Display the relative occurrence and co-occurrence of events in a sample
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
R
data
man
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
README.md
appveyor.yml

README.md

Travis-CI Build Status AppVeyor Build status CRAN_Status_Badge CRAN Downloads

Mondrian

The unique function of the Mondrian package, named mondrian, allows representing in a single graph the relative occurrence and co-occurrence of events measured in a sample. As examples, the package was applied to describe the occurrence and co-occurrence of different species of bacterial or viral symbionts infecting arthropods at the individual level. The graphics allows determining the prevalence of each symbiont and the patterns of multiple infections (i.e. how different symbionts share or not the same individual hosts). We named the package after the famous painter as the graphical output recalls Mondrian’s paintings.

Installing Mondrian

To install the development version from GitHub:

  1. Install the release version of devtools from CRAN with install.packages("devtools").

  2. Make sure you have a working development environment.

    • Windows: Install Rtools.
    • Mac: Install Xcode from the Mac App Store.
    • Linux: Install a compiler and various development libraries (details vary across different flavors of Linux).
  3. Then:

library(devtools)
install_github("aursiber/Mondrian")

The stable version can be installed from CRAN using:

install.packages("Mondrian")

Once installed, the package can be loaded using:

library("Mondrian")

The web application of Mondrian

A web application (a Shiny application) is available to use the functionalities of the Mondrian package in an interactive way. In this application, two examples are shown. The user can also upload its own data and compute the mondrian function on it. The display output can then be saved.

The MONDRIAN Shiny app can be found at: http://lbbe-shiny.univ-lyon1.fr/MondrianShiny/

Articles which use Mondrian functionalities

  • Competitive outcome of multiple infections in a behavior-manipulating virus/wasp interaction. Martinez et al. (2015). Ecology and Evolution, 5(24):5934–5945. doi: 10.1002/ece3.1749

  • Nuclear and cytoplasmic differentiation among Mediterranean populations of Bemisia tabaci: testing the biological relevance of cytotypes. Terraz et al. (2014). Pest Management Science, 70:1503-1513. doi: 10.1002/ps.3792

  • Endosymbiont diversity among sibling weevil species competing for the same resource. Merville et al. (2013). BMC Evolutionary Biology, 13:28. doi: 10.1186/1471-2148-13-28

  • Distribution of Bemisia tabaci (Homoptera: Aleyrodidae) biotypes and their associated symbiotic bacteria on host plants in West Africa. Gnankiné et al. (2013). Insect Conservation and Diversity, 6(3):411-421. doi: 10.1111/j.1752-4598.2012.00206.x

  • Endosymbiont metacommunities, mtDNA diversity and the evolution of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex. Gueguen et al. (2010). Molecular Ecology, 19(19):4365-76. doi: 10.1111/j.1365-294X.2010.04775.x