Analysis of Multivariate Event Times


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Documentation for package ‘mets’ version 1.2.6

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A B C D E F G H I J K L M N O P R S T

mets-package Analysis of Multivariate Events

-- A --

aalenfrailty Aalen frailty model
ace.family.design For internal use
addCums Simulation of recurrent events data based on cumulative hazards
alpha2kendall For internal use
alpha2spear For internal use
ascertained.pairs For internal use

-- B --

back2timereg Convert to timereg object
base1cumhaz rate of CRBSI for HPN patients of Copenhagen
base44cumhaz rate of Occlusion/Thrombosis complication for catheter of HPN patients of Copenhagen
base4cumhaz rate of Mechanical (hole/defect) complication for catheter of HPN patients of Copenhagen
basecumhaz Plotting the baslines of stratified Cox
basehazplot.phreg Plotting the baslines of stratified Cox
bicomprisk Estimation of concordance in bivariate competing risks data
binomial.twostage Fits Clayton-Oakes or bivariate Plackett (OR) models for binary data using marginals that are on logistic form. If clusters contain more than two times, the algoritm uses a compososite likelihood based on all pairwise bivariate models.
binomial.twostage.time Fits Clayton-Oakes or bivariate Plackett (OR) models for binary data using marginals that are on logistic form. If clusters contain more than two times, the algoritm uses a compososite likelihood based on all pairwise bivariate models.
biprobit Bivariate Probit model
biprobit.time Bivariate Probit model
biprobit.vector Bivariate Probit model
blocksample Block sampling
Bootcovariancerecurrence Estimation of covariance for bivariate recurrent events with terminal event
BootcovariancerecurrenceS Estimation of covariance for bivariate recurrent events with terminal event
Bootphreg Wild bootstrap for Cox PH regression
bplot Plotting the baslines of stratified Cox
bptwin Liability model for twin data
bptwin.time Liability model for twin data

-- C --

casewise Estimates the casewise concordance based on Concordance and marginal estimate using prodlim but no testing
casewise.bin Estimates the casewise concordance based on Concordance and marginal estimate using timereg and performs test for independence
casewise.test Estimates the casewise concordance based on Concordance and marginal estimate using timereg and performs test for independence
CCbinomial.twostage For internal use
cif Cumulative incidence with robust standard errors
cifreg CIF regression
ClaytonOakes Clayton-Oakes model with piece-wise constant hazards
cluster.index Finds subjects related to same cluster
coarse.clust For internal use
coefmat For internal use
concordance.cor Concordance Computes concordance and casewise concordance
concordanceCor Concordance Computes concordance and casewise concordance
concordanceTwinACE For internal use
concordanceTwostage For internal use
cor.cif Cross-odds-ratio, OR or RR risk regression for competing risks
corsim.prostate For internal use
corsim.prostate.random For internal use
count.history Counts the number of previous events of two types for recurrent events processes
covarianceRecurrent Estimation of covariance for bivariate recurrent events with terminal event
covarianceRecurrentS Estimation of covariance for bivariate recurrent events with terminal event
covfr Predictions from proportional hazards model
covfridstrata Predictions from proportional hazards model
covfridstrataCov Predictions from proportional hazards model
covIntH1dM1IntH2dM2 Simulation of recurrent events data based on cumulative hazards
cumContr GOF for Cox covariates in PH regression
cumsumidstratasum Predictions from proportional hazards model
cumsumidstratasumCov Predictions from proportional hazards model
cumsumstrata Predictions from proportional hazards model
cumsumstratasum Predictions from proportional hazards model

