James F. Saracco, Rodney B. Siegel, and Robert L. Wilkerson. 2011. Occupancy modeling of black-backed woodpeckers on burned Sierra Nevada forests. Ecosphere 2:art31.


Supplement

Data and R and WinBUGS code for running the occupancy model described in the paper.
Ecological Archives
C002-004-S1
.

Copyright


Authors
File list (downloads)
Description


Author(s)

James F. Saracco
The Institute for Bird Populations
P.O. Box 1346
Point Reyes Station, CA 94956-1346
E-mail: jsaracco@birdpop.org

Rodney B. Siegel
The Institute for Bird Populations
P.O. Box 1346
Point Reyes Station, CA 94956-1346
E-mail: rsiegel@birdpop.org

Robert L. Wilkerson
The Institute for Bird Populations
P.O. Box 1346
Point Reyes Station, CA 94956-1346
E-mail: bwilkerson@birdpop.org


File list

bbwo_occ.r -- (MD5: c32c59d390e4c2472d85a9a83bcc2064)

bbwo_dat.txt -- (MD5: a1f979c217060a8b2d03e12957c32059)

Description

The 'bbwo_occ.r' script reads in data from 'bbwo_dat.txt', writes a model file for WinBUGS ('bbwoEAmodel.txt'), runs the model in WinBUGS (via the R2WinBUGS package) and stores results in an R list called 'out'.

The file 'bbwo_dat.txt' contains encounter history and covariate data used in the occupancy model. Fields include:

  1. fire – Name of fire area designated by the USDA Forest Service
  2. point – Four-character alpha-numeric identifier for survey points
  3. int.1 – Indicator variable denoting whether a Black-backed Woodpecker was encountered (1) or not encountered (0) during the first 3-min passive survey interval.
  4. int.2 – Indicator variable denoting whether a Black-backed Woodpecker was encountered (1) or not encountered (0) during the second 2-min passive survey interval. NAs indicate no data recorded for that interval
  5. int.3 – Indicator variable denoting whether a Black-backed Woodpecker was encountered (1) or not encountered (0) during the first call-broadcast survey interval.
  6. int.4 – Indicator variable denoting whether a Black-backed Woodpecker was encountered (1) or not encountered (0) during the second call-broadcast survey interval. NAs indicate no data recorded for that interval
  7. int.5 – Indicator variable denoting whether a Black-backed Woodpecker was encountered (1) or not encountered (0) during the third call-broadcast survey interval. NAs indicate no data recorded for that interval
  8. fa – Age of fire area (i.e., time since most recent burn) in years (range = 1–10)
  9. lat – Latitude of survey point in decimal degrees
  10. snag.ct – Number of stems counted from the survey point using a 10 basal area factor (BAF) timber cruising crutch
  11. cc – Change in percent canopy cover at the survey point based on satellite derived relativized difference normalized burn ratio score RdNBR (Miller et al. 2009. Remote Sensing of Environment 113:645–656) summarized at 8,100-m2 (90 m × 90 m pixel) resolution by averaging 900-m2 (30 m × 30 m pixel) values from Geographic Information System (GIS) coverages provided by the USDA Forest Service (J. D. Miller) using the raster package (http://cran.r-project.org/web/packages/raster/vignettes/Raster.pdf) in R
  12. elev.res – Residuals from a regression of survey-point elevation (m) on survey-point latitude

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