Supplement 1. Data and R and WinBUGS code for running the occupancy model described in the paper.

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:

fire – Name of fire area designated by the USDA Forest Service
point – Four-character alpha-numeric identifier for survey points
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.
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
int.3 – Indicator variable denoting whether a Black-backed Woodpecker was encountered (1) or not encountered (0) during the first call-broadcast survey interval.
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
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
fa – Age of fire area (i.e., time since most recent burn) in years (range = 1–10)
lat – Latitude of survey point in decimal degrees
snag.ct – Number of stems counted from the survey point using a 10 basal area factor (BAF) timber cruising crutch
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
elev.res – Residuals from a regression of survey-point elevation (m) on survey-point latitude