-- D --

daggr aggregating for for data frames
daggregate aggregating for for data frames
Dbvn Derivatives of the bivariate normal cumulative distribution function
dby Calculate summary statistics grouped by
dby2 Calculate summary statistics grouped by
dby2<- Calculate summary statistics grouped by
dby<- Calculate summary statistics grouped by
dbyr Calculate summary statistics grouped by
dcor summary, tables, and correlations for data frames
dcount summary, tables, and correlations for data frames
dcut Cutting, sorting, rm (removing), rename for data frames
dcut<- Cutting, sorting, rm (removing), rename for data frames
ddrop Cutting, sorting, rm (removing), rename for data frames
ddrop<- Cutting, sorting, rm (removing), rename for data frames
dermalridges Dermal ridges data (families)
dermalridgesMZ Dermal ridges data (monozygotic twins)
deval summary, tables, and correlations for data frames
deval2 summary, tables, and correlations for data frames
dfactor relev levels for data frames
dfactor<- relev levels for data frames
dhead list, head, print, tail
divide.conquer Split a data set and run function
divide.conquer.timereg Split a data set and run function from timereg and aggregate
dkeep Cutting, sorting, rm (removing), rename for data frames
dkeep<- Cutting, sorting, rm (removing), rename for data frames
dlag Lag operator
dlag<- Lag operator
dlev relev levels for data frames
dlev<- relev levels for data frames
dlevel relev levels for data frames
dlevel<- relev levels for data frames
dlevels relev levels for data frames
dlist list, head, print, tail
dmean summary, tables, and correlations for data frames
dmeansd summary, tables, and correlations for data frames
dmvn Multivariate normal distribution function
dnames Cutting, sorting, rm (removing), rename for data frames
dnames<- Cutting, sorting, rm (removing), rename for data frames
dnumeric relev levels for data frames
dnumeric<- relev levels for data frames
dprint list, head, print, tail
dquantile summary, tables, and correlations for data frames
drcumhaz Rate for leaving HPN program for patients of Copenhagen
dreg Regression for data frames with dutility call
drelev relev levels for data frames
drelev<- relev levels for data frames
drelevel relev levels for data frames
drelevel<- relev levels for data frames
drename Cutting, sorting, rm (removing), rename for data frames
drename<- Cutting, sorting, rm (removing), rename for data frames
dreshape Fast reshape
drm Cutting, sorting, rm (removing), rename for data frames
drm<- Cutting, sorting, rm (removing), rename for data frames
dsample Block sampling
dscalar summary, tables, and correlations for data frames
dsd summary, tables, and correlations for data frames
dsort Sort data frame
dsort2 Sort data frame
dsort<- Sort data frame
dspline Simple linear spline
dspline<- Simple linear spline
dstr summary, tables, and correlations for data frames
dsubset summary, tables, and correlations for data frames
dsum summary, tables, and correlations for data frames
dsummary summary, tables, and correlations for data frames
dtab tables for data frames
dtable tables for data frames
dtail list, head, print, tail
dtrans Transform that allows condition
dtrans<- Transform that allows condition
dtransform Transform that allows condition
dtransform<- Transform that allows condition
dunique Cutting, sorting, rm (removing), rename for data frames

-- E --

easy.binomial.twostage Fits two-stage binomial for describing depdendence in binomial data using marginals that are on logistic form using the binomial.twostage funcion, but call is different and easier and the data manipulation is build into the function. Useful in particular for family design data.
easy.survival.twostage Wrapper for easy fitting of Clayton-Oakes or bivariate Plackett models for bivariate survival data
EVaddGam Relative risk for additive gamma model
eventpois Extract survival estimates from lifetable analysis
extendCums Simulation of illness-death model

-- F --

familycluster.index Finds all pairs within a cluster (family)
familyclusterWithProbands.index Finds all pairs within a cluster (famly) with the proband (case/control)
fast.approx Fast approximation
fast.cluster For internal use
fast.pattern Fast pattern
fast.reshape Fast reshape
faster.reshape For internal use
folds For internal use
force.same.cens For internal use

-- G --

ghaplos ghaplos haplo-types for subjects of haploX data
gof.phreg GOF for Cox PH regression
gofG.phreg Stratified baseline graphical GOF test for Cox covariates in PH regression
gofM.phreg GOF for Cox covariates in PH regression
gofZ.phreg GOF for Cox covariates in PH regression
Grandom.cif Additive Random effects model for competing risks data for polygenetic modelling
grouptable For internal use

-- H --

hapfreqs hapfreqs data set
haplo.surv.discrete Discrete time to event haplo type analysis
haploX haploX covariates and response for haplo survival discrete survival

-- I --

ilap For internal use
ipw Inverse Probability of Censoring Weights
ipw2 Inverse Probability of Censoring Weights

-- J --

jumptimes For internal use

-- K --

kendall.ClaytonOakes.twin.ace For internal use
kendall.normal.twin.ace For internal use
km Kaplan-Meier with robust standard errors

-- L --

lifecourse Life-course plot
lifetable Life table
lifetable.formula Life table
lifetable.matrix Life table
LinSpline Simple linear spline
logitSurv Proportional odds survival model
loglikMVN Multivariate normal distribution function

-- M --

make.pairwise.design For internal use
make.pairwise.design.competing For internal use
matdoubleindex Predictions from proportional hazards model
matplot.mets.twostage For internal use
mdi Predictions from proportional hazards model
mena Menarche data set
mets.options Set global options for 'mets'
migr Migraine data
mlogit Multinomial regression based on phreg regression
multcif Multivariate Cumulative Incidence Function example data set

-- N --

nonparcuminc For internal use
np np data set
npc For internal use

-- O --

object.defined For internal use
or.cif Cross-odds-ratio, OR or RR risk regression for competing risks
or2prob Estimate parameters from odds-ratio

