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StrainRanking (version 1.2)

Ranking of Pathogen Strains

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.

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Version

Install

install.packages('StrainRanking')

Monthly Downloads

131

Version

1.2

License

GPL (>= 2.0) | file LICENSE

Maintainer

Samuel Soubeyrand

Last Published

November 29th, 2017

Functions in StrainRanking (1.2)

PathogenCompositionMoryzaeMadagascar

Compositions of Magnaporthe oryzae collected in Madagascar
PathogenCompositionPsyringaeClades

Compositions of Pseudomonas syringae at the clade resolution
DGobj-class

Class "DGobj"
DGobj.rawdata

Construction of a DG object from raw data
PathogenCompositionPsyringaeHaplotypes

Compositions of Pseudomonas syringae at the haplotype resolution
DGobj.simul.mechanistic

Simulation of a DG object under a mechanistic model
PathogenCompositionMoryzaeChina

Compositions of Magnaporthe oryzae collected in China
DGobj.simul.regression

Simulation of a DG object under a regression model
powderymildew

Demographic and genetic real data
PathogenCompositionPtriticinaKalango

Compositions of Puccinia triticina in Kalango crops
StrainRanking-package

Ranking of Pathogen Strains
ranking.strains

Method for ranking pathogen strains
PathogenCompositionPtriticinaGalibier

Compositions of Puccinia triticina in Galibier crops
generation.alpha.3strains

Generation of parameters for the simulations under the regression model
gmcpic.test

Function implementing the Generalized Monte Carlo plug-in test with calibration (GMCPIC test)
PathogenCompositionPsyringaePhylogroups

Compositions of Pseudomonas syringae at the phylogroup resolution