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Logistic-Exposure Analyses of Nest Survival

Terry L. Shaffer

This resource consists of downloadable computer code (SAS and R) for performing logistic-exposure analyses of nest survival described in the following publications:

Shaffer, T. L. 2004. A unified approach to analyzing nest success. Auk 121:526-540.

Shaffer, T. L. and F. R. Thompson III. 2007. Making meaningful estimates of nest survival with model-based methods. Studies in Avian Biology 34:84-95.

Related papers:

Heisey, D. M., T. L. Shaffer, and G. C. White. 2007. The ABC's of nest survival: theory and application from a biostatistical perspective. Studies in Avian Biology 34:13-33.

Rotella, J., S. Dinsmore, and T. Shaffer. 2004. Modeling nest-survival data: a comparison of recently developed methods that can be implemented in MARK and SAS. Animal Biodiversity and Conservation 27.1:187-205.

The following programs illustrate 1) logistic-exposure modeling of nest survival, 2) computation of AIC-based model-selection criteria, and 3) computation of model-averaged regression coefficients and unconditional standard errors. These programs accompany Shaffer (2004).

Downloading Instructions:

To download a file, click on the appropriate link below. The file will then either 1) open within your browser or 2) prompt you to save the file to a local drive on your computer. To view a file saved to a local drive, you will need to open the file using SAS or a text editor.

Program and Macro Files (SAS 8.2):

LOGEXPOS.SAS ( 14K) -- the main SAS program
AIC_MAC.SAS ( 15K) -- file containing SAS macros for AIC computations and model-averaging (This file is needed to run LOGEXPOS.SAS)

Program and Macro Files (SAS 9.1):

LOGEXPOS_SAS9.SAS ( 14K) -- the main SAS program
AIC_MAC_SAS9.SAS ( 15K) -- file containing SAS macros for AIC computations and model-averaging (This file is needed to run LOGEXPOS_SAS9.SAS)

Output from the Above Program:

LOGEXPOS.OUT ( 23K) -- SAS output file from running LOGEXPOS.SAS
LOGEXPOS.LOG ( 33K) -- SAS log file from running LOGEXPOS.SAS

The following SAS programs and macro code were developed in concert with Shaffer and Thompson (2007). The programs provide all the functionality of the above programs and more. The primary added feature is macro code that facilitates making model-based predictions of nest survival from multiple models. Several macros included with the above programs have also been embellished. Included is a sample program that illustrates several of the analyses described in Shaffer and Thompson (2007). Refer to documentation in the sample program for a description of the examples and instructions for running them.

Program and Macro Archive File:

SAS 9.1: logistic-exposure-sample-program-27June2005.ZIP ( 62K)
R Software: Logistic-exposure link function (courtesy of Mark Herzog, mherzog@prbo.org)

This resource should be cited as:

Shaffer, Terry L. 2004. Logistic-Exposure Analyses of Nest Survival. Jamestown, ND: Northern Prairie Wildlife Research Center Online. http://www.npwrc.usgs.gov/resource/birds/nestsurv/index.htm (Version 28AUG2008)

Terry Shaffer, Northern Prairie Wildlife Research Center, U.S. Geological Survey, 8711 37th Street Southeast, Jamestown, North Dakota 58401, USA.

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