An R package for the analysis of biological image data, especially tracings of single neurons.
As of v1.0 there is a released version on CRAN.
install.packages('nat')It you wish to run the package tests, it is necessary to install with
dependencies=TRUE.
Interim source code packages for released versions are available from our lab repository:
# when binary packages are preferred (e.g. mac/windows)
install.packages('nat',repos=c('http://jefferislab.org/R',getOption("repos")),
type='both')
# when source packages are the default (e.g. linux)
install.packages('nat',repos=c('http://jefferislab.org/R',getOption("repos")))Note the specification of both the jefferislab.org repository and the default
CRAN repository in order to ensure that package dependencies are installed from
CRAN and the main package is installed from our repository. Note also that it is
necessary to specify type='both' on platforms where binary packages are the
norm (Windows/MacOS X) since nat is only provided as a source package on our
repository.
You can, however, download the tar ball,
and run R CMD INSTALL on it, or use the devtools package to install the development version:
# install.packages("devtools")
devtools::install_github("nat", "jefferis")Note: Windows users need Rtools and devtools to install this way.
nat is self sufficient for core functionality, but the transformation of 3d data using Computational Morphometry Toolkit (CMTK) registrations depends on an external installation of that toolkit. CMTK binaries can be downloaded for Windows, Linux and Mac at http://www.nitrc.org/projects/cmtk/. Source code is available from the same site or an unofficial mirror repository at https://github.com/jefferis/cmtk. We have extensive experience of using CMTK under linux (where we compile from source) and mac (where we compile or use the MacOSX-10.6-x86_64.dmg binary installers). We have also used neurodebian to install as part of the travis continuous integration setup (see the project's .travis.yml file).