TDRcalibrate-class {diveMove} | R Documentation |
This class holds information produced at various stages of dive analysis. Methods are provided for extracting data from each slot.
## S4 method for signature 'TDRcalibrate, logical': attendance(obj, ignoreZ) ## S4 method for signature 'TDRcalibrate, numeric, ## missing': extractDive(obj, diveNo) ## S4 method for signature 'TDRcalibrate, missing': getDAct(x) ## S4 method for signature 'TDRcalibrate, character': getDAct(x, y) ## S4 method for signature 'TDRcalibrate, missing': getDPhaseLab(x) ## S4 method for signature 'TDRcalibrate, numeric': getDPhaseLab(x, diveNo) ## S4 method for signature 'TDRcalibrate, missing': getGAct(x) ## S4 method for signature 'TDRcalibrate, character': getGAct(x, y) ## S4 method for signature 'TDRcalibrate, missing': plot(x, diveNo=seq(unique(getDAct(x, "dive.id"))), labels="phase.id", surface=FALSE, ...)
x, obj |
"TDRcalibrate" object. |
ignoreZ |
logical indicating whether to ignore trivial aquatic periods. |
diveNo |
numeric vector with dive numbers to plot. |
labels |
one of “phase.id” or “dive.phase”,
specifying whether to label observations based on the gross phase ID
of the "TDR" object, or based on each dive
phase, respectively. |
surface |
logical indicating whether to plot surface readings. |
... |
further arguments to plotDive . |
y |
string; “dive.id”, “dive.activity”, or
“postdive.id” in the case of getDAct , to extract the
numeric dive ID, the factor identifying dive phases in each dive, or
the numeric postdive ID, respectively. In the case of
getGAct it should be one of “phase.id”,
“trip.act”, “trip.beg”, or “trip.end”, to
extract the numeric phase ID for each observation, a factor
indicating what major activity the observation corresponds to, or
the beginning and end times of each phase in the record, respectively. |
This is perhaps the most important class in diveMove, as it holds all the information necessary for calculating requested summaries for a TDR.
The tdr
slot contains the time, zero-offset corrected depth,
and possibly calibrated or uncalibrated speed. See
readTDR
and the accessor function getTDR
for this slot. Convenient access to each vector in this slot is
available through getTime
, getDepth, and
getSpeed.
The slot gross.activity holds, as a list, a vector (named
phase.id
) numbering each major activity phase found in the
record, a factor (named trip.act
) labelling each row as being
on-land, at-sea, or leisure at-sea activity. These two elements are
as long as there are rows in tdr
. This slot also contains two
more vectors: one with the beginning time of each phase, and another
with the ending time; both represented as POSIXct
objects. See
detPhase
.
The slot dive.activity
contains a data.frame, again with as
many rows as those in tdr
, consisting of three vectors named:
dive.id
, which is an integer vector, sequentially numbering
each dive (rows that are not part of a dive are labelled 0),
dive.activity is a factor which completes that in trip.act
above, further identifying rows in the record belonging to a dive.
The third vector in dive.activity
is an integer vector
sequentially numbering each postdive interval (all rows that belong to
a dive are labelled 0). See detDive
, and
getDAct
to access all or any one of these vectors.
dive.phases
is a slot corresponding to a factor that labels
each row in the record as belonging to a particular phase of a dive.
See labDivePhase
, and getDPhaseLab
to
access this slot.
land.threshold
, sea.threshold
, dive.threshold
,
and speed.calib.coefs
are each a single number representing
parameters used for detecting phases, and calibrating the TDR. Except
for the latter, these are mostly for internal use, and hence do not
have an accessor function. See getSpeedCoef
for
accessing speed.calib.coefs
.
The plot method for this class creates an interactive plot of the
"TDR"
object, labelling the identified
observations with a chosen factor from the corresponding
"TDRcalibrate"
object. The argument
surface
allows for the inclusion/exclusion of identified
surface readings.
Objects can be created by calls of the
form new("TDRcalibrate", ...)
. The objects of this class
contain information necessary to divide the record into sections
(e.g. land/water), dive/surface, and different sections within dives.
They also contain the parameters used to calibrate speed and criteria
to divide the record into phases.
tdr
:"TDR"
, with concurrent
time, depth, and possibly speed (if "TDRspeed"
). See
Details
.gross.activity
:"list"
, must be
the same as value returned by detPhase
.dive.activity
:"data.frame"
,
must be the same as value returned by detDive
.dive.phases
:"factor"
, must be
the same as value returned by labDivePhase
.land.threshold
:"numeric"
the
temporal criteria used for detecting periods on land that should
be considered as at-sea.sea.threshold
:"numeric"
the
temporal criteria used for detecting periods at-sea that should
not be considered as foraging time.dive.threshold
:"numeric"
the
criteria used for defining a dive.speed.calib.coefs
:"numeric"
the intercept and slope derived from the speed calibration
procedure.
signature(obj = "TDRcalibrate", ignoreZ =
"logical")
: generates an attendance table for the TDR record;
the duration of each dry and wet phase.signature(x = "TDRcalibrate", y = "missing")
:
extracts a data frame with vectors identifying all readings to a
particular dive and postdive number, and a factor identifying all
readings to a particular activity.signature(x = "TDRcalibrate", y =
"character")
: as the method for missing y
, but selects a
particular vector to extract.signature(x = "TDRcalibrate", diveNo =
"missing")
: extracts a factor identifying all readings to a
particular dive phase.signature(x = "TDRcalibrate", diveNo =
"numeric")
: as the method for missing y
, but selects
data from a particular dive number to extract.signature(obj = "TDRcalibrate", diveNo =
"numeric", id = "missing")
: extract particular dives.signature(x = "TDRcalibrate", y = "missing")
:
extracts elements that divide the data into major wet and dry
activities.signature(x = "TDRcalibrate", y =
"character")
: as the method for missing y
, but extracts
particular elements.signature(object = "TDRcalibrate")
: prints
informative summary of the data.signature(x = "TDRcalibrate")
: extracts the
TDR
object.signature(x = "TDRcalibrate")
: extracts
the speed calibration coefficients.signature(x = "TDRcalibrate", y = "missing")
:
plot the TDR object, labelling identified sections of it (see
Usage
and Details
).
Sebastian P. Luque spluque@gmail.com
TDR-class
for links to other classes in the
package