ovenbird                package:secr                R Documentation

_O_v_e_n_b_i_r_d _M_i_s_t-_n_e_t_t_i_n_g _D_a_t_a_s_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     Data from a multi-year mist-netting study of ovenbirds (_Seiurus
     aurocapilla_) at a site in Maryland, USA.

_U_s_a_g_e:

     data(ovenbird)

_D_e_t_a_i_l_s:

     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). 
     Recaptures within a day are not included in this dataset, so each
     bird occurs at most once per day and the detector type is 'multi'
     rather than 'proximity'.  Although several individuals were
     captured in more than one year, no use is made of this information
     in the analyses presently offered in 'secr'. 

     The data are provided as a multi-session 'capthist' object
     'ovenCH'.  Sex is coded as a categorical individual covariate ('M'
     or 'F').

     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 in press).  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.

_S_o_u_r_c_e:

     D. K. Dawson (ddawson@usgs.gov) and M. G. Efford unpublished data.

_R_e_f_e_r_e_n_c_e_s:

     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. (2010) Bird density estimated from
     acoustic signals. _Journal of Applied Ecology_ in press.

     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.

_S_e_e _A_l_s_o:

     'capthist'

_E_x_a_m_p_l_e_s:

     ## Not run: 

     ## 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 = 'multi')
     temp <- read.captures('ovencapt.txt', colClasses=c('character',
         'character', 'numeric', 'numeric', 'character'))
     ovenCH <- make.capthist(temp, netsites0509, covnames=c('Sex','Age'))

     ## End(Not run)

     require (graphics)
     data(ovenbird)
     par(mfrow = c(1,5), mar = c(1,1,4,1))
     plot(ovenCH, tracks = TRUE, varycol = TRUE)

     counts(ovenCH, 'n')

     ## Not run: 

     ## 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)
     ovenbird.model.1

     ## fit net avoidance model
     ovenbird.model.1b <- secr.fit(ovenCH, mask = ovenmask, model =
         list(g0~b))
     ovenbird.model.1b

     ## End(Not run)

     ## compare & average pre-fitted models
     AIC(ovenbird.model.1, ovenbird.model.1b)
     model.average(ovenbird.model.1, ovenbird.model.1b)

     ## select one year to plot
     plot(ovenbird.model.1b, newdata = data.frame(session = '2005', 
         b = 0))

