mets: Analysis of Multivariate Event Times

Implementation of various statistical models for multivariate event history data. Including multivariate cumulative incidence models, and bivariate random effects probit models (Liability models). Also contains two-stage binomial modelling that can do pairwise odds-ratio dependence modelling based marginal logistic regression models. This is an alternative to the alternating logistic regression approach (ALR).

Install the latest version of this package by entering the following in R:
install.packages("mets")
AuthorKlaus K. Holst and Thomas Scheike
Date of publication2017-03-30 21:36:03 UTC
MaintainerKlaus K. Holst <klaus@holst.it>
LicenseGPL (>= 2)
Version1.2.2
https://github.com/kkholst/mets

View on CRAN

Man pages

aalenfrailty: Aalen frailty model

back2timereg: Convert to timereg object

bicomprisk: Estimation of concordance in bivariate competing risks data

binomial.twostage: Fits Clayton-Oakes or bivariate Plackett (OR) models for...

biprobit: Bivariate Probit model

blocksample: Block sampling

bptwin: Liability model for twin data

casewise: Estimates the casewise concordance based on Concordance and...

casewise.test: Estimates the casewise concordance based on Concordance and...

ClaytonOakes: Clayton-Oakes model with piece-wise constant hazards

cluster.index: Finds subjects related to same cluster

concordance: Concordance Computes concordance and casewise concordance

cor.cif: Cross-odds-ratio, OR or RR risk regression for competing...

daggregate: aggregating for for data frames

Dbvn: Derivatives of the bivariate normal cumulative distribution...

dby: Calculate summary statistics grouped by

dcor: summary, tables, and correlations for data frames

dcut: Cutting, sorting, rm (removing), rename for data frames

dermalridges: Dermal ridges data (families)

dermalridgesMZ: Dermal ridges data (monozygotic twins)

divide.conquer: Split a data set and run function

divide.conquer.timereg: Split a data set and run function from timereg and aggregate

dlag: Lag operator

dprint: list, head, print, tail

drelevel: relev levels for data frames

dsort: Sort data frame

dtable: tables for data frames

dtransform: Transform that allows condition

easy.binomial.twostage: Fits two-stage binomial for describing depdendence in...

easy.survival.twostage: Wrapper for easy fitting of Clayton-Oakes or bivariate...

EVaddGam: Relative risk for additive gamma model

eventpois: Extract survival estimates from lifetable analysis

familycluster.index: Finds all pairs within a cluster (family)

familyclusterWithProbands.index: Finds all pairs within a cluster (famly) with the proband...

fast.approx: Fast approximation

fast.pattern: Fast pattern

fast.reshape: Fast reshape

Grandom.cif: Additive Random effects model for competing risks data for...

internal: For internal use

ipw: Inverse Probability of Censoring Weights

ipw2: Inverse Probability of Censoring Weights

lifecourse: Life-course plot

lifetable.matrix: Life table

mena: Menarche data set

mets.options: Set global options for 'mets'

mets-package: Analysis of Multivariate Events

migr: Migraine data

multcif: Multivariate Cumulative Incidence Function example data set

np: np data set

phreg: Fast Cox PH regression

plack.cif: plack Computes concordance for or.cif based model, that is...

print.casewise: prints Concordance test

prt: Prostate data set

random.cif: Random effects model for competing risks data

simAalenFrailty: Simulate from the Aalen Frailty model

simClaytonOakes: Simulate from the Clayton-Oakes frailty model

simClaytonOakesWei: Simulate from the Clayton-Oakes frailty model

summary.cor: Summary for dependence models for competing risks

survival.twostage: Twostage survival model for multivariate survival data

test.conc: Concordance test Compares two concordance estimates

tetrachoric: Estimate parameters from odds-ratio

twinbmi: BMI data set

twin.clustertrunc: Estimation of twostage model with cluster truncation in...

