Jay E. Jones, Andrew J. Kroll, Jack Giovanini, Steven D. Duke, and Matthew G. Betts. 2011. Estimating thresholds in occupancy when species detection is imperfect. Ecology 92:2299–2309.

Supplement

R code for estimating thresholds while accounting for variable detection and data for estimating thresholds for forest birds, Oregon, USA, 2007–2008.
Ecological Archives E092-199-S1.

Copyright

Authors
File list (downloads)
Description

Author(s)

Jay E. Jones
Weyerhaeuser Company
WTC 1B20
PO Box 9777
Federal Way, WA, 98063-9777
USA
Email: jay.jones@weyerhaeuser.com

Andrew J. Kroll
Weyerhaeuser Company
WTC 1A5
PO Box 9777
Federal Way, WA, 98063-9777
USA

Jack Giovanini
Weyerhaeuser Company
WTC 1B20
PO Box 9777
Federal Way, WA, 98063-9777
USA

Steven D. Duke
Weyerhaeuser Company
WTC 1B20
PO Box 9777
Federal Way, WA, 98063-9777
USA

Matthew G. Betts
Department of Forest Ecosystems and Society
321 Richardson Hall
Oregon State University, OR, 97331
USA

File list

Supplement_Avian data.csv
Supplement_R code.r

Description

The Supplement_Avian data.csv file contains data on stand-level habitat covariates and visit-specific detections of avian species, Oregon, USA, 2008–2009. Column definitions
  1. Stand id
  2. Percent cover of conifer species
  3. Percent cover of broadleaf species
  4. Percent cover of deciduous broadleaf species
  5. Percent cover of hardwood species
  6. Percent cover of hardwood species in a 2000 m radius circle around each sample stand
  7. Elevation (m) of stand
  8. Age of stand
  9. Year of sampling
  10. Visit number
  11. Detection of Magnolia Warbler on Visit 1
  12. Detection of Magnolia Warbler on Visit 2
  13. Detection of Orange-crowned Warbler on Visit 1
  14. Detection of Orange-crowned Warbler on Visit 2
  15. Detection of Swainson’s Thrush on Visit 1
  16. Detection of Swainson’s Thrush on Visit 2
  17. Detection of Willow Flycatcher on Visit 1
  18. Detection of Willow Flycatcher on Visit 2
  19. Detection of Wilson’s Warbler on Visit 1
  20. Detection of Wilson’s Warbler on Visit 1

Checksum values are:

Column 2 (Percent cover of conifer species – CONIFER): SUM = 5862.83
Column 3 (Percent cover of broadleaf species – BROAD): SUM = 7043.17
Column 4 (Percent cover of deciduous broadleaf species – DECBROAD): SUM = 5475.17
Column 5 (Percent cover of hardwood species – HARDWOOD): SUM = 2151.96
Column 6 (Percent cover of hardwood species in a 2000 m radius circle around each sample stand– HWD2000): SUM = 3486.07
Column 7 (Stand elevation – ELEVM): SUM = 83240.58
Column 8 (Stand age – AGE): SUM = 1537; NA indicates a stand was harvested in 2008
Column 9 (Year of sampling – YEAR): SUM = 425792
Column 11 (MGWA.1): SUM = 70
Column 12 (MGWA.2): SUM = 71
Column 13 (OCWA.1): SUM = 121
Column 14 (OCWA.2): SUM = 76
Column 15 (SWTH.1): SUM = 90
Column 16 (SWTH.2): SUM = 95
Column 17 (WIFL.1): SUM = 85
Column 18 (WIFL.2): SUM = 85
Column 19 (WIWA.1): SUM = 36
Column 20 (WIWA.2): SUM = 37

The Supplement_R code.r file is R source code for simulation and empirical analyses conducted in Jones et al.