diveMove (version 0.6-9)

detPhase: Detect phases of activity from depth readings

Description

Functions to identify sections of a TDR record displaying one of three possible activities: on-land, at-sea, and at-sea leisure.

Usage

detPhase(time, depth, landerr, seaerr, ...)
getAct(time, act, interval)

Arguments

time

POSIXct object with date and time for all depths.

depth

numeric vector with depth readings.

landerr

land error threshold in seconds. On-land phases shorter than this threshold will be considered as at-sea.

seaerr

at-sea leisure threshold in seconds. At-sea phases shorter than this threshold will be considered as at-sea leisure.

act

A numeric vector indicating the activity for every element of time.

interval, ...

sampling interval in seconds.

Value

• A list with components; the first 4 are returned by detPhase and the rest by getAct:
• phase.id
  numeric vector identifying each activity phase, starting from 1 for every input record.
• trip.act
  factor with levels L indicating land, W indicating at-sea, U for underwater (above dive criterion), D for diving, Z for at-sea leisure animal activities. Only L, W, and Z are actually represented.
• trip.beg
  a POSIXct object as long as the number of unique activity phases identified, indicating the start times for each activity phase.
• trip.end
  a POSIXct object as long as the number of unique activity phases identified, indicating the end times for each activity phase.
• time.br
  a factor dividing the factor act in phases.
• time.peract
  duration of each phase defined by time.br.
• beg.time
  POSIXct object; beginning time for each phase.
• end.time
  POSIXct object; ending time for each phase.

Details

detPhase first creates a factor with value L (on-land) for rows with NAs for depth and value W (at-sea) otherwise. It subsequently calculates the duration of each of these phases of activity. If the duration of an on-land phase (L) is less than landerr, then the values in the factor for that phase are changed to W (at-sea). The duration of phases is then recalculated, and if the duration of a phase of at-sea activity is less than seaerr, then the corresponding value for the factor is changed to Z (at-sea leisure). The durations of all phases are recalculated a third time to provide final phase durations.

getAct takes a factor indicating different activity phases, their associated time, and the sampling interval to return a factor uniquely identifying each phase of activity, i.e. labelling them. In addition, it returns the duration of each phase, and their beginning and end times.

See Also

detDive