-- P --

p11.binomial.twostage.RV For internal use
pbvn Multivariate normal distribution function
pcif Extract survival estimates from lifetable analysis
phreg Fast Cox PH regression
phreg.par Fast Cox PH regression
piecewise.data For internal use
piecewise.twostage For internal use
plack.cif plack Computes concordance for or.cif based model, that is Plackett random effects model
plack.cif2 plack Computes concordance for or.cif based model, that is Plackett random effects model
plot.covariace.recurrent Estimation of covariance for bivariate recurrent events with terminal event
plotConfRegion Plotting the baslines of stratified Cox
plotcr For internal use
plotSurvd Discrete time to event haplo type analysis
pmvn Multivariate normal distribution function
ppch Piecewise constant hazard distribution
pred.cif.boot Wild bootstrap for Cox PH regression
predict.phreg Predictions from proportional hazards model
predictPairPlack For internal use
predictSurvd Discrete time to event haplo type analysis
print.casewise prints Concordance test
prob.exceed.recurrent Estimation of probability of more that k events for recurrent events process
prob.exceedBiRecurrent Estimation of probability of more that k events for recurrent events process
prob.exceedRecurrent Estimation of probability of more that k events for recurrent events process
procform For internal use
procform3 For internal use
procformdata For internal use
prt Prostate data set

-- R --

random.cif Random effects model for competing risks data
randomDes Twostage survival model for multivariate survival data
readPhreg Fast Cox PH regression
recmarg Fast recurrent marginal mean when death is possible
recurrentMarginal Fast recurrent marginal mean when death is possible
recurrentMarginalgam Simulation of recurrent events data based on cumulative hazards
revcumsum Predictions from proportional hazards model
revcumsumidstratasum Predictions from proportional hazards model
revcumsumidstratasumCov Predictions from proportional hazards model
revcumsumstrata Predictions from proportional hazards model
revcumsumstratasum Predictions from proportional hazards model
rmvn Multivariate normal distribution function
robust.basehaz.phreg Predictions from proportional hazards model
robust.phreg Fast Cox PH regression
rpch Piecewise constant hazard distribution
rr.cif Cross-odds-ratio, OR or RR risk regression for competing risks

-- S --

scoreMVN Multivariate normal distribution function
showfitsim Simulation of recurrent events data based on cumulative hazards
sim For internal use
simAalenFrailty Simulate from the Aalen Frailty model
simbinClaytonOakes.family.ace For internal use
simbinClaytonOakes.pairs For internal use
simbinClaytonOakes.twin.ace For internal use
simBinFam For internal use
simBinFam2 For internal use
simBinPlack For internal use
simClaytonOakes Simulate from the Clayton-Oakes frailty model
simClaytonOakes.family.ace For internal use
simClaytonOakes.twin.ace For internal use
simClaytonOakesLam Simulate from the Clayton-Oakes frailty model
simClaytonOakesWei Simulate from the Clayton-Oakes frailty model
simCompete.simple For internal use
simCompete.twin.ace For internal use
simCox For internal use
simFrailty.simple For internal use
simGlm Discrete time to event haplo type analysis
simMultistate Simulation of illness-death model
simnordic For internal use
simnordic.random For internal use
simRecurrent Simulation of recurrent events data based on cumulative hazards
simRecurrentGamma Simulation of recurrent events data based on cumulative hazards
simRecurrentII Simulation of recurrent events data based on cumulative hazards II
simRecurrentTS Simulation of recurrent events data based on cumulative hazards: Two-stage model
simSurvFam For internal use
slope.process Estimates the casewise concordance based on Concordance and marginal estimate using timereg and performs test for independence
squareintHdM Simulation of recurrent events data based on cumulative hazards
summary.cor Summary for dependence models for competing risks
sumstrata Predictions from proportional hazards model
surv.boxarea For internal use
survival.iterative Survival model for multivariate survival data
survival.twostage Twostage survival model for multivariate survival data
survival.twostage.fullse Twostage survival model for multivariate survival data

-- T --

tailstrata Predictions from proportional hazards model
test.conc Concordance test Compares two concordance estimates
tetrachoric Estimate parameters from odds-ratio
tie.breaker Fast recurrent marginal mean when death is possible
twin.clustertrunc Estimation of twostage model with cluster truncation in bivariate situation
twin.polygen.design For internal use
twinbmi BMI data set
twinlm Classic twin model for quantitative traits
twinlm.strata Classic twin model for quantitative traits
twinlm.time Liability model for twin data
twinsim Simulate twin data
twinstut Stutter data set
twostage.aalen Twostage survival model for multivariate survival data
twostage.cox.aalen Twostage survival model for multivariate survival data
twostage.coxph Twostage survival model for multivariate survival data
twostage.fullse For internal use
twostage.phreg Twostage survival model for multivariate survival data
twostageMLE Twostage survival model fitted by pseudo MLE