detPhase {diveMove} | R Documentation |
Functions to identify sections of a TDR record displaying one of three possible activities: on-land, at-sea, and at-sea leisure.
detPhase(time, depth, landerr=65, seaerr=3605, ...) getAct(time, act, interval)
time |
chron 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 chron units (d). |
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.
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 chron object as long as the number of unique activity phases identified, with start times for each activity phase. |
trip.end |
a chron object as long as the number of unique activity phases identified, with 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 |
beginning time for each phase. |
end.time |
ending time for each phase. |
Sebastian P. Luque spluque@gmail.com