New version of vegan released to CRAN (1.17-9) Why I love open source!
I've recently been looking at [Martin Trauth](http://www.geo.uni-potsdam.de/member-details/show/108.html 'Martin Trauth's web page at The University of Potsdam Institute of Earth and Environmental Science')'s book MATLAB® Recipes for Earth Sciences to try to understand what some of my palaeoceanography colleagues are doing with their data analyses (lots of frequency domain time series techniques and a preponderance of filters). Whilst browsing, the recurrence plot section caught my eye as something to look into further, both for palaeo-based work but also for work on ecological thresholds and tipping points.
In a recurrence plot, the recurrences of a phase space are plotted. As we tend not to have the phase space, just the time series of observations, we embed the observed series to produce the m dimensional phase space. A key feature of the recurrence plot is the time delay included during embedding. There is an embed() function in R but it does not handle the time delay aspects that one needs for the recurrence plot, so I decided to write my own. The results are shown below in my function Embed(). It has been written to replicate the standard R embed() function where d = 1 (i.e. no time delay), which is a useful check that it is doing the right thing.
x: the time series, observed at regular intervals.
m: the number of dimensions to embed x into.
as.embed: logical; should we return the embedded time series in the order that embed() would?
So what does embedding do? Without additional time delay, embed() and Embed() produce a matrix with m columns containing the original time series and lagged versions of it, each column a lag 1 version of the previous column. Incomplete rows, that arise due to the lagging of the series with itself, are discarded. You can see this in the identical calls to embed() and Embed() shown above. There were 10 observations in the series, and we asked for 4 lag 1 versions of this series. Hence each of the series in the embedded version contains just seven observations; we loose three observations because the 2nd, 3rd, and 4th columns are progressively shifted by 1 time unit relative to the original series.
Time delay embedding allows for additional delay between the lagged versions of the original series. If d = 2, then each of the m - 1 new series is lagged by 2 time intervals. This is shown in the final example above, with Embed(1:10, m = 4, d = 2), where the entries within the rows are offset by 2. However, the embedded series now contain just four observations.
How we use this to produce a recurrence plot will be covered in a separate post.