secr (version 2.5.0)

ovensong: Ovenbird Acoustic Dataset

Description

Data from an acoustic survey of ovenbirds (Seiurus aurocapilla) at a site in Maryland, USA.

Usage

data(ovensong)

source

D. K. Dawson ([e-mail]) and M. G. Efford unpublished data.

Details

In June 2007 D. K. Dawson and M. G. Efford used a moving 4-microphone array to survey breeding birds in deciduous forest at the Patuxent Research Refuge near Laurel, Maryland, USA. The data for ovenbirds were used to demonstrate a new method for analysing acoustic data (Dawson and Efford 2009). See ovenbird for mist-netting data from the same site over 2005--2009, and for other background. Over five days, four microphones were placed in a square (21-m side) centred at each of 75 points in a rectangular grid (spacing 50 m); on each day points 100 m apart were sampled sequentially. Recordings of 5 minutes duration were made in .wav format on a 4-channel digital sound recorder. The data are estimates of average power on each channel (microphone) for the first song of each ovenbird distinguishable in a particular 5-minute recording. Power was estimated with the sound analysis software Raven Pro 1.4 (Charif et al. 2008), using a window of 0.7 s duration and frequencies between 4200 and 5200 Hz, placed manually at the approximate centre of each ovenbird song. Sometimes this frequency range was obscured by insect noise so an alternative 1000-Hz range was measured and the values were adjusted by regression. The data are provided as a single-session, single-occasion capthist object signalCH. The `signal' attribute contains the power measurement in decibels for each detected sound on each channel where the power threshold is exceeded. As the threshold signal (attribute cutval = 35) is less than any signal value in this dataset, all detection histories are complete (1,1,1,1) across microphones. For analysis Dawson and Efford applied a higher threshold that treated weaker signals as `not detected' (see Examples). The row names of signalCH (e.g. "3755AX") are formed from a 4-digit number indicating the sampling location (one of 75 points on a 50-m grid) and a letter A--D to distinguish individual ovenbirds within a 5-minute recording; `X' indicates power values adjusted by regression. The default model for sound attenuation is a log-linear decline with distance from the source (linear decline on dB scale). Including a spherical spreading term in the sound attenuation model causes the likelihood surface to become multimodal in this case. Newton-Raphson, the default maximization method in secr.fit, is particularly inclined to settle on a local maximum; in the example below we use a set of starting values that have been found by trial and error to yield the global maximum. Two fitted models are included (see Examples for details). ll{ Object Description signalCH capthist object ovensong.model.1 fitted secr model -- spherical spreading ovensong.model.2 fitted secr model -- no spherical spreading }

References

Charif, R. A., Waack, A. M. and Strickman, L. M. (2008) Raven Pro 1.3 User's Manual. Cornell Laboratory of Ornithology, Ithaca, New York. 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 Borchers, D. L. (2009) Population density estimated from locations of individuals on a passive detector array. Ecology 90, 2676--2682.

See Also

capthist, ovenbird, detection functions

Examples

summary(signalCH)
traps(signalCH)
signal(signalCH)

## apply signal threshold
signalCH.525 <- subset(signalCH, cutval = 52.5)

## models with and without spherical spreading
omask <- make.mask(traps(signalCH), buffer = 200)
ostart <- c(log(20), 80, log(0.1), log(2))
ovensong.model.1 <- secr.fit( signalCH.525, mask = omask, 
    start = ostart, detectfn = 11 ) 
ovensong.model.2 <- secr.fit( signalCH.525, mask = omask, 
    start = ostart, detectfn = 10 )

## compare fit of models
AIC(ovensong.model.1, ovensong.model.2)

## density estimates, dividing by 75 to allow for replication
collate(ovensong.model.1, ovensong.model.2)[1,,,"D"]/75

## plot attenuation curves cf Dawson & Efford (2009) Fig 5
pars1 <- predict(ovensong.model.1)[c("beta0", "beta1"), "estimate"]
pars2 <- predict(ovensong.model.2)[c("beta0", "beta1"), "estimate"]
attenuationplot(pars1, xval=0:150, spherical = TRUE, ylim = c(40,110))
attenuationplot(pars2, xval=0:150, spherical = FALSE, add = TRUE, 
    col = "red")
## spherical spreading only
pars1[2] <- 0  
attenuationplot(pars1, xval=0:150, spherical = TRUE, add = TRUE, lty=2)