# A package for analysing phototaxis and thermotaxis by *Dictyostelium* slugs

This is a small package of statistical and graphical functions to accompany the article by **Fisher, P.R**. & Annesley, S.J. (2006). Slug phototaxis, thermotaxis and spontaneous turning behaviour. *Methods in Molecular Biology.* 346, 137-170. Ed. L Eichinger & Humana Press. It contains three major functions (and associated auxiliary functions and tables) for the graphical and statistical analysis of slug phototaxis and thermotaxis data – *acorn* (for __ac__curacy of __or__ientation a__n__alysis based on the ordinary von Mises distribution for unidirectional data), *bimstat* (__bim__odal __stat__istics based on the von Mises distribution for bidirectional data), and *vmtests.on.files* (__v__on __M__ises distribution–based __tests__ __on__ __files__ containing data sets for which κ is hypothesized to be equal in the two-sample and multisample cases). Both *acorn* and *bimstat* produce a circular plot of the data along with estimates of the relevant parameters (μ and κ for *acorn*, α and κ for *bimstat*), along with confidence limits and tests of their significance (against H_{0} that κ = 0 in *acorn* using the Rayleigh test, against H_{0} that α = 0 in *bimstat* using the LR likelihood ratio test). In each case the data is in the form of one or more files containing a data set consisting of digitized start and endpoints for slug trails in the form “n x1 y1 x2 y2” where n is the slug (or line) number, x1 and y1 are the xy coordinates of the start point, x2 and y2 are the xy coordinates of the endpoint.

The following examples of the use of *acorn* and *bimstat* are provided in the package. The commands that produced the output are shown in each case within the plot - they used the data files called "phototaxis_demo" and "bimodal_demo", both of which are provided as part of the *DirStats* package.

The implementation of the statistical and graphical analysis in *DirStats* depends on prior installation of the R Environment for Statistical Computing. R can be downloaded from the Comprehensive R Archive Network (CRAN). Precompiled versions are available for Windows, Macintosh and Linux platforms, while the source code is available for porting to other platforms. The directional statistics analysis described here requires the *circular*, *CircStats* and *Bhat* packages as well as the R base package. These packages are also available through CRAN. Once R and the required packages have been downloaded and R installed, *DirStats* should be downloaded and saved as a plain text file called *DirStats.R* in the R home folder. To install the code, simply run R and type the command *source (“DirStats.R”)*. Save R on exit and the functions in *DirStats* will then be available permanently. To see the examples above in R use the command *DirStats.demo() * after installing *DirStats.R*.

For more details on how to use *DirStats* please consult **Fisher, P.R.** & Annesley, S.J. (2006). Slug phototaxis, thermotaxis and spontaneous turning behaviour. *Methods in Molecular Biology. 346, 137-170.* Ed. L Eichinger & F. Rivero. In "Dictyostelium discoideum Protocols." Humana Press.