twinlm: Classic twin model for quantitative traits

twinsim: Simulate twin data

twinstut: Stutter data set

Functions

aalenfrailty Man page
ace.family.design Man page
alpha2kendall Man page
alpha2spear Man page
ascertained.pairs Man page
back2timereg Man page
bicomprisk Man page
binomial.twostage Man page
binomial.twostage.time Man page
biprobit Man page
biprobit.time Man page
biprobit.vector Man page
blocksample Man page
bptwin Man page
bptwin.time Man page
casewise Man page
casewise.bin Man page
casewise.test Man page
CCbinomial.twostage Man page
ClaytonOakes Man page
cluster.index Man page
coarse.clust Man page
coefmat Man page
concordance Man page
concordance.twin.ace Man page
concordance.twostage Man page
cor.cif Man page
corsim.prostate Man page
corsim.prostate.random Man page
daggr Man page
daggregate Man page
Dbvn Man page
dby Man page
dby<- Man page
dby2 Man page
dby2<- Man page
dbyr Man page
dcor Man page
dcount Man page
dcut Man page
dcut<- Man page
ddrop Man page
ddrop<- Man page
dermalridges Man page
dermalridgesMZ Man page
deval Man page
deval2 Man page
dfactor Man page
dfactor<- Man page
dhead Man page
divide.conquer Man page
divide.conquer.timereg Man page
dkeep Man page
dkeep<- Man page
dlag Man page
dlag<- Man page
dlev Man page
dlev<- Man page
dlevel Man page
dlevel<- Man page
dlevels Man page
dlist Man page
dmean Man page
dmeansd Man page
dnames Man page
dnames<- Man page
dnumeric Man page
dnumeric<- Man page
dprint Man page
dquantile Man page
drelev Man page
drelev<- Man page
drelevel Man page
drelevel<- Man page
drename Man page
drename<- Man page
dreshape Man page
drm Man page
drm<- Man page
dsample Man page
dscalar Man page
dsd Man page
dsort Man page
dsort<- Man page
dstr Man page
dsubset Man page
dsum Man page
dsummary Man page
dtab Man page
dtable Man page
dtail Man page
dtrans Man page
dtrans<- Man page
dtransform Man page
dtransform<- Man page
dunique Man page
easy.binomial.twostage Man page
easy.survival.twostage Man page
EVaddGam Man page
eventpois Man page
familycluster.index Man page
familyclusterWithProbands.index Man page
fast.approx Man page
fast.cluster Man page
faster.reshape Man page
fast.pattern Man page
fast.reshape Man page
folds Man page
force.same.cens Man page
Grandom.cif Man page
grouptable Man page
ilap Man page
ipw Man page
ipw2 Man page
jumptimes Man page
kendall.ClaytonOakes.twin.ace Man page
kendall.normal.twin.ace Man page
lifecourse Man page
lifetable Man page
lifetable.formula Man page
lifetable.matrix Man page
loglikMVN Man page
make.pairwise.design Man page
make.pairwise.design.competing Man page
matplot.mets.twostage Man page
mena Man page
mets.options Man page
mets-package Man page
migr Man page
multcif Man page
nonparcuminc Man page
np Man page
npc Man page
object.defined Man page
or2prob Man page
or.cif Man page
p11.binomial.twostage.RV Man page
pbvn Man page
pcif Man page
phreg Man page
phreg.par Man page
piecewise.data Man page
piecewise.twostage Man page
plack.cif Man page
plack.cif2 Man page
plotcr Man page
pmvn Man page
predictPairPlack Man page
print.casewise Man page
procform Man page
procform3 Man page
prt Man page
random.cif Man page
rr.cif Man page
scoreMVN Man page
sim Man page
simAalenFrailty Man page
simbinClaytonOakes.family.ace Man page
simbinClaytonOakes.pairs Man page
simbinClaytonOakes.twin.ace Man page
simBinFam Man page
simBinFam2 Man page
simBinPlack Man page
simClaytonOakes Man page
simClaytonOakes.family.ace Man page
simClaytonOakes.twin.ace Man page
simClaytonOakesWei Man page
simCompete.simple Man page
simCompete.twin.ace Man page
simCox Man page
simnordic Man page
simnordic.random Man page
simSurvFam Man page
slope.process Man page
summary.cor Man page
surv.boxarea Man page
survival.twostage Man page
survival.twostage.fullse Man page
test.conc Man page
tetrachoric Man page
twinbmi Man page
twin.clustertrunc Man page
twinlm Man page
twinlm.strata Man page
twinlm.time Man page
twin.polygen.design Man page
twinsim Man page
twinstut Man page
twostage.aalen Man page
twostage.cox.aalen Man page
twostage.coxph Man page
twostage.fullse Man page
twostage.phreg Man page

