surveyReport | R Documentation |
This function creates a report about a camera trapping survey and species records. It uses a camera trap station information table and a record table (generated with recordTable
) as input. Output tables can be saved and a zip file for simple data sharing can be created easily.
surveyReport (recordTable,
CTtable,
speciesCol = "Species",
stationCol = "Station",
cameraCol,
setupCol,
retrievalCol,
CTDateFormat = "%Y-%m-%d",
CTHasProblems = FALSE,
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
Xcol,
Ycol,
sinkpath,
makezip
)
recordTable |
data.frame containing a species record table as given by |
CTtable |
data.frame containing information about location and trapping period of camera trap stations (equivalent to |
speciesCol |
character. name of the column specifying Species ID in |
stationCol |
character. name of the column specifying Station ID in |
cameraCol |
character. name of the column specifying Camera ID in |
setupCol |
character. name of the column containing camera setup dates in |
retrievalCol |
character. name of the column containing camera retrieval dates in |
CTDateFormat |
character. The date format in columns |
CTHasProblems |
logical. Are there periods of camera malfunction specified in |
recordDateTimeCol |
character. The name of the column containing date and time of records in |
recordDateTimeFormat |
character. The date/time format of column |
Xcol |
character. name of the column specifying x coordinates in |
Ycol |
character. name of the column specifying y coordinates in |
sinkpath |
character. The directory into which the survey report is saved (optional) |
makezip |
logical. Create a zip file containing tables, plots and maps in |
The value of CTDateFormat
should be interpretable by as.Date
. CTDateFormat
defaults to "YYYY-MM-DD", e.g. "2014-10-31". See strptime
for how to format date and time strings in R.
If CTHasProblems
is set to TRUE, the function tries to find columns ProblemX_from
and ProblemX_to
in CTtable
(X
designates numbers from 1 to n in which a camera or station was not operational). If there are no such columns all stations are assumed to have been operational uninterruptedly from setup to retrieval.
An invisible list containing 5 data.frames
.
survey_dates |
station and image date ranges, number of total and active trap nights, number of cameras per station |
species_by_station |
species numbers by station |
events_by_species |
number of events and stations by species |
events_by_station |
number of events for every species by station (only species that were recorded) |
events_by_station2 |
number of events for all species at all stations (including species that were not recorded) |
The output will be saved to a .txt file if sinkpath
is defined.
If makezip
is TRUE, a zip file will be created in sinkpath
. It contains single-species activity plots, detection maps (if Xcol
and Ycol
are defined), the survey report tables, the record table and the camera trap station table, and an example R script.
Juergen Niedballa
recordTable
data(camtraps)
data(recordTableSample)
reportTest <- surveyReport (recordTable = recordTableSample,
CTtable = camtraps,
speciesCol = "Species",
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
CTDateFormat = "%d/%m/%Y",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S")
class(reportTest) # a list with
length(reportTest) # 5 elements
reportTest[[1]] # camera trap operation times and image date ranges
reportTest[[2]] # number of species by station
reportTest[[3]] # number of events and number of stations by species
reportTest[[4]] # number of species events by station
reportTest[[5]] # number of species events by station including 0s (non-observed species)
# with camera problems
reportTest_problem <- surveyReport (recordTable = recordTableSample,
CTtable = camtraps,
speciesCol = "Species",
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
CTDateFormat = "%d/%m/%Y",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
CTHasProblems = TRUE)
reportTest_problem$survey_dates
## Not run:
# run again with sinkpath defined
reportTest <- surveyReport (recordTable = recordTableSample,
CTtable = camtraps,
speciesCol = "Species",
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
CTDateFormat = "%d/%m/%Y",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
sinkpath = getwd())
# have a look at the text file
readLines(list.files(getwd(), pattern = paste("survey_report_", Sys.Date(), ".txt", sep = ""),
full.names = TRUE))
## End(Not run)
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