Construct a matrix of daily camera trap station operation for use in
detectionHistory and spatialDetectionHistory,
where it is needed for calculating trapping effort per occasion. It is also
used in surveyReport to calculate the number of trap nights
durig a survey. If several cameras were deployed per station, the matrix can
contain camera- or station-specific trap operation information, or
information about sessions during repeated surveys.
cameraOperation(
CTtable,
stationCol = "Station",
cameraCol,
sessionCol,
setupCol,
retrievalCol,
hasProblems = FALSE,
byCamera,
allCamsOn,
camerasIndependent,
dateFormat = "ymd",
occasionStartTime = 0,
writecsv = FALSE,
outDir
)data.frame containing information about location and trapping period of camera trap stations
character. name of the column specifying Station ID in
CTtable
character. name of the column specifying Camera ID in
CTtable (optional). If empty, 1 camera per station is assumed.
character. name of the column specifying session ID in
CTtable (optional). Use it for creating multi-session / multi-season
detection histories (unmarked: unmarkedMultFrame;
secr: capthist )
character. name of the column containing camera setup dates
in CTtable
character. name of the column containing camera
retrieval dates in CTtable
logical. If TRUE, function will look for columns
specifying malfunction periods in CTtable (naming convention:
ProblemX_from and ProblemX_to, where X is a number)
logical. If TRUE, camera operation matrix is computed by
camera, not by station (requires cameraCol)
logical. Takes effect only if cameraCol is defined
and if byCamera is FALSE. If allCamsOn = TRUE, all cameras at
a station need to be operational for the station to be operational (e.g. 1
camera out of 2 malfunctioning renders the station inoperational). Output
values can be 1/0/NA only (all cameras at a station operational/ at least 1
camera not operational/ no camera set up). If allCamsOn = FALSE, at
least 1 active camera makes a station operational.
logical. Return number of active camera traps by
station? Only if byCamera is FALSE and allCamsOn is FALSE. If
camerasIndependent is TRUE, output values will be the number of
operational cameras at a station. If camerasIndependent is FALSE, the
value is 1 if at least 1 camera was operational, otherwise 0. In both cases,
values are NA if no camera was set up.
character. The format of columns setupCol and
retrievalCol (and potential problem columns) in CTtable. Must
be interpretable by either as.Date or the "orders" argument
parse_date_time in lubridate. Can be a date
or (since version 2.1) a date-time.
integer. time of day (the full hour) at which to
begin occasions. Replaces occasionStartTime from
detectionHistory and spatialDetectionHistory.
logical. Should the camera operation matrix be saved as a .csv?
character. Directory into which csv is saved
A matrix. Row names always indicate Station IDs. If
sessionCol and/or cameraCol are defined, they are contained in
the row names also (camera ID only if byCamera = TRUE). Column names
are dates.
Legend: NA: camera(s) not set up, 0: camera(s) not
operational, 1 (or higher): number of operational camera(s) or an indicator
for whether the station was operational (depending on
camerasIndependent and allCamsOn)
cameraCol is NULL by default, meaning the function assumes there was
1 camera per station in CTtable. If more than 1 camera was deployed
per station, cameraCol needs to be specified to identify individual
cameras within a station. Likewise, sessionCol can be used to if
camera trap stations were operated during multiple sessions / trapping
seasons.
dateFormat defaults to "YYYY-MM-DD", e.g. "2014-10-31", but can be
any other date format or date-time also. It can be specified either in the
format required by strptime or the 'orders' argument in
parse_date_time in lubridate. In the example
above, "YYYY-MM-DD" would be specified as "%Y-%m-%d" in base R or "ymd"
in lubridate.
Since version 2.1, dateFormat can be a date-time. That makes it possible to specify the exact time cameras were set up / retrieved / malfunctioned / worked again. This information is used to calculate the daily trapping effort more precisely on days with incomplete effort.
Previously, setup and retrival day were counted as 1, indicating a whole day of effort on those days. Since version 2.1, setup and retrieval are assumed to have happened at 12 noon (resulting in daily effort of 0.5 instead of 1). Users can also specify the exact time cameras were set up (by providing a date-time in the setup / retrieval / problem columns). See vignette 3 for more details.
If hasProblems is TRUE, the function tries to find columns
ProblemX_from and ProblemX_to in CTtable. X is a
consecutive number from 1 to n, specifying periods in which a camera or
station was not operational. If hasProblems is FALSE, cameras are
assumed to have been operational uninterruptedly from setup to retrieval
(see camtraps for details).
allCamsOn only has an effect if there was more than 1 camera at a
station. If TRUE, for the station to be considered operational, all cameras
at a station need to be operational. If FALSE, at least 1 active camera
renders the station operational. Argument camerasIndependent defines
if cameras record animals independently (it thus only has an effect if there
was more than 1 camera at a station). This is the case if an observation at
one camera does not increase the probability for detection at another camera
(cameras face different trails at a distance of one another).
Non-independence occurs if an animal is likely to trigger both camers (as
would be the case with 2 cameras facing each other).
If camerasIndependent is TRUE, 2 active cameras at a station will
result in a station operation value of 2 in the resulting matrix, i.e., 2
independent trap days at 1 station and day. If camerasIndependent is
FALSE, 2 active cameras will return value 1, i.e., 1 trap night at 1 station
per day.
