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.

Author
Youyi Fong <youyifong@gmail.com>, Saheli Datta, Krisztian Sebestyen
Date of publication
2016-07-10 11:55:52
Maintainer
Youyi Fong <youyifong@gmail.com>
License
GPL-2
Version
2016.7-9

View on CRAN

Man pages

aa.prop.list
Amino Acid Properties
chi.norm
A Transformation of Chi-squared Random Variable
cloud9
9-Component Mixture Dirichlet Prior for Protein Sequences
dirichlet_functions
Functions related to mixture Dirichlet distribution
getSeqKernel
Protein Sequence Kernels
krm
Kernel-based Regression Models
krm.most
Kernel-based Regression Model Maximum of adjusted Score Test
krm.score.test
Adjusted Score Test
profile_HMM
Functions related to profile HMM
seq_alignment
Functions Related to Sequence Alignment
seq_read_write
Read a Fasta Sequence File
sim.liu
Simulate sDataset

Files in this package

krm
krm/inst
krm/inst/misc
krm/inst/misc/sim1.fasta
krm/inst/misc/y1.txt
krm/inst/misc/SETpfamseed_aligned_for_testing.fasta
krm/inst/unitTests
krm/inst/unitTests/runRUnitTests.R
krm/inst/unitTests/Makefile
krm/inst/unitTests/runit.krm.score.test.R
krm/inst/unitTests/report.txt
krm/inst/unitTests/runit.getSeqKernel.R
krm/inst/unitTests/runit.krm.most.R
krm/tests
krm/tests/doRUnit.R
krm/src
krm/src/Makevars
krm/src/DirichletRV.h
krm/src/Observable.h
krm/src/MI_kernel.cpp
krm/src/StatPlus.h
krm/src/MixtureDirichletRV.h
krm/src/score_var.cpp
krm/src/MathPlus.h
krm/src/MixtureDirichletRV.cpp
krm/src/ProteinSequence.cpp
krm/src/DirichletRV.cpp
krm/src/ProteinSequence.h
krm/src/rvgs.h
krm/src/RandomPlus.h
krm/src/U.h
krm/src/rvgs.cpp
krm/src/Makevars.win
krm/src/var_Q.cpp
krm/NAMESPACE
krm/data
krm/data/cloud9.rda
krm/data/aa.prop.list.rda
krm/R
krm/R/dirichlet_functions.R
krm/R/EQQ.R
krm/R/krm.score.test.R
krm/R/sim.liu.R
krm/R/seq_read_write.R
krm/R/profile_HMM.R
krm/R/krm.most.R
krm/R/getSeqKernel.r
krm/R/misc.R
krm/R/seq_alignment.R
krm/MD5
krm/DESCRIPTION
krm/ChangeLog
krm/man
krm/man/getSeqKernel.Rd
krm/man/chi.norm.Rd
krm/man/krm.score.test.Rd
krm/man/aa.prop.list.Rd
krm/man/seq_alignment.Rd
krm/man/sim.liu.Rd
krm/man/cloud9.Rd
krm/man/krm.Rd
krm/man/krm.most.Rd
krm/man/dirichlet_functions.Rd
krm/man/profile_HMM.Rd
krm/man/seq_read_write.Rd