Installation

Installing via the plasmogenepi R-universe

The fastest and simplest way to install PlasmoSim is via the plasmogenepi R-universe as follows:

install.packages('PlasmoSim', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org'))

However, this may not work for some chips, in which case backup instructions are presented below.

Assuming everything installed correctly, we need to load the package:

library(PlasmoSim)

You can test that the package is loaded and working by running the following command, which should produce this output:

check_PlasmoSim_loaded()

## PlasmoSim loaded successfully!

Installing Manually

Installing Rcpp

PlasmoSim relies on the Rcpp package, which requires the following OS-specific steps:

• Windows
  • Download and install the appropriate version of Rtools for your version of R. On installation, ensure you check the box to arrange your system PATH as recommended by Rtools
• Mac OS X
  • Download and install XCode
  • Within XCode go to Preferences : Downloads and install the Command Line Tools
• Linux (Debian/Ubuntu)

  • Install the core software development utilities required for R package development as well as LaTeX by executing

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

Installing and loading PlasmoSim

Next, in R, ensure that you have the devtools package installed by running

install.packages("devtools", repos = 'http://cran.us.r-project.org')

Then install the PlasmoSim package directly from GitHub by running

devtools::install_github("mrc-ide/PlasmoSim")

If you have any problems installing then please raise an issue on github.

Assuming everything installed correctly, we need to load the package:

library(PlasmoSim)

You can test that the package is loaded and working by running the following command, which should produce this output:

check_PlasmoSim_loaded()

## PlasmoSim loaded successfully!