R/obsolete_bwcompatibility.R

In kleinbub/rIP: Synchronization of physiological and behavioral time-series of two interacting agents.

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# Here goes deprecated and obsolete functions calls, that will eventually get deleted
# 
# #' @rdname extractEpochs
# #' @export
# catExtractLong = function(x, signal="", epochStream="",by="",FUN=""){stop("this function has been renamed to extractEpochs ")}
# 
# 
# 
## legacyPeakFinder is an old version of peakFinder not implementing max time
legacyPeakFinder = function(x, sgol_p = 2, sgol_n = 25, mode=c("peaks","valleys","both"), correctionRangeSeconds = 0.5){
  which.minmax = function(x, pv){if(pv=="p") which.max(x) else if(pv=="v") which.min(x)}
  
  sampRate = frequency(x)
  smooth_x = signal::sgolayfilt(x,  p =sgol_p, n = sgol_n, m=0)
  fdderiv1  = diff(smooth_x)
  mode = match.arg(mode)
  pik = sign(embed(fdderiv1,2)) #embed appaia al segnale il segnale laggato di 1 samp
  s = pik[,2] - pik[,1] #that's where the magic happens

  if(mode=="peaks") {
    pikboo = c(s ==  2, FALSE) #embed perde 1 sample, quindi aggiungi un FALSE alla fine
    piksam = which(pikboo) #in quali sample c'è un'inversione di segno della derivata?
    pv = rep("p",length(piksam))
  } else if(mode=="valleys") {
    pikboo = c(s == -2, FALSE)
    piksam = which(pikboo)
    pv = rep("v",length(piksam))
  } else if(mode=="both") {
    pikboo = c(abs(s) ==  2, FALSE)
    piksam = which(pikboo)
    s = s[s!=0]
    pv = s
    pv[s>0] = "p"
    pv[s<0] = "v"
  }

  #correzione manuale: cerca il valore più alto nei dintorni del cambio di derivata
  for(v in seq_along(piksam)){
    #individua il range con 0.5s prima e dopo la valle della derivata (esclusi gli estremi inzio e fine ts)
    search_interval = x[
      max(1,piksam[v]-correctionRangeSeconds*sampRate):min(length(x),piksam[v]+correctionRangeSeconds*sampRate)
    ]
    #trova il più piccolo e aggiorna pikmsam
    if(mode=="peaks")
      piksam[v] = max(1, piksam[v]+  (which.max(search_interval) - round(length(search_interval)/2)))
    else if (mode=="valleys")
      piksam[v] = max(1, piksam[v]+  (which.min(search_interval) - round(length(search_interval)/2)))
    else
      piksam[v] = max(1, piksam[v]+  (which.minmax(search_interval,pv[v]) - round(length(search_interval)/2)))

    piksam[v] = min(piksam[v], length(x))
  }
  #ricrea pikmboo dai sample corretti
  pikboo = rep(F,length(pikboo))
  pikboo[piksam] = T
  piks = time(x)[piksam]
  list("bool" = pikboo,
       "samples" = piksam,
       "seconds" = piks,
       "type" = pv)
}


#' #vecchio "get"
#' 
#' 
#' 
#' #' @export
#' frequency.DyadSignal = function(x){attr(x,"SR")}


#' @export
signalDecimate = function (signal, newSampRate) {stop("this function has been deprecated. Use resample and signalFilter instead")}