Database to detion histories

Usage

DBdetectionHistory(
  con,
  ProjectShortName,
  Species,
  Iteration = 1,
  byCamera,
  occasionStartTime = 0,
  camerasIndependent = TRUE,
  output = "binary",
  occasionLength = 1,
  includeEffort = TRUE,
  day1 = "station",
  ...
)

Arguments

con: database connection string (as returned via weda_connect())
ProjectShortName: Project short name (single value/project must be provided)
Species: Common species name/s to obtain detection histories for (e.g. Leadbeater's Possum)
Iteration: Iteration of survey (only single value allowed, loop function if multiple iterations required)
byCamera: passed to camtrapR: logical. If TRUE, camera operability matrix is computed by camera, not by station (requires cameraCol)
occasionStartTime: passed to camtrapR: integer. time of day (the full hour) at which to begin occasions. Replaces occasionStartTime from detectionHistory and spatialDetectionHistory.
camerasIndependent: passed to camtrapR: 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.
output: passed to camtrapR: character. Return binary detections ("binary") or counts of detections ("count")
occasionLength: passed to camtrapR: integer. occasion length in days
includeEffort: passed to camtrapR: logical. Compute trapping effort (number of active camera trap days per station and occasion)?
day1: passed to camtrapR: character. When should occasions begin: station setup date ("station"), first day of survey ("survey"), a specific date (e.g. "2015-12-31")?
...: additional arguments passed to camtrapR::detectionHistory()

Value

Depending on the value of includeEffort and scaleEffort, a list with either 1, 2 or 3 elements. The first element is the species detection history. The second is the optional effort matrix and the third contains the effort scaling parameters.

detection_history: A species detection matrix
effort: A matrix giving the number of active camera trap days per station and occasion (= camera trapping effort). It is only returned if includeEffort = TRUE
effort_scaling_parameters: Scaling parameters of the effort matrix. It is only returned if includeEffort and scaleEffort are TRUE

Examples


if (FALSE) { # \dontrun{
con <- weda::weda_connect(password = keyring::key_get(service = "ari-dev-weda-psql-01",
                                                     username = "psql_user"), username = "psql_user")

lbp_det_hist <- DBdetectionHistory(con,
                                  ProjectShortName = "FPSP_LBPCT",
                                  Species = "Leadbeater's Possum",
                                  Iteration = 1,
                                  byCamera = TRUE,
                                  occasionStartTime = 0,
                                  camerasIndependent = TRUE,
                                  output = "binary",
                                  occasionLength = 1,
                                  includeEffort = FALSE,
                                  scaleEffort = FALSE,
                                  day1 = "station")
                                  } # }