StrainRanking v1.2

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Ranking of Pathogen Strains

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.

Functions in StrainRanking

Name Description
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
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Details

Type Package
Date 2017-11-25
License GPL (>= 2.0) | file LICENSE
NeedsCompilation yes
Packaged 2017-11-27 19:48:57 UTC; samuelsoubeyrand
Repository CRAN
Date/Publication 2017-11-29 23:45:52 UTC

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