In mrc-ide/PlasmoMAPI: Mapping Plasmodium Spatial Connectivity from Genetic Data

Installing Rcpp

PlasmoMAPI 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 PlasmoMAPI

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 PlasmoMAPI package directly from GitHub by running

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

If you have any problems installing, please check the Known issues page to see if there is a known solution. If not then please raise an issue on github.

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

library(PlasmoMAPI)

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

check_PlasmoMAPI_loaded()

mrc-ide/PlasmoMAPI documentation built on Oct. 1, 2020, 9:41 a.m.