| read.capthist {secr} | R Documentation |
Data in the DENSITY formats for capture data and trap layouts may be
imported as a capthist object for analysis in secr. Data in
a capthist object may also be exported in these formats for use
in DENSITY (Efford 2012). read.capthist inputs data from text
files and constructs a capthist object in one step using the
functions read.traps and make.capthist. Data may also be
read from Excel spreadsheets if the package readxl is installed (see
secr-datainput.pdf).
read.capthist(captfile, trapfile, detector = "multi", fmt = c("trapID","XY"),
noccasions = NULL, covnames = NULL, trapcovnames = NULL,
cutval = NULL, verify = TRUE, noncapt = "NONE", tol = 0.01, snapXY = FALSE,
markocc = NULL, ...)
write.capthist(object, filestem = deparse(substitute(object)),
sess = "1", ndec = 2, covariates = FALSE, tonumeric = TRUE, ...)
captfile |
name of capture data file |
trapfile |
name of trap layout file or (for a multi-session captfile) a vector of file names, one for each session |
detector |
character value for detector type (‘single’, ‘multi’, ‘proximity’, etc.) |
fmt |
character value for capture format (‘trapID’ or ‘XY’) |
noccasions |
number of occasions on which detectors were operated |
covnames |
character vector of names for individual covariate fields in ‘captfile’ |
trapcovnames |
character vector of names for detector covariate fields in ‘trapfile’ |
cutval |
numeric, threshold of signal strength for ‘signal’ detector type |
verify |
logical if TRUE then the resulting capthist object is
checked with |
noncapt |
character value; animal ID used for ‘no captures’ |
tol |
numeric, snap tolerance in metres |
snapXY |
logical; if TRUE then fmt = 'XY' uses nearest trap within tol |
markocc |
integer vector distinguishing marking occasions (1) from sighting occasions (0) |
... |
other arguments passed to |
object |
|
filestem |
character value used to form names of output files |
sess |
character session identifier |
ndec |
number of digits after decimal point for x,y coordinates |
covariates |
logical or a character vector of covariates to export |
tonumeric |
logical for whether factor and character covariates should be converted to numeric values on output |
read.capthist
captfile should record one detection on each line. A detection
comprises a session identifier, animal identifier, occasion number (1,
2,...,S where S is the number of occasions), and a
detector identifier (fmt = "trapID") or X- and Y-coordinates
(fmt = "XY"). Each line of trapfile has a detector
identifier and its X- and Y-coordinates. In either file type the
identifiers (labels) may be numeric or alphanumeric values. Values
should be separated by blanks or tabs unless (i) the file name ends in
‘.csv’ or (ii) sep = "," is passed in ..., in which case commas
are assumed. Blank lines and any text after ‘#’ are ignored. For further
details see secr-datainput.pdf,
make.capthist and ‘Data formats’ in the help for DENSITY.
The noccasions argument is needed only if there were no
detections on the final occasion; it may be a positive integer (constant
across all sessions) or a vector of positive integers, one for each
session. covnames is needed only when captfile includes
individual covariates. Likewise for trapcovnames and
detector covariates. Values of noccasions and covnames
are passed directly to make.capthist, and trapcovnames is
passed to read.traps.
A session identifier is required even for single-session
capture data. In the case of data from multiple sessions,
trapfile may be a vector of file names, one for each session.
Additional data may be coded as for DENSITY. Specifically,
captfile may include extra columns of individual covariates, and
trapfile may code varying usage of each detector over occasions
and detector covariates.
markocc is needed only if sightings of unmarked animals are potentially
recorded on some occasions. If the data span multiple sessions with differing
combinations of marking and sighting occasions then markocc may be a
list with one vector per session.
The function read.telemetry is a simplified version of
read.capthist for telemetry data.
write.capthist
For a single-session analysis, DENSITY requires one text file of
capture data and one text file with detector coordinates (the 'trap
layout' file). write.capthist constructs names for these files
by appending ‘capt.txt’ and ‘trap.txt’ to filestem which
defaults to the name of the capthist object. If filestem is
empty then output goes to the console.
If object contains multiple sessions with differing
traps then a separate trap layout file is exported for each
session and each file name includes the session name. All capture data
are exported to one file regardless of the number of sessions. The
DENSITY format used is ‘TrapID’ except when x-y coordinates are
specific to a detection (i.e., polygon and transect detectors).
covariates controls the export of both detector and individual
covariates. If it is TRUE or FALSE then it is taken to apply to
both. A vector of covariate names is used as a lookup for both
detector and capthist covariate fields: covariates are exported if
their name matches; this may be used to export any combination of
(uniquely named) detector and capthist covariates.
Existing text files will be replaced without warning. In the case of a
multi-session capthist file, session names are taken from
object rather than sess. Session names are truncated to
17 characters with blanks and commas removed.
To export data in comma-delimited (‘.csv’) format, pass sep =
"," in .... The resulting files have extension ‘.csv’ rather than
‘.txt’ and may be opened with spreadsheet software.
write.capthist does not work for mark–resight data.
The original DENSITY formats accommodate ‘single’, ‘multi’ and ‘proximity’
data. Data for the newer detector types (‘count’, ‘signal’, ‘polygon’,
‘polygonX’, ‘transect’, ‘transectX’ and ‘telemetryonly’) may be input using the
DENSITY formats with minor variations. They may also be output with
write.capthist, but a warning is given that DENSITY does not
understand these data types. See detector and
secr-datainput.pdf for more.
The ... argument is useful for some special cases. For example, if
your input uses ‘;’ instead of ‘#’ for comments (‘;’ is also valid in
DENSITY) then set comment.char = ";" in read.capthist.
In a similar fashion, write comma- or tab-separated values by
setting sep = "," or sep = "\t" respectively.
The arguments of count.fields are a subset of those of
read.table so ... is limited to any of {sep, quote,
skip, blank.lines.skip, comment.char}.
If you fail to set fmt correctly in read.capthist then the
error message from verify may be uninformative.
Efford, M. G. (2012) DENSITY 5.0: software for spatially explicit capture–recapture. Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand https://www.otago.ac.nz/density/.
read.telemetry, read.traps, make.capthist,
write.captures, write.traps, read.table
## export ovenbird capture histories
## the files "ovenCHcapt.txt" and "ovenCHtrap.txt" are
## placed in the current folder (check with getwd() or dir())
## Not run:
write.capthist(ovenCH)
## End(Not run)