strum: STRUctural Modeling of Latent Variables for General Pedigree

Implements a broad class of latent variable and structural equation models for general pedigree data.

Install the latest version of this package by entering the following in R:
install.packages("strum")
AuthorNathan Morris [aut, cre], Yeunjoo Song [aut], Stephen Cahn [ctb]
Date of publication2015-06-12 06:43:35
MaintainerNathan Morris <nathan.morris@cwru.edu>
LicenseGPL (>= 2)
Version0.6.2

View on CRAN

Functions

allRandomEffects Man page
allRandomEffects<- Man page
allRandomEffects<-,strumVirtualModel-method Man page
allRandomEffects,strumVirtualModel-method Man page
ascertainment Man page
ascertainment<- Man page
ascertainment<-,strumVirtualModel-method Man page
ascertainment,strumVirtualModel-method Man page
coding Man page
coding<- Man page
coding<-,strumMarker-method Man page
coding,strumMarker-method Man page
covariatePhenotypes Man page
covariatePhenotypes,strumVirtualModel-method Man page
createSimModel Man page
createStrumData Man page
createStrumMarker Man page
createStrumModel Man page
dataType Man page
dataType<- Man page
dataType<-,strumData-method Man page
dataType,strumData-method Man page
dataVals Man page
dataVals<- Man page
dataVals<-,strumData-method Man page
dataVals,strumData-method Man page
errorRate Man page
errorRate<- Man page
errorRate<-,strumMarker-method Man page
errorRate,strumMarker-method Man page
fittedParameters Man page
fittedParameters<- Man page
fittedParametersCovMatrix Man page
fittedParametersCovMatrix<- Man page
fittedParametersCovMatrix<-,strumFittedModel-method Man page
fittedParametersCovMatrix,strumFittedModel-method Man page
fittedParameters<-,strumFittedModel-method Man page
fittedParameters,strumFittedModel-method Man page
formulas Man page
formulas<- Man page
formulas<-,strumVirtualModel-method Man page
formulas,strumVirtualModel-method Man page
haplotypes Man page
haplotypes<- Man page
haplotypes<-,strumMarker-method Man page
haplotypes,strumMarker-method Man page
ibd Man page
ibdMarker Man page
ibdMarker<- Man page
ibdMarker<-,strumIBD-method Man page
ibdMarker,strumIBD-method Man page
ibdMatrix Man page
ibdMatrix<- Man page
ibdMatrix<-,strumIBD-method Man page
ibdMatrix,strumIBD-method Man page
ibd,strumData-method Man page
importHapmapData Man page
importIBD Man page
importIBD,strumData-method Man page
intervalIBD Man page
intervalIBD<- Man page
intervalIBD<-,strumMarker-method Man page
intervalIBD,strumMarker-method Man page
markerFacts Man page
markerFacts<- Man page
markerFacts<-,strumMarker-method Man page
markerFacts,strumMarker-method Man page
markerInfo Man page
markerInfo<- Man page
markerInfo<-,strumSimModel-method Man page
markerInfo,strumSimModel-method Man page
missingRate Man page
missingRate<- Man page
missingRate<-,strumMarker-method Man page
missingRate,strumMarker-method Man page
mutationRate Man page
mutationRate<- Man page
mutationRate<-,strumMarker-method Man page
mutationRate,strumMarker-method Man page
paramNames Man page
paramNames<- Man page
paramNames<-,strumVirtualModel-method Man page
paramNames,strumVirtualModel-method Man page
phi Man page
phi<- Man page
phi<-,strumData-method Man page
phi,strumData-method Man page
plot,strumModel-method Man page
plot,strumSimModel-method Man page
plot,strumVirtualModel-method Man page
populationRecombRate Man page
populationRecombRate<- Man page
populationRecombRate<-,strumMarker-method Man page
populationRecombRate,strumMarker-method Man page
returnIBD Man page
returnIBD<- Man page
returnIBD<-,strumMarker-method Man page
returnIBD,strumMarker-method Man page
show,strumData-method Man page
show,strumFittedModel-method Man page
show,strumIBD-method Man page
show,strumMarker-method Man page
show,strumModel-method Man page
show,strumSimModel-method Man page
show,strumVirtualModel-method Man page
simulateStrumData Man page
strum Man page
[<-,strumData,ANY,ANY,ANY-method Man page
[,strumData,ANY,ANY,ANY-method Man page
strumData-class Man page
[[<-,strumData-method Man page
[[,strumData-method Man page
$<-,strumData-method Man page
$,strumData-method Man page
strumFittedModel-class Man page
strumIBD-class Man page
strumMarker-class Man page
strumModel-class Man page
strum-package Man page
strumSimModel-class Man page
strumVirtualModel-class Man page
traitMissingRate Man page
traitMissingRate<- Man page
traitMissingRate<-,strumSimModel-method Man page
traitMissingRate,strumSimModel-method Man page
varList Man page
varList<- Man page
varList<-,strumVirtualModel-method Man page
varList,strumVirtualModel-method Man page

Files

inst
inst/extdata
inst/extdata/hap20snp10.Rdata
inst/extdata/example_ped.csv
inst/extdata/example_raw.csv
inst/extdata/GENIBD.chr1Ped.ibd
inst/doc
inst/doc/strum-example.R inst/doc/strum-intro.R
inst/doc/strum-intro.Rnw
inst/doc/strum-example.Rnw
inst/doc/strum-example.pdf
inst/doc/strum-intro.pdf
inst/include
inst/include/utils.h
src
src/Makevars
src/computeInterval.cpp
src/computeLLDeriv.cpp
src/computeQ.cpp
src/Makevars.win
NAMESPACE
R
R/strum.R R/06strumData.R R/utils.R R/estimateCovariance.R R/02strumModel.R R/03strumFittedModel.R R/estimateDerivative.R R/01strumSimModel.R R/fitModel.R R/estimateParameter.R R/05strumIBD.R R/createModel.R R/simulateData.R R/00strumVirtualModel.R R/generateStartValue.R R/04strumMarker.R R/createMarker.R R/createData.R
vignettes
vignettes/figures
vignettes/figures/fig_linkage.png
vignettes/figures/fig_model7.png
vignettes/figures/fig_association.png
vignettes/figures/fig_model4.png
vignettes/figures/fig_model8.png
vignettes/figures/fig_model1.png
vignettes/figures/fig_model9.png
vignettes/figures/fig_model0.png
vignettes/figures/fig_model3.png
vignettes/figures/fig_model5.png
vignettes/figures/fig_model6.png
vignettes/figures/fig_model2.png
vignettes/strum-intro.Rnw
vignettes/strum-example.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/strumVirtualModel-class.Rd man/simulateStrumData.Rd man/strumMarker-class.Rd man/createStrumData.Rd man/strum.Rd man/strumData-class.Rd man/importHapmapData.Rd man/strumModel-class.Rd man/createSimModel.Rd man/createStrumModel.Rd man/strum-package.Rd man/createStrumMarker.Rd man/strumFittedModel-class.Rd man/strumSimModel-class.Rd man/strumIBD-class.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.