Package: krm 2022.10-17

krm: Kernel Based Regression Models

Implements several methods for testing the variance component parameter in regression models that contain kernel-based random effects, including a maximum of adjusted scores test. Several kernels are supported, including a profile hidden Markov model mutual information kernel for protein sequence. This package is described in Fong et al. (2015) <doi:10.1093/biostatistics/kxu056>.

Authors:Youyi Fong [cre], Saheli Datta [aut], Krisztian Sebestyen [aut], Steve Park [ctb], Dave Geyer [ctb]

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manual.pdf |manual.html✨
card.svg |card.png
krm/json (API)

# Install 'krm' in R:
install.packages('krm', repos = c('https://youyifong.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • aa.prop.list - Amino Acid Properties
  • cloud9 - 9-Component Mixture Dirichlet Prior for Protein Sequences

On CRAN:

Conda:

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

cpp

1.00 score 1 stars 5 scripts 194 downloads 32 exports 1 dependencies

Last updated from:96e5c5c18e. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK118
linux-devel-x86_64OK106
source / vignettesOK181
linux-release-arm64OK110
linux-release-x86_64OK125
macos-release-arm64OK103
macos-release-x86_64OK188
macos-oldrel-arm64OK120
macos-oldrel-x86_64OK257
windows-develOK121
windows-releaseOK97
windows-oldrelOK110
wasm-releaseOK101

Exports:aa2arabicalignment2countalignment2trancountarabic2arabicFilearabic2fastaFilecalcPairwiseIdentitychi.normddirichletdmdirichletfastaFile2arabicFilegetSeqKernelhmmMargLlikkrm.mostkrm.score.testlogIntegrateDirichletlogIntegrateMixDirichletmodifyDirichletrdirichletreadArabicFilereadBlockFilereadFastaFilereadPriorFromFilereadSelexAsMatrixreadSelexFileremoveGaprmdirichletselexFile2arabicFilesim.liu.2007sim.liu.2008string2arabicstringList2arabicFilewriteFastaFile

Dependencies:kyotil

Readme and manuals

Help Manual

Help pageTopics
Amino Acid Propertiesaa.prop.list
Functions Related to Sequence Alignmentalignment2count alignment2trancount calcPairwiseIdentity removeGap
A Transformation of Chi-squared Random Variablechi.norm
9-Component Mixture Dirichlet Prior for Protein Sequencescloud9
Functions related to mixture Dirichlet distributionddirichlet dmdirichlet logIntegrateDirichlet logIntegrateMixDirichlet modifyDirichlet rdirichlet rmdirichlet
Protein Sequence KernelsgetSeqKernel
Functions related to profile HMMhmmMargLlik readPriorFromFile
Kernel-based Regression Modelskrm
Kernel-based Regression Model Maximum of adjusted Score Testkrm.most
Adjusted Score Testkrm.score.test
Read a Fasta Sequence Fileaa2arabic arabic2arabicFile arabic2fastaFile fastaFile2arabicFile readArabicFile readBlockFile readFastaFile readSelexAsMatrix readSelexFile selexFile2arabicFile string2arabic stringList2arabicFile writeFastaFile
Simulate sDatasetsim.liu.2007 sim.liu.2008