Package: malaria.em 2.0
Xiaohong Li
malaria.em: EM Estimation of Malaria Haplotype Probabilities from Multiply Infected Human Blood Samples
Using EM algorithm to estimate malaria haplotype probabilities and the number of infections from multiply infected human blood samples. Estimated haplotype probabilities and their standard error are reported.
Authors:
malaria.em_2.0.tar.gz
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malaria.em.pdf |malaria.em.html✨
malaria.em/json (API)
| # Install 'malaria.em' in R: |
| install.packages('malaria.em', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/plasmogenepi/malaria.em/issues
- geno - EM Estimation of Malaria Haplotype Probabilities and Number of Infections from Multiply Infected Human Blood Samples
Last updated 2 months agofrom:8e020ad607. Checks:1 OK, 7 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 05 2025 |
| R-4.5-win | NOTE | Feb 05 2025 |
| R-4.5-mac | NOTE | Feb 05 2025 |
| R-4.5-linux | NOTE | Feb 05 2025 |
| R-4.4-win | NOTE | Feb 05 2025 |
| R-4.4-mac | NOTE | Feb 05 2025 |
| R-4.3-win | NOTE | Feb 05 2025 |
| R-4.3-mac | NOTE | Feb 05 2025 |
Exports:findCandidatesForAllGenotypesfindHaplotypeCandidateOneGenotypefunOfLambdagenAllHaploSetListgenAllHaploSetList.cgenAllHaploSetList.CgenAllHaploSetList.C.alldatagenAllHaploSetList.c.igenAllHaploSetListForOneGenotypegetAllCoefficientQij.CgetallConfig.CgetAllHaplotypesgetAllQij.CgetAllScore.C.emgetallWeight.C.emgetCoefficientQij.CgetDesignforAllGenotypes.additive.allhaplotypegetDesignforOneGenotype.additivegetDesignforOneGenotype.additive.allhaplotypegetHaplotypesWithLocigetLocitypeFromOneGenotypegetNextHaploSetgetNextIndexgetoneHaploSet.vector.CgetOneHaplotypegetoneL.C.emgetOneNumset.CgetOneQij.CgetoneQij.vector.CgetOneScore.C.emgetOneScore.haplotype.emgetoneWeight.C.emgetStd.emgetVector.CGinvhaploSet2GenotypeisLastSetlogLmalaria.emnewton.glmnum.unique.allelenum.unique.allele.locusprint.malaria.emsortGenotypestoGenotypes
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| EM Estimation of Malaria Haplotype Probabilities and Number of Infections from Multiply Infected Human Blood Samples | findCandidatesForAllGenotypes findHaplotypeCandidateOneGenotype funOfLambda genAllHaploSetList genAllHaploSetList.C genAllHaploSetList.c genAllHaploSetList.C.alldata genAllHaploSetList.c.i genAllHaploSetListForOneGenotype geno getAllCoefficientQij.C getallConfig.C getAllHaplotypes getAllQij.C getAllScore.C.em getallWeight.C.em getCoefficientQij.C getDesignforAllGenotypes.additive.allhaplotype getDesignforOneGenotype.additive getDesignforOneGenotype.additive.allhaplotype getHaplotypesWithLoci getLocitypeFromOneGenotype getNextHaploSet getNextIndex getoneHaploSet.vector.C getOneHaplotype getoneL.C.em getOneNumset.C getOneQij.C getoneQij.vector.C getOneScore.C.em getOneScore.haplotype.em getoneWeight.C.em getStd.em getUniqueGenotype getUniqueGenotypeCount getVector.C Ginv haploSet2Genotype isLastSet logL malaria.em newton.glm num.unique.allele num.unique.allele.locus print.malaria.em sortGenotypes toGenotypes |