camtrapR (version 0.98.0)

cameraOperation: Create a camera operability matrix

Description

Construct a matrix of daily camera operability for use in detectionHistory and spatialDetectionHistory, where is needed for calculating trapping effort per occasion. If there were several cameras per station, the matrix can contain camera- or station-specific trap operation information.

Usage

cameraOperation(CTtable, 
  stationCol, 
  cameraCol, 
  setupCol, 
  retrievalCol, 
  hasProblems = FALSE,
  byCamera, 
  allCamsOn, 
  camerasIndependent,
  dateFormat = "%Y-%m-%d", 
  writecsv = FALSE, 
  outDir
)

Arguments

CTtable

data.frame containing information about location and trapping period of camera trap stations

stationCol

character. name of the column specifying Station ID in CTtable

cameraCol

character. name of the column specifying Camera ID in CTtable (optional). If empty, 1 camera per station is assumed.

setupCol

character. name of the column containing camera setup dates in CTtable

retrievalCol

character. name of the column containing camera retrieval dates in CTtable

hasProblems

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)

byCamera

logical. If TRUE, camera operability matrix is computed by camera, not by station (requires cameraCol)

allCamsOn

logical. If TRUE, all cameras of a station need to be operational for a station to be operational (only relevant if byCamera is FALSE). Output values will be 1/0/NA only (all cameras at a station operational/ at least 1 camera not operational

camerasIndependent

logical. Sum up number of active camera traps by station? Only if byCamera is FALSE and allCamsOn is FALSE. If camerasIndependent is TRUE, output values will the number of operational cameras at a station. If c

dateFormat

character. The format of columns setupCol and retrievalCol. Should be interpretable by as.Date

writecsv

logical. Should the camera operability matrix be saved as a .csv?

outDir

character. Directory into which csv is saved

Value

• A matrix. Row names indicate Station ID (camera ID 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)/camera(s) were operational (depending on camerasIndependent and allCamsOn)

Details

cameraCol is NULL by default. The function will check if there is more than 1 entry for any station in CTtable and returns an error if TRUE. In that case cameraCol needs to be specified to identify individual cameras within a station. dateFormat defaults to "YYYY-MM-DD", e.g. "2014-10-31". See strptime for formatting options. If hasProblems is TRUE, the function tries to find columns ProblemX_from and ProblemX_to in CTtable. X designates consecutive numbers from 1 to n 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 it is set to TRUE, all cameras at a station need to be operational for the station to be considered operational. If FALSE, at least 1 active station renders the station operational. Argument camerasIndependent defines if cameras at a station are considered independent (it thus only has an effect if there was more than 1 camera at a station). Independence occurs 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 any animal observation is likely to be made by both cameras (as would be the case with 2 cameras facing each other). If camerasIndependent is TRUE, 2 active cameras at a station will give a station operation value of 2, i.e., 2 independent trap nights at 1 station. If camerasIndependent is FALSE, 2 active cameras will return value 1, i.e., 1 trap nights at 1 station (which is made up of 2 )

Examples

data(camtraps)

# no problems/malfunction
camop_no_problem <- cameraOperation(CTtable      = camtraps,
                                    stationCol   = "Station",
                                    setupCol     = "Setup_date",
                                    retrievalCol = "Retrieval_date",
                                    writecsv     = FALSE,
                                    hasProblems  = FALSE,
                                    dateFormat   = "%d/%m/%Y"
)

# with problems/malfunction
camop_problem <- cameraOperation(CTtable      = camtraps,
                                 stationCol   = "Station",
                                 setupCol     = "Setup_date",
                                 retrievalCol = "Retrieval_date",
                                 writecsv     = FALSE,
                                 hasProblems  = TRUE,
                                 dateFormat   = "%d/%m/%Y"
)

camop_no_problem
camop_problem