SFREEMAP is an analytical approach to obtain accurate, per-branch expectations of numbers of state transitions and dwelling times. It also provides an intuitive way of visualizing the results by integrating over the posterior and summarizing the parameters onto a target reference topology (such as a consensus or MAP tree) provided by the user.
Paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1554-7
First install R and dependencies according to your operating system (see below), then install the package from CRAN, github or source, as described in the following sections.
If you are using a Debian/Ubuntu based distribution, install the following packages.
sudo apt-get install r-base-core libblas-dev liblapack-dev libmagick++-devInstall the latest version of Rtools for Windows following http://cran.r-project.org/bin/windows/Rtools/.
You might need to install install Xcode command line tools:
xcode-select --installThe most up to date version from Github can be installed using devtools. Devtools itself has a different set of
dependencies depending on the OS you are on, for some install.packages('devtools') on R console might be enough,
for Debian/Ubuntu the easiest way is with sudo apt install r-cran-devtools.
After installing devtools you can run the lines below on R to install sfreemap.
Use build_vignettes = TRUE parameter to install_github if you want to build usage examples as well.
require(devtools)
install_github('dpasqualin/sfreemap')If you don't want to install devtools you can also clone the repository and install it using R command line.
You will need git installed on your system.
git clone https://github.com/dpasqualin/sfreemap.git
R CMD build sfreemap && R CMD INSTALL sfreemap
If you want to look at the reference manual, load R and type the following commands. A new tab will open in your web browser with the description of all available functions.
require(sfreemap)
help(package = "sfreemap", help_type = "html")
The following command will open a new tab in your browser with a link to the vignettes, if you chose to install it.
browseVignettes("sfreemap")
For development you are gonna need a few extra packages:
# On Fedora libssl-dev might be called libssh2-devel, and on OS X might be just libssh2
sudo apt-get install texlive-full zlib1g-dev libcurl4-openssl-dev libssl-dev