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.

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
```

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!