Row names depend on the input arguments and contain the station name and
potentially session and camera names (if sessionCol and/or
cameraCol are defined).
Naming convention is (since version 1.2) Bold information are from
the columns stationCol, sessionCol and cameraCol in
CTtable:
Station
Station__SESS_SessionID
Station__CAM_CameraID
Station__SESS_SessionID__CAM_CameraID
Session are designated with prefix "__SESS_", cameras with prefix "__CAM_". Therefore, these are reserved words and may not be part of station, session or camera names. Here's what it may look like in real life:
Station1
Station1__SESS_2019
Station1__CAM_1024152
Station1__SESS_2019__CAM_1024152
Functions detectionHistory and spatialDetectionHistory recognize these and use the information accordingly.
Setting camerasIndependent according to the sampling situation
is important for the functions detectionHistory and
spatialDetectionHistory, if sampling effort (the number of
active trap nights in a occasion) is to be computed and returned.
data(camtraps)
# no problems/malfunction
camop_no_problem <- cameraOperation(CTtable = camtraps,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
writecsv = FALSE,
hasProblems = FALSE,
dateFormat = "dmy"
)
# with problems/malfunction
camop_problem <- cameraOperation(CTtable = camtraps,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
writecsv = FALSE,
hasProblems = TRUE,
dateFormat = "dmy"
)
# with problems/malfunction / dateFormat in strptime format
camop_problem_lubridate <- cameraOperation(CTtable = camtraps,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
writecsv = FALSE,
hasProblems = TRUE,
dateFormat = "%d/%m/%Y"
)
camop_no_problem
#> 2009-04-02 2009-04-03 2009-04-04 2009-04-05 2009-04-06 2009-04-07
#> StationA 0.5 1.0 1.0 1 1 1
#> StationB NA 0.5 1.0 1 1 1
#> StationC NA NA 0.5 1 1 1
#> 2009-04-08 2009-04-09 2009-04-10 2009-04-11 2009-04-12 2009-04-13
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-14 2009-04-15 2009-04-16 2009-04-17 2009-04-18 2009-04-19
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-20 2009-04-21 2009-04-22 2009-04-23 2009-04-24 2009-04-25
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-26 2009-04-27 2009-04-28 2009-04-29 2009-04-30 2009-05-01
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-05-02 2009-05-03 2009-05-04 2009-05-05 2009-05-06 2009-05-07
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-05-08 2009-05-09 2009-05-10 2009-05-11 2009-05-12 2009-05-13
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-05-14 2009-05-15 2009-05-16 2009-05-17
#> StationA 0.5 NA NA NA
#> StationB 1.0 1 0.5 NA
#> StationC 1.0 1 1.0 0.5
camop_problem
#> 2009-04-02 2009-04-03 2009-04-04 2009-04-05 2009-04-06 2009-04-07
#> StationA 0.5 1.0 1.0 1 1 1
#> StationB NA 0.5 1.0 1 1 1
#> StationC NA NA 0.5 1 1 1
#> 2009-04-08 2009-04-09 2009-04-10 2009-04-11 2009-04-12 2009-04-13
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-14 2009-04-15 2009-04-16 2009-04-17 2009-04-18 2009-04-19
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-20 2009-04-21 2009-04-22 2009-04-23 2009-04-24 2009-04-25
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-26 2009-04-27 2009-04-28 2009-04-29 2009-04-30 2009-05-01
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-05-02 2009-05-03 2009-05-04 2009-05-05 2009-05-06 2009-05-07
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-05-08 2009-05-09 2009-05-10 2009-05-11 2009-05-12 2009-05-13
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 0 0
#> 2009-05-14 2009-05-15 2009-05-16 2009-05-17
#> StationA 0.5 NA NA NA
#> StationB 1.0 1 0.5 NA
#> StationC 0.0 0 0.0 0
camop_problem_lubridate
#> 2009-04-02 2009-04-03 2009-04-04 2009-04-05 2009-04-06 2009-04-07
#> StationA 0.5 1.0 1.0 1 1 1
#> StationB NA 0.5 1.0 1 1 1
#> StationC NA NA 0.5 1 1 1
#> 2009-04-08 2009-04-09 2009-04-10 2009-04-11 2009-04-12 2009-04-13
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-14 2009-04-15 2009-04-16 2009-04-17 2009-04-18 2009-04-19
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-20 2009-04-21 2009-04-22 2009-04-23 2009-04-24 2009-04-25
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-04-26 2009-04-27 2009-04-28 2009-04-29 2009-04-30 2009-05-01
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-05-02 2009-05-03 2009-05-04 2009-05-05 2009-05-06 2009-05-07
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 1 1
#> 2009-05-08 2009-05-09 2009-05-10 2009-05-11 2009-05-12 2009-05-13
#> StationA 1 1 1 1 1 1
#> StationB 1 1 1 1 1 1
#> StationC 1 1 1 1 0 0
#> 2009-05-14 2009-05-15 2009-05-16 2009-05-17
#> StationA 0.5 NA NA NA
#> StationB 1.0 1 0.5 NA
#> StationC 0.0 0 0.0 0