Package: StrainRanking 1.2

Samuel Soubeyrand

StrainRanking: 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.

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

StrainRanking_1.2.tar.gz
StrainRanking_1.2.tar.gz(r-4.5-noble)StrainRanking_1.2.tar.gz(r-4.4-noble)
StrainRanking_1.2.tgz(r-4.4-emscripten)StrainRanking_1.2.tgz(r-4.3-emscripten)
StrainRanking.pdf |StrainRanking.html✨
StrainRanking/json (API)

# Install 'StrainRanking' in R:
install.packages('StrainRanking', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.18 score 15 scripts 136 downloads 1 mentions 8 exports 0 dependencies

Last updated 7 years agofrom:7d01116099. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-linux-x86_64NOTEDec 01 2024

Exports:DGobj.rawdataDGobj.simul.mechanisticDGobj.simul.regressiongeneration.alpha.3strainsgmcpic.testranking.strainsshowsummary

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Ranking of Pathogen StrainsStrainRanking-package StrainRanking
Class '"DGobj"'DG DG class DG object DGobj DGobj-class names,DGobj-method show,DGobj-method summary,DGobj-method [,DGobj-method [<-,DGobj-method
Construction of a DG object from raw dataDGobj.rawdata
Simulation of a DG object under a mechanistic modelDGobj.simul.mechanistic
Simulation of a DG object under a regression modelDGobj.simul.regression
Generation of parameters for the simulations under the regression modelgeneration.alpha.3strains
Function implementing the Generalized Monte Carlo plug-in test with calibration (GMCPIC test)gmcpic.test
Compositions of Magnaporthe oryzae collected in ChinaChina MoryzaeChina PathogenCompositionMoryzaeChina
Compositions of Magnaporthe oryzae collected in MadagascarMadagascar MoryzaeMadagascar PathogenCompositionMoryzaeMadagascar
Compositions of Pseudomonas syringae at the clade resolutionClades PathogenCompositionPsyringaeClades PsyringaeClades
Compositions of Pseudomonas syringae at the haplotype resolutionHaplotypes PathogenCompositionPsyringaeHaplotypes PsyringaeHaplotypes
Compositions of Pseudomonas syringae at the phylogroup resolutionPathogenCompositionPsyringaePhylogroups Phylogroups PsyringaePhylogroups
Compositions of Puccinia triticina in Galibier cropsGalibier PathogenCompositionPtriticinaGalibier PtriticinaGalibier
Compositions of Puccinia triticina in Kalango cropsKalango PathogenCompositionPtriticinaKalango PtriticinaKalango
Demographic and genetic real datapowderymildew
Method for ranking pathogen strainsranking.strains