Abstract
Currently R is the most popular software for data analyses among biologists. Here, we present bwimage, a package designed to describe patterns from black and white images. The package can be used for a wide range of applications. We implemented functions previously described in the literature to calculate parameters designed originally, but not exclusively, for vegetation structures. Additionally, we propose a new parameter: the aggregation index. We demonstrate applications for field work, providing examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure. We provide advice and illustrated examples of how to produce high quality images for analyses.
Highlights
The facility to obtain high quality digital images creates the opportunity to measure natural variables using image analyses
Francesco Chianucci, The Council for Agricultural Research and Economics (CREA) Research Centre for Forestry and Wood, Arezzo, Italy This article is included in the RPackage gateway
If the user is not acquainted with scale and threshold processing and/or images were captured under different light conditions, we recommend the scale and application of threshold algorithms in a native image editor software, such as GIMP6, and subsequent usage of the resulting images with the bwimage package
Summary
1. Francesco Chianucci , The Council for Agricultural Research and Economics (CREA) Research Centre for Forestry and Wood, Arezzo, Italy. This article is included in the RPackage gateway. 2. Roy Francis, Uppsala University, Uppsala, Sweden National Bioinformatics Infrastructure Sweden, Uppsala, Sweden. Any reports and responses or comments on the article can be found at the end of the article. Dr Roy Francis was included in the Acknowledgments section. Any further responses from the reviewers can be found at the end of the article
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