logfile, append = TRUE)
  }

  structure(list(outliers = moall, y = y, yadj = yadj, cval = cval,
    fit0 = fit.wo.outliers, # initial model fitted without outliers
    fit = stage2$fit, effects = oeff, times = outtimes), 
    class = "tsoutliers")
}