README.md

In dpasqualin/sfreemapr: Simulation-Free Stochastic Mapping

THIS PACKAGE IS FOR TESTING ONLY

This is a first version of the sfreemap package, written entirely in R, and used only for comparison between versions in my thesis.

Package Requirements for Production

You need to have R installed on your system. If you are using a debian/ubuntu based distribution, just type the following command in a terminal.

sudo apt-get install r-base-core

Package Requirements for Development

sudo apt-get install r-base-core texlive-full

R Dependencies

Install

Before installing sfreemapr make sure you have the package phytools:

install.packages('phytools')
install.packages('devtools')
install_github('dpasqualin/sfreemapr')

If you have troubles installing the devtools package, try downloading sfreemapr and then building and installing it using the following commands:

git clone https://github.com/dpasqualin/sfreemapr.git
R CMD check sfreemapr && R CMD build sfreemapr && R CMD INSTALL sfreemapr

If you choose to install using the command above, the documentation will be available in the directory sfreemapr.Rcheck.

Example

require(sfreemapr) # load package
tree <- pbtree(n=100,scale=1) # create a tree with 100 taxa
Q <- matrix(c(-1,1,1,-1),2,2) # create a transition rate matrix
rownames(Q)<-colnames(Q)<-letters[1:nrow(Q)] # give name to the states
tree <- sim.history(tree,Q,anc="a") # simulate a history for the tree

# estimate the history
sm <- sfreemapr.map(tree, tree$states, Q='empirical')
sfreemapr.pie_plot(sm) # plot the result
sfreemapr.describe(sm) # numerical summary of the result

dpasqualin/sfreemapr documentation built on May 15, 2019, 10:45 a.m.