Publication details
R project: powerful tool for vegetation data analysis and visualization.
| Authors | |
|---|---|
| Year of publication | 2007 |
| Type | Article in Proceedings |
| Conference | Proceedings of the Fifth Symposium of Vegetation Diversity in Taiwan |
| MU Faculty or unit | |
| Citation | |
| Field | Ecology |
| Keywords | R-project; R-users; vegetation ecologists |
| Description | I can imagine the feeling of R novice, who has just opened the R program for the fist time: disappointment. Its user interface is very simple, in reality it offers only empty command console – almost no menu, no buttons, no wizard, simply nothing interesting. Anything you want to do, every simple operation, starting with importing the data and followed by some simple calculation or graph drawing, everything has to be written manually step by step using functions with numerous arguments... and if you need help? You are welcome, up-to-date R reference manual has 1532 pages... R is simply NOT a kind of point-and-click software, so if you need just quickly draw summary of your data or calculate one-way ANOVA, forget about R and go for Statistica or just do it in Excel. R is nothing less than a programming language with software environment together – you are not limited by any software engineer’s imaginations, you just create what you need by yourself. The main power of R is in the fact that everything is under one roof – you don’t need to transform the data between different software packages neither taking care about data format. In R, you can proceed from data importing through data analyzing and ending up with data visualization. Another powerful feature of R is its openness. There is comprehensive library of various packages contributed by others, and you are welcome to download them together with help files and use them for your data. Do you need some specific analysis and you cannot find appropriate software? R library most probably already contains the package, which will offer you the functions you are looking for, it just needs a bit of searching. Do you publish novel approach for data analysis in your paper and you want others to use it and cite your publication? Just attach simple R script in electronic attachment, so as everybody can apply this algorithm on his own data, or – even better – publish a package, which will contain appropriate functions. If we search Web of Science for papers using R project for data analysis or visualization, we can see that majority of R users are among ecologists. Papers using R are frequently published in journals such as Ecology, Journal of Applied Ecology, American Naturalists or Biological Conservation. Use of R is definitely not European domain – the most productive R users are Americans, followed by mixture of nations from all continents. Number of papers using R during last three years has rapidly increased, from tens in 2005 up to thousands in 2007. What can R project bring to vegetation ecologists? In my conference presentation, I will try to answer different aspects of this question. R offers several packages designed for analysis of vegetation data, including species response modeling, ordination analysis, cluster analysis and methods of classification and regression trees. You can also find more advanced analytical tools, such as random forest or simulation algorithms of Hubbell’s neutral models. R also offers comprehensive and flexible tools of data visualization, producing required figures in printing quality. Last but not least, R can be also connected to other software as a stand-alone analytical utility – we tried to connect R with JUICE in order to allow quick ordination analysis of relevé data and species response curve modeling. There is still much to do with R development and removing bugs from new R release, but once R is stable and available on various platforms, it has good chance to become standard analytical tool for both university students and scientists. |
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