README.md

In dpasqualin/sfreemap: Simulation Free Stochastic Mapping

SFREEMAP

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

Installation

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.

Debian/Ubuntu

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++-dev

Windows

Install the latest version of Rtools for Windows following http://cran.r-project.org/bin/windows/Rtools/.

MAC OS

You might need to install install Xcode command line tools:

xcode-select --install

From Github using devtools

The 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')

From source

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

Documentation

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")

Development

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

dpasqualin/sfreemap documentation built on July 5, 2023, 10:52 a.m.