Publications by » R
Tinier 0.5.0
I had some time on my hands in the last few weeks while I wait to start a new job, so I went back to the tinieR package to fiddle around! New things – petit_plot I’d long wanted to find a way to export plots directly from R into pre-tinified image files, and although I’d found a way to do it for ggplot2 plots, doing it with base R plots and...
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Visualize dynamic data from R in 3d
In this video i demonstrate a nice feature of Bio7 to visualize 3d data created in “R” dynamically. The data for the points is generated in “R” and then transferred to the OpenGL view of Bio7. In the first example a random plot is generated and updated. In the second example 10000 random (lighted) spheres are normally distributed. Finall...
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Ecological Modelling with “R”
Here i present some Books and Articles about Ecological Modelling and “R”. Since “R” is integrated in Bio7 all the presented methods in the Books and Articles can also be useful together with Bio7. Books: Ellner, Stephen P. & Guckenheimer, John (2006). Dynamic Models in Biology. Princeton University Press Bolker B (2008) Ecological Models...
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Plots in R and the ImageJ visualization
If you plot data in R and you would like to display the same data in the ImageJ view it is necessary to transfer the data matrix to ImageJ. The first thing which can be noticed is that the image data is displayed rotated because of the Bio7 approach to transfer data forth and back in the following way: imagedata(x,y) whereas (x0,y0) can be found ...
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Image Data and Classification with R
03.08.2010 In this post i would like to demonstrate the ability of R to handle and classify image data with the help of ImageJ and Rserve bundled and implemented in Bio7. In general R is a very useful application for image analysis and plenty of “pure” R packages for image analysis are already available. But the combination of a scientific im...
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New R features in Bio7 1.5
Bio7 1.5 has been released and comes with new functionalities for R. For all who don’t know Bio7 here is a short description: Bio7 is a integrated development environment for ecological modelling based on the Rich-Client-Platform concept of the Java IDE Eclipse. The Bio7 platform contains several perspectives which arrange several views for a s...
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Image Classification Limits Part 2
Recently i released the first 64-bit versions of Bio7 bundled with a 64-bit Java Virtual Machine. I’m always curious how far i can go using both applications together to do image analysis (especially classification) with huge images coming e.g. from satellites. The transfer of the images in Bio7 is realized with a combination of ImageJ and R co...
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Shared Ecological Modelling References
05.06.2011 Today i started to create a list of books and articles about ecological modelling. In this list you will not only find general books about modelling but also books about spatial analysis, image analysis and other (in my opinion) important techniques useful in the context of ecological modelling. For the collection i use “Zotero” wh...
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Image Data from ImageJ to R and Vice Versa
In recent years many R packages have been developed to enable image analysis in R. As an alternative the combination of R with a powerful image analysis software like ImageJ offers many advanced image analysis interfaces and algorithms not yet available in R. Bio7 integrates both applications in a Rich Client Plattform based on Eclipse interfaced...
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Landscape Metrics with R, SDMTools, ImageJ and Bio7
01.02.2012 Landscape metrics were developed to analyze spatial patterns of landscapes (e.g. composition and spatial arrangement). In R it is possible to calculate these metrics with the “SDMTools” package. Bio7 offers an easy to use interface to R and ImageJ and can use these tools to simplify a workflow to analyze image data (e.g. vegetation...
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