StrainRanking-package: Ranking of Pathogen Strains

Description Details Author(s) References

Description

Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics, using demographic and genetic data sampled in the curse of the epidemics. This package also includes the GMCPIC test.

Details

Package: StrainRanking
Type: Package
Version: 1.2
Date: 2017-11-25
License: GPL (>=2.0)
Depends: methods

To rank pathogen strains using the method of Soubeyrand et al. (2014), create a DG object (Demographic and Genetic data set) with one of the three construction functions (DGobj.rawdata, DGobj.simul.regression and DGobj.simul.mechanistic) and apply the ranking.strains function. Other construction functions returning a DG object might be written to extend the approach proposed by Soubeyrand et al. (2014).

Author(s)

Soubeyrand, S., Tollenaere, C., Haon-Lasportes, E. and Laine, A.-L.

Maintainer: samuel.soubeyrand@inra.fr

References

Soubeyrand S., Tollenaere C., Haon-Lasportes E. & Laine A.-L. (2014). Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics. PLOS ONE 9(1): e86591.

Soubeyrand S, Garreta V, Monteil C, Suffert F, Goyeau H, Berder J, Moinard J, Fournier E, Tharreau D, Morris C, Sache I (2017). Testing differences between pathogen compositions with small samples and sparse data. Phytopathology 107: 1199-1208. http://doi.org/10.1094/PHYTO-02-17-0070-FI


StrainRanking documentation built on May 2, 2019, 3:38 p.m.