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 accuracy of orientation
analysis based on the ordinary von Mises distribution for
unidirectional
data), bimstat (bimodal statistics
based on the von Mises distribution for bidirectional data), and vmtests.on.files (von Mises
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 H0 that κ = 0 in acorn
using the Rayleigh test, against H0 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) via the R Home Page at http://www.r-project.org/.
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 (http://www.latrobe.edu.au/mcbg/DirStats.R) 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.