| ovenbird {secr} | R Documentation |
Data from a multi-year mist-netting study of ovenbirds (Seiurus aurocapilla) at a site in Maryland, USA.
ovenCH
ovenCHp
ovenbird.model.1
ovenbird.model.D
ovenmask
From 2005 to 2009 D. K. Dawson and M. G. Efford conducted a capture–recapture survey of breeding birds in deciduous forest at the Patuxent Research Refuge near Laurel, Maryland, USA. The forest was described by Stamm, Davis & Robbins (1960), and has changed little since. Analyses of data from previous mist-netting at the site by Chan Robbins were described in Efford, Dawson & Robbins (2004) and Borchers & Efford (2008).
Forty-four mist nets (12 m long, 30-mm mesh) spaced 30 m apart on the perimeter of a 600-m x 100-m rectangle were operated for approximately 9 hours on each of 9 or 10 non-consecutive days during late May and June in each year. Netting was passive (i.e. song playback was not used to lure birds into the nets). Birds received individually numbered bands, and both newly banded and previously banded birds were released at the net where captured. Sex was determined in the hand from the presence of a brood patch (females) or cloacal protuberance (males). A small amount of extra netting was done by other researchers after the main session in some years.
This dataset comprises all records of adult (after-hatch-year) ovenbirds caught during the main session in each of the five years 2005–2009. One ovenbird was killed by a predator in the net in 2009, as indicated by a negative net number in the dataset. Sex was determined in the hand from the presence of a brood patch (females) or cloacal protuberance (males). Birds are listed by their band number (4-digit prefix, ‘.’, and 5-digit number).
The data are provided as a multi-session capthist object
‘ovenCHp’. Sex is coded as a categorical individual covariate ("M"
or "F").
Recaptures at the same site within a day are not included in this dataset,
so ovenCHp has detector type ‘proximity’. Previous versions of secr
provided only a trimmed version of these data, retaining only one capture
per bird per day (ovenCH with detector type ‘multi’). That may be
obtained from ovenCHp as shown in the examples.
Although several individuals were captured in more than one year, no use is made of this information in the analyses presently offered in secr.
An analysis of the data for males in the first four years showed that they tended to avoid nets after their first capture within a season (Dawson & Efford 2009). While the species was present consistently, the number of detections in any one year was too small to give reliable estimates of density; pooling of detection parameters across years helped to improve precision.
Included with the data are a mask and two models fitted to ovenCH as in
Examples.
| Object | Description |
| ovenCH | multi-session capthist object (as multi-catch) |
| ovenCHp | multi-session capthist object (as binary proximity) |
| ovenbird.model.1 | fitted secr model -- null |
| ovenbird.model.D | fitted secr model -- trend in density across years |
| ovenmask | mask object |
D. K. Dawson (ddawson@usgs.gov) and M. G. Efford unpublished data.
Borchers, D. L. and Efford, M. G. (2008) Spatially explicit maximum likelihood methods for capture-recapture studies. Biometrics 64, 377–385.
Dawson, D. K. and Efford, M. G. (2009) Bird population density estimated from acoustic signals. Journal of Applied Ecology 46, 1201–1209.
Efford, M. G., Dawson, D. K. and Robbins C. S. (2004) DENSITY: software for analysing capture-recapture data from passive detector arrays. Animal Biodiversity and Conservation 27, 217–228.
Stamm, D. D., Davis, D. E. and Robbins, C. S. (1960) A method of studying wild bird populations by mist-netting and banding. Bird-Banding 31, 115–130.
## commands used to create ovenCH from the input files
## "netsites0509.txt" and "ovencapt.txt"
## for information only - these files not distributed
# netsites0509 <- read.traps(file = "netsites0509.txt",
# skip = 1, detector = "proximity")
# temp <- read.table("ovencapt.txt", colClasses=c("character",
# "character", "numeric", "numeric", "character"))
# ovenCHp <- make.capthist(temp, netsites0509, covnames = "Sex")
# ovenCHp <- reduce(ovenCHp, dropunused = FALSE) # drop repeat detections
par(mfrow = c(1,5), mar = c(1,1,4,1))
plot(ovenCHp, tracks = TRUE, varycol = TRUE)
par(mfrow = c(1,1), mar = c(5,4,4,2) + 0.1) ## defaults
counts(ovenCHp, "n")
## Not run:
## trimmed version of data - for consistency with earlier versions
ovenCH <- reduce(ovenCHp, outputdetector = "multi", dropunused = FALSE)
## array constant over years, so build mask only once
ovenmask <- make.mask(traps(ovenCH)[["2005"]], type = "pdot",
buffer = 400, spacing = 15, detectpar = list(g0 = 0.03,
sigma = 90), nocc = 10)
## fit constant-density model
ovenbird.model.1 <- secr.fit(ovenCH, mask = ovenmask)
## fit temporal trend in density (Session capitalized)
ovenbird.model.D <- secr.fit(ovenCH, mask = ovenmask,
model = list(D ~ Session))
## compare pre-fitted models
AIC(ovenbird.model.1, ovenbird.model.D)
## End(Not run)