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## $Id: stampDive.R 600 2014-01-30 03:31:47Z sluque $
"stampDive" <- function(x, ignoreZ=TRUE)
{
## Value: A data frame; stamping each dive with phase number it belongs
## to, activity during that phase, and trip start and end time
## --------------------------------------------------------------------
## Arguments: x=TDRcalibrate object, ignoreZ=ignore Z phases?
## --------------------------------------------------------------------
## Author: Sebastian Luque
## --------------------------------------------------------------------
if (!is(x, "TDRcalibrate")) stop ("x needs to be a TDRcalibrate object")
act <- getGAct(x, "activity")
diveid <- getDAct(x, "dive.id")
if (ignoreZ) {
tt <- getTime(getTDR(x))
interval <- getDtime(getTDR(x))
act[act == "Z"] <- "L"
attlist <- .rleActivity(tt, act, interval) # recalculate
phaseid <- as.numeric(attlist[[1]]) # what phase.id is now
} else {
attlist <- getGAct(x)
phaseid <- getGAct(x, "phase.id")
}
beg <- rep(attlist[[3]], table(phaseid))
end <- rep(attlist[[4]], table(phaseid))
phase.no <- numeric(length(act)) # vector of 0s
phaseid[act == "L"] <- 0 # dry phase.id should be 0
## make a sequence for phase.id > 0 from 1:number of such phases
phase.no[act != "L"] <- rep(seq(along=table(phaseid[phaseid > 0])),
table(phaseid[phaseid > 0]))
ok <- match(unique(diveid[diveid > 0]), diveid) # required subscripts
phase.no <- phase.no[ok]
activity <- act[ok]
data.frame(phase.no, activity, beg=beg[ok], end=end[ok])
}
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