cameraOperation: Create a camera trap station operability matrix

In carlopacioni/camtrapRdeluxe: A R package that builds on camtrapR to provide more functionalities and flexibility

Create a camera trap station operability matrix

Description

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

Usage

cameraOperation(CTtable, 
  stationCol = "Station", 
  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. 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.
camerasIndependent	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.
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

Details

cameraCol is NULL by default. The function then assumes there was 1 camera per station CTtable. In more than 1 camera was deployed per station, 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 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.

Value

A matrix. Row names indicate Station IDs (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) or an indicator for whether the station was operational (depending on camerasIndependent and allCamsOn)

Note

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.

Author(s)

Juergen Niedballa

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

carlopacioni/camtrapRdeluxe documentation built on Nov. 29, 2023, 3:37 a.m.