| surveyReport {camtrapR} | R Documentation |
Create a report about a camera trapping survey and species detections
Description
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.
Usage
surveyReport(
recordTable,
CTtable,
camOp,
speciesCol = "Species",
stationCol = "Station",
cameraCol,
setupCol,
retrievalCol,
CTDateFormat = "ymd",
CTHasProblems = "deprecated",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS",
Xcol,
Ycol,
sinkpath,
makezip
)
Arguments
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 |
camOp |
camera operation matrix created with
|
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 format of columns |
CTHasProblems |
deprecated (since version 2.1) |
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 |
Details
dateFormat defaults to "YYYY-MM-DD", e.g. "2014-10-31". It can be
specified either in the format required by strptime or
the 'orders' argument in parse_date_time in
lubridate. In the example above, "YYYY-MM-DD" would be specified as
"%Y-%m-%d" or "ymd".
recordDateTimeFormat defaults to the "YYYY-MM-DD HH:MM:SS"
convention, e.g. "2014-09-30 22:59:59". recordDateTimeFormat can be
interpreted either by base-R via strptime or in
lubridate via parse_date_time (argument
"orders"). lubridate will be used if there are no "%" characters in
recordDateTimeFormat.
For "YYYY-MM-DD HH:MM:SS", recordDateTimeFormat would be either
"%Y-%m-%d %H:%M:%S" or "ymd HMS". For details on how to specify date
and time formats in R see strptime or
parse_date_time.
Note: as of version 2.1, argument CTHasProblems is deprecated and
defunct. Please use camOp instead to provide information about
periods of camera activity and malfunction. If camOp is not provided
the legacy version of surveyReport (from camtrapR 2.0.3) will be run with a
warning.
Value
An invisible list containing 5 data.frames.
survey_dates |
station and image date ranges, number of total and active trap days (calendar days and taking into account independent effort of multiple cameras, if applicable), 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.
Author(s)
Juergen Niedballa
See Also
Examples
data(camtraps)
data(recordTableSample)
# since version 2.1, camera operation matrix is required as input
camop_no_problem <- cameraOperation(CTtable = camtraps,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
writecsv = FALSE,
hasProblems = FALSE,
dateFormat = "dmy"
)
reportTest <- surveyReport (recordTable = recordTableSample,
CTtable = camtraps,
camOp = camop_no_problem,
speciesCol = "Species",
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
CTDateFormat = "dmy",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS")
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
camop_problem <- cameraOperation(CTtable = camtraps,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
writecsv = FALSE,
hasProblems = TRUE,
dateFormat = "dmy"
)
reportTest_problem <- surveyReport (recordTable = recordTableSample,
CTtable = camtraps,
camOp = camop_problem,
speciesCol = "Species",
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
CTDateFormat = "dmy",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS")
reportTest_problem$survey_dates
## if camOp is missing, the legacy version (from 2.0.3) will be used:
reportTest_problem_old <- surveyReport (recordTable = recordTableSample,
CTtable = camtraps,
# camOp = camop_problem,
speciesCol = "Species",
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
CTDateFormat = "dmy",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS")
## Not run:
# run again with sinkpath defined
reportTest <- surveyReport (recordTable = recordTableSample,
CTtable = camtraps,
camOp = camop_no_problem,
speciesCol = "Species",
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
CTDateFormat = "dmy",,
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS",
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)