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Microhabitat effects on small mammal occupancy at the spatial scale of individual traps
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analysis_trapocc_binomial.R
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model_trapocc_binomial.R

README.md

hee-mammal-habitat

An analysis of the effects of microhabitat characteristics (vegetation, litter, coarse woody debris, etc.) on habitat use by small mammals, and how this interaction was influenced by silviculture (i.e., timber harvest). To analyze habitat use at the finest scale possible, we conducted an occupancy analysis in which individual trap locations were the occupancy units of interest. The analysis was conducted with capture data for four small mammal species captured at 32 Hardwood Ecosystem Experiment (HEE) sites in 2007-2011. In 2008-2009, a subset of these sites were harvested under different management regimes. Therefore, of the 5 study years, 2 were pre-harvest and 3 post-harvest.

The results are published in the following article:

Kellner, Kenneth F.; Swihart, Robert K. 2014. Changes in small mammal microhabitat use following silvicultural disturbance. American Midland Naturalist 172: 348-358.

Metadata

The 'analysis_trapocc_binomial.R file contain the framework of the Bayesian analysis in JAGS for the project. Additional information is provided in the comments of the file. The model used in the BUGS language is contained in the file model_trapocc_binomial.R.

The data subfolder contains example CSV files representative of the actual data used in this study. I do not currently have permission to publish the complete raw data. Columns in each CSV file are described below.

  1. example_captures.csv contains the raw small mammal capture records from a single year and have been processed to fix errors. Each row represents a single capture/trap record and the following columns are available:

    • Grid - the trapping grid ID number
    • Check - the check day/time identification (5 days with 2 checks/day; 1P = day 1, PM; 3A = day 3, AM, etc.)
    • Trap - the trap ID; each grid had 3 rows designated by letters with 9 traps in each row designated by numbers.
    • Species - the small mammal species captured, if applicable. Represented by a code (WFMO = white-footed mouse, EACH = eastern chipmunk, SHSH = short-tailed shrew, PIVO = pine vole).
    • id - the tag ID for the animal, if it was eartagged.
    • Fate - The fate of the animal and/or trap, most impmortantly '1' for new capture, '2' for re-capture, and '7' or '8' for missing/disturbed trap, etc.
  2. example_grid_covs.csv contains information about each trapping grid location:

    • temp1-5 - Mean daily temperature for each of the 5 trapping days (measured on-site).
    • jd1-5 - Julian day for each of the trapping days.
    • aspect - The site aspect; 1 for northeast and 0 for southwest.
  3. example_microsite.csv contains values for microhabitat variables at each trapping grid location:

    • grid - the trapping grid ID number.
    • trap - the trap location ID.
    • herb - percent herbaceous plant cover.
    • wood - percent woody plant cover.
    • cwd - length of coarse woody debris in a 1m radius around trap location (m).
    • litter - litter depth (cm).
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