Files

inst
inst/misc
inst/misc/ipw.png
inst/misc/cifMZ.png
inst/misc/pcif2.png
inst/misc/sim-cens-ts.r
inst/misc/cumh.png
inst/misc/binfam.rda
inst/misc/obs
inst/misc/obs/workshop.R inst/misc/obs/workshop-ts.R
inst/misc/obs/workshop.org
inst/misc/obs/workshop.html
inst/misc/workshop-src.org
inst/misc/conc2.png
inst/misc/pcifl.png
inst/misc/phenotype1.rda
inst/misc/twinbmi.R inst/misc/run-all.R
inst/misc/concordance.png
inst/misc/pcif.png
inst/misc/orgmode1.css
inst/misc/twinbmi2.rda
inst/misc/mets1.png
inst/misc/mena.html
inst/misc/pairwise-competing-risks-ace.r
inst/misc/workshop-run.html
inst/misc/pairwise-twostage.r
inst/misc/casewisea.png
inst/misc/cif2.png
inst/misc/binomialtwostage.R
inst/misc/menalong.rda
inst/misc/orgmode2.css
inst/misc/sim-nordic-twin.r
inst/misc/workshop.html
inst/devel
inst/devel/bptwin2.R inst/devel/dreg.R
inst/doc
inst/doc/quantitative-twin.pdf
inst/doc/quantitative-twin.ltx
inst/doc/binomial-family.pdf
inst/doc/basic-dutils.ltx
inst/doc/binomial-twin.ltx
inst/doc/binomial-case-control-ascertainment.pdf
inst/doc/binomial-family.ltx
inst/doc/binomial-twin.pdf
inst/doc/binomial-case-control-ascertainment.ltx
inst/doc/basic-dutils.pdf
inst/documentation
inst/documentation/dutils.org
inst/include
inst/include/mets_RcppExports.h
inst/include/mets.h
tests
tests/testthat
tests/testthat/test_dutils.R tests/testthat/test_reshape.R tests/testthat/test_approx.R tests/testthat/test_claytonoakes.R tests/test-all.R
src
src/mvn.cpp
src/twostage.h
src/Makevars
src/mvt.f
src/mvn.h
src/cor.cpp
src/fastcox.h
src/tvpackAux.c
src/binomial-twostage.cpp
src/tools.h
src/tvpack.f
src/survival-twostage.cpp
src/apply.cpp
src/tools.cpp
src/fastcox.cpp
src/prop-odd.cpp
src/claytonoakes.cpp
src/clusterindex.cpp
src/aalenfrailty.cpp
src/Makevars.win
src/init.c
src/RcppExports.cpp
src/biprobit.cpp
src/randomF77.c
NAMESPACE
demo
demo/models.R demo/tools.R
demo/00Index
demo/mets.R
NEWS
data
data/mena.rda
data/dermalridgesMZ.rda
data/migr.txt.gz
data/dermalridges.rda
data/np.txt.gz
data/multcif.txt.gz
data/twinstut.txt.gz
data/datalist
data/twinbmi.txt.gz
data/prt.rda
R
