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Original R software for estimating overlap of activity patterns
This software was used in preparing Refs [1 and 2], but it is now superceded by the overlap package.
The data from [Ref 2] are in file traptimes.txt. The file setup.R reads the data into R and also imports a set of functions that are used in the analyses (these functions are in the file ovlcode.R).
The file
example.R provides simple
examples of how to estimate overlap, including a bootstrap confidence
interval. To run the example (which should take less than a minute on a
modern PC), follow these steps:
- copy ALL the R files and the data file into a directory on your computer
- start R and click on File|Change dir... to select the directory where you stored the files
- Install the CRAN package circular if it is not already installed. ...
-
At the R prompt (> ) type
source("example.R")
The files figure1.R and figure2.R produce the two figures in ref [2]. These files are included for the benefit of anyone interested in producing similar graphs, but they are not extensively commented.
References
[1] Ridout, M.S. & Linkie, M. (2009) Estimating overlap of daily activity patterns from camera trap data. Journal of Agricultural, Biological and Environmental Statistics, 14, 322-337.] doi: 10.1198/jabes.2009.08038 [pdf]
[2] Linkie, M. & Ridout, M.S. (2011) Assessing tiger-prey interactions in Sumatran rainforests. Journal of Zoology, 284, 224-229. doi: 10.1111/j.1469-7998.2011.00801.x [pdf]