R/erp.t.R

In erpR: Event-Related Potentials (ERP) Analysis, Graphics and Utility Functions

erp.t <-
  function(base1, base2,numbers1,numbers2=numbers1, startmsec=NULL, endmsec=NULL, electrode, smo = NULL, paired=TRUE, alpha=0.05, erplist1=NULL, erplist2=erplist1, sig=NULL, main=electrode, col=c("blue", "red"), p.adjust.method="none", ...) {
    
    # preliminary checks
    if (is.null(erplist1)|is.null(erplist2)){
      stop("two erplist objects (erplist1 and erplist2) containing ERP data frames must be specified!", call.=F)
    }
    
    #electrode checks
    if (!electrode%in%names(erplist1[[1]])) {
      stop("The electrode specified is not in the data frames contained in the erplist1", call.=F)
    }
    
    if (!electrode%in%names(erplist2[[1]])) {
      stop("The electrode specified is not in the data frames contained in the erplist2", call.=F)
    }
    
    
    #### object checks
    object.names1=paste(base1, numbers1, sep="")
    if (any(!object.names1%in%names(erplist1))){
      missing.objects1=object.names1[!object.names1%in%names(erplist1)]
      missing.object.collist1=paste(missing.objects1, "\n", sep="")
      stop("The following objects are not contained in the erplist1 specified:\n", missing.object.collist1, call.=F)
    }
    #### object checks
    object.names2=paste(base2, numbers2, sep="")
    if (any(!object.names2%in%names(erplist2))){
      missing.objects2=object.names2[!object.names2%in%names(erplist2)]
      missing.object.collist2=paste(missing.objects2, "\n", sep="")
      stop("The following objects are not contained in the erplist2 specified:\n", missing.object.collist2, call.=F)
    }
    
    ### get startmsec from the first object
    erplist = erplist1
    erpdf = erplist[[1]]
    
    if(!is.null(attr(erpdf, "startmsec")) & !is.null(attr(erpdf, "endmsec"))){
      startmsec=attr(erpdf, "startmsec")
      endmsec=attr(erpdf, "endmsec")
    }
    
    if (is.null(startmsec)|is.null(endmsec)){
      stop("startmsec and endmsec must be specified", call.=F)
    }
    
    
    #retrieve the call that can be used with erp and erp.add
    mycall=match.call()
    mycall.list=as.list(mycall)
    
    #create the object for the future call of erp
    mycall.erp=mycall.list[names(mycall.list)%in%as.list(names(as.list(args(erp))))]
    #notice the second part of this line of code. Basically I retrive the args of funciton erp, transform in a list. Then I take only the args in call that match
    # with args of function erp, to avoid to call for args unexpected from the function erp.
    mycall.erp$el=as.name("e1") # this is for a fake initial plot, it does not matter if it is e1 or e2.
    mycall.erp$type="n" # this is for the fake initial plot.
    
    
    #create the object for the future call of erp
    mycall.erp.add=mycall.list[names(mycall.list)%in%c("lty", "smo", "col", "lwd", "startmsec", "endmsec", "interval")]
    
    
    #### PARTE 1: STATISTICHE PER ELETTRODO ####
    if (is.null(numbers2)){
      numbers2=numbers1}
    
    
    if (is.null(sig)){
      

      alltemp.results=mass.t.test(base1=base1, base2=base2, numbers1=numbers1, numbers2=numbers2, startmsec=startmsec, endmsec=endmsec, paired=paired, 
                                  erplist1=erplist1, erplist2=erplist2, electrodes=electrode, p.adjust.method=p.adjust.method)$sig
    }

if (!is.null(sig)){
  alltemp.results=sig
}

##### PARTE 2 CREO DATAFRAME PER SCALP




alldata1=grandaverage(base=base1, numbers1, erplist=erplist1)
alldata2=grandaverage(base=base2,numbers2, erplist=erplist2)



e1=alldata1[,electrode]
e2=alldata2[,electrode]


do.call("erp", mycall.erp[-1])

# plotto le bande di significativita
######################
abline(v=grep(TRUE, alltemp.results[,electrode]), col="lightgray", lwd=3)
#######################
if (!is.null(smo)){
  e1=smooth.spline(e1, spar=smo)$y
  e2=smooth.spline(e2, spar=smo)$y
}

mycall.erp.add$el = as.name("e1")
mycall.erp.add$col = col[1]

do.call("erp.add", mycall.erp.add)		

mycall.erp.add$el = as.name("e2")
mycall.erp.add$col = col[2]

do.call("erp.add", mycall.erp.add)		



print(col)
invisible(alltemp.results)
}