R/dtable.R R/aalenfrailty.R R/pmvn.R R/onload.R R/predict.biprobit.R R/plot.bptwin.R R/utils.R R/plotcr.R R/sim.clayton.oakes.R R/twinsim.R R/Dbvn.R R/sim-nordic-twin.R R/jumptimes.R R/cor.R R/fastreshape.R R/cumh.R R/twinlm.time.R R/biprobit.time.R R/daggregate.R R/casewise.R R/lifetable.R R/score.biprobit.R R/dprint.R R/summary.biprobit.R R/bicomprisksim.R R/phreg.R R/twinlm.R R/clusterindex-reshape.R R/npc.R R/bicomprisk.R R/claytonakes.R R/summary.bptwin.R R/mets-package.R R/methodstwinlm.R R/procformula.R R/blocksample.R R/normal0.R R/options.R R/twostage.R R/prop-odds.R R/RcppExports.R R/sim.bptwin.R R/ipw.R R/print.biprobit.R R/surv.boxarea.R R/coef.biprobit.R R/exmarg.R R/lifecourse.R R/fastpattern.R R/dby.R R/fastcluster.R R/dsort.R R/print.summary.biprobit.R R/fastapprox.R R/phreg.par.R R/biprobit.R R/logLik.biprobit.R R/dutils.R R/dtransform.R R/marginalprobit.R R/tetrachor.R R/biprobit.strata.R R/twin.clustertrunc.r R/bptwin.R R/divide.conquer.R R/binomial.twostage.R R/force.same.cens.R R/vcov.biprobit.R
vignettes
vignettes/binomial-family.org
vignettes/basic-dutils.org
vignettes/binomial-twin.org
vignettes/marg1.jpg
vignettes/mets.bib
vignettes/quantitative-twin.ltx
vignettes/scatter2.jpg
vignettes/scatter1.jpg
vignettes/quantitative-twin.org
vignettes/basic-dutils.ltx
vignettes/binomial-twin.ltx
vignettes/binomial-case-control-ascertainment.org
vignettes/binomial-family.ltx
vignettes/binomial-case-control-ascertainment.ltx
vignettes/header.org
MD5
build
build/vignette.rds
DESCRIPTION
man
man/fast.approx.Rd man/lifetable.matrix.Rd man/tetrachoric.Rd man/twin.clustertrunc.Rd man/Dbvn.Rd man/ipw2.Rd man/mena.Rd man/casewise.test.Rd man/test.conc.Rd man/dprint.Rd man/multcif.Rd man/mets-package.Rd man/simClaytonOakesWei.Rd man/aalenfrailty.Rd man/internal.Rd man/back2timereg.Rd man/daggregate.Rd man/dtransform.Rd man/twinlm.Rd man/plack.cif.Rd man/simAalenFrailty.Rd man/twinstut.Rd man/eventpois.Rd man/cor.cif.Rd man/divide.conquer.timereg.Rd man/drelevel.Rd man/dsort.Rd man/bptwin.Rd man/twinbmi.Rd man/casewise.Rd man/prt.Rd man/migr.Rd man/random.cif.Rd man/summary.cor.Rd man/binomial.twostage.Rd man/simClaytonOakes.Rd man/ClaytonOakes.Rd man/concordance.Rd man/lifecourse.Rd man/survival.twostage.Rd man/dcor.Rd man/dermalridgesMZ.Rd man/dtable.Rd man/fast.reshape.Rd man/dermalridges.Rd man/Grandom.cif.Rd man/blocksample.Rd man/phreg.Rd man/familyclusterWithProbands.index.Rd man/EVaddGam.Rd man/easy.binomial.twostage.Rd man/biprobit.Rd man/twinsim.Rd man/cluster.index.Rd man/dlag.Rd man/easy.survival.twostage.Rd man/ipw.Rd man/dby.Rd man/familycluster.index.Rd man/divide.conquer.Rd man/mets.options.Rd man/np.Rd man/print.casewise.Rd man/fast.pattern.Rd man/dcut.Rd man/bicomprisk.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.