View source: R/spatialDetectionHistory.R
spatialDetectionHistory | R Documentation |
capthist
object for spatial capture-recapture analyses from camera-trapping data
This function generates spatial detection histories of individuals of a species for spatial capture-recapture analyses with package secr
. Data are stored in a capthist
object. The capthist
object contains detection histories, camera-trap station location and possibly individual and station-level covariates. Detection histories can have adjustable occasion length and occasion start time (as in the function detectionHistory
).
spatialDetectionHistory(recordTableIndividual,
species,
camOp,
CTtable,
output,
stationCol = "Station",
speciesCol = "Species",
sessionCol,
Xcol,
Ycol,
stationCovariateCols,
individualCol,
individualCovariateCols,
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
occasionLength,
minActiveDaysPerOccasion,
occasionStartTime = 0,
maxNumberDays,
day1,
buffer,
includeEffort = TRUE,
scaleEffort = FALSE,
binaryEffort,
timeZone,
makeRMarkInput
)
recordTableIndividual |
data.frame. the record table with individual IDs created by |
species |
character. the species for which to compute the detection history |
camOp |
The camera operability matrix as created by |
CTtable |
data.frame. contains station IDs and coordinates. Same as used in |
output |
character. Return individual counts ("count") or binary observations ("binary")? |
stationCol |
character. name of the column specifying Station ID in |
speciesCol |
character. name of the column specifying species in |
sessionCol |
character. name of the column specifying session IDs, either in |
Xcol |
character. name of the column specifying x coordinates in |
Ycol |
character. name of the column specifying y coordinates in |
stationCovariateCols |
character. name of the column(s) specifying station-level covariates in |
individualCol |
character. name of the column specifying individual IDs in |
individualCovariateCols |
character. name of the column(s) specifying individual covariates in |
recordDateTimeCol |
character. name of the column specifying date and time in |
recordDateTimeFormat |
format of column |
occasionLength |
integer. occasion length in days |
minActiveDaysPerOccasion |
integer. minimum number of active trap days for occasions to be included (optional) |
occasionStartTime |
integer. time of day (the full hour) at which to begin occasions. |
maxNumberDays |
integer. maximum number of trap days per station (optional) |
day1 |
character. When should occasions begin: station setup date ("station"), first day of survey ("survey"), a specific date (e.g. "2015-12-31")? |
buffer |
integer. Makes the first occasion begin a number of days after station setup. (optional) |
includeEffort |
logical. Include trapping effort (number of active camera trap days per station and occasion) as usage in |
scaleEffort |
logical. scale and center effort matrix to mean = 0 and sd = 1? Currently not used. Must be FALSE. |
binaryEffort |
logical. Should effort be binary (1 if >1 active day per occasion, 0 otherwise)? |
timeZone |
character. must be an argument of |
makeRMarkInput |
logical. If |
The function creates a capthist
object by combining three different objects: 1) a record table of identified individuals of a species, 2) a camera trap station table with station coordinates and 3) a camera operation matrix computed with cameraOperation
. The record table must contain a column with individual IDs and optionally individual covariates. The camera trap station table must contain station coordinates and optionally station-level covariates. The camera operation matrix provides the dates stations were active or not and the number of active stations.
day1
defines if each stations detection history will begin on that station's setup day (day1 = "station"
) or if all station's detection histories have a common origin (the day the first station was set up if day1 = "survey"
or a fixed date if, e.g. day1 = "2015-12-31"
).
includeEffort
controls whether an effort matrix is computed or not. If TRUE, effort will be used for object usage
information in a traps
. binaryEffort
makes the effort information binary. scaleEffort
is currently not used and must be set to FALSE. The reason is that usage
can only be either binary, or nonnegative real values, whereas scaling effort would return negative values.
The number of days that are aggregated is controlled by occasionLength
. occasionStartTime
can be used to make occasions begin another hour than midnight (the default). This may be relevant for nocturnal animals, in which 1 whole night would be considered an occasion.
Output can be returned as individual counts per occasion (output = "count"
) or as binary observation (output = "binary"
).
Argument sessionCol
can be used to a create multi-session capthist
object. There are two different ways in which the argument is interpreted. It depends on whether a column with the name you specify in argument sessionCol
exists in recordTableIndividual
or in CTtable
. If sessionCol
is found in recordTableIndividual
, the records will be assigned to the specified sessions, and it will be assumed that all camera trap station were used in all sessions. Alternatively, if sessionCol
is found inCTtable
, it will be assumed that only a subset of stations was used in each session, and the records will be assigned automatically (using the station IDs to identify which session they belong into). In both cases, session information must be provided as a sequence of integer numbers beginnign with 1, i.e., you provide the session number directly in sessionCol
. See session
for more information about sessions in secr.
capthist
objects (as created by spatialDetectionHistory
for spatial capture-recapture analyses) expect the units of coordinates (Xcol
and col
in CTtable
) to be meters. Therefore, please use a suitable coordinate system (e.g. UTM).
Output depends on argument makeRMarkInput
:
makeRMarkInput = FALSE |
A |
makeRMarkInput = TRUE |
A data frame for use in RMark |
Please note the section about defining argument timeZone
in the vignette on data extraction (accessible via vignette("DataExtraction")
or online (https://cran.r-project.org/package=camtrapR/vignettes/DataExtraction.html)).
Juergen Niedballa
secr RMark
data(recordTableIndividualSample)
data(camtraps)
# create camera operation matrix (with problems/malfunction)
camop_problem <- cameraOperation(CTtable = camtraps,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
writecsv = FALSE,
hasProblems = TRUE,
dateFormat = "%d/%m/%Y"
)
sdh <- spatialDetectionHistory(recordTableIndividual = recordTableIndividualSample,
species = "LeopardCat",
camOp = camop_problem,
CTtable = camtraps,
output = "binary",
stationCol = "Station",
speciesCol = "Species",
Xcol = "utm_x",
Ycol = "utm_y",
individualCol = "Individual",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
occasionLength = 10,
day1 = "survey",
includeEffort = TRUE,
timeZone = "Asia/Kuala_Lumpur"
)
# missing space in species = "LeopardCat" was introduced by recordTableIndividual
# (because of CRAN package policies.
# In your data you can have spaces in your directory names)
summary(sdh)
plot(sdh, tracks = TRUE)
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