filterRecordTable: Filter species record table for temporal independence

In jniedballa/camtrapR: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

Filter species record table for temporal independence

Description

Filter species record table for temporal independence

Usage

filterRecordTable(
  recordTable,
  minDeltaTime = 0,
  deltaTimeComparedTo,
  speciesCol = "Species",
  stationCol,
  cameraCol,
  camerasIndependent,
  recordDateTimeCol = "DateTimeOriginal",
  recordDateTimeFormat = "ymd HMS",
  removeDuplicateRecords = TRUE,
  exclude,
  timeZone,
  writecsv = FALSE,
  outDir,
  eventSummaryColumn,
  eventSummaryFunction,
  quiet = FALSE
)

Arguments

recordTable	data frame as created by recordTable.
minDeltaTime	integer. Time difference between records of the same species at the same station to be considered independent (in minutes)
deltaTimeComparedTo	character. For two records to be considered independent, must the second one be at least minDeltaTime minutes after the last independent record of the same species ("lastIndependentRecord"), or minDeltaTime minutes after the last record ("lastRecord")?
speciesCol	character. name of the column specifying species in recordTable
stationCol	character. Name of the camera trap station column. Assuming "Station" if undefined.
cameraCol	character. Name of the column specifying cameras in recordTable (optional).
camerasIndependent	logical. If TRUE, species records are considered to be independent between cameras at a station.
recordDateTimeCol	character. Name of the column specifying date and time in recordTable.
recordDateTimeFormat	character. Format of column recordDateTimeCol in recordTable
removeDuplicateRecords	logical. If there are several records of the same species at the same station (also same camera if cameraID is defined) at exactly the same time, show only one?
exclude	character. Vector of species names to be excluded from the record table
timeZone	character. Must be a value returned by OlsonNames
writecsv	logical. Should the record table be saved as a .csv?
outDir	character. Directory to save csv to. If NULL and writecsv = TRUE, recordTable will be written to inDir.
eventSummaryColumn	character. A column in the record table (e.g. from a metadata tag) by to summarise non-independent records (those within minDeltaTime of a given record) with a user-defined function (eventSummaryFunction)
eventSummaryFunction	character. The function by which to summarise eventSummaryColumn of non-independent records, e.g. "sum", "max" (optional)
quiet	logical. If TRUE, suppress printing of progress.

Value

A data frame containing species records and additional information about stations, date, time, filtered for temporal independence.

Author(s)

Juergen Niedballa

Examples

if (Sys.which("exiftool") != ""){        # only run example if ExifTool is available

# set directory with camera trap images in station directories
wd_images_ID_species <- system.file("pictures/sample_images_species_dir", 
                                    package = "camtrapR")
                                    
# create record table without temporal filtering
rec_table <- recordTable(inDir                  = wd_images_ID_species,
                        IDfrom                 = "directory",
                        minDeltaTime           = 0,
                        exclude                = "UNID",
                        timeZone               = "Asia/Kuala_Lumpur",
                        removeDuplicateRecords = TRUE
                        )
                        
# filter for 60 minutes temporal independence
rec_table_filt <- filterRecordTable(recordTable         = rec_table, 
                                    minDeltaTime        = 60, 
                                    stationCol          = "Station",
                                    deltaTimeComparedTo = "lastIndependentRecord")
 nrow(rec_table)
 nrow(rec_table_filt)
 
 }

jniedballa/camtrapR documentation built on April 7, 2024, 9:08 p.m.