Analysis of Multivariate Event Times

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Documentation for package ‘mets’ version 1.3.10

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

-- A --

aalenMets Fast Additive Hazards Model with Robust Standard Errors
ace_family_design Concordance Probability from Twostage Model
ACTG175 ACTG175, block randomized study from speff2trial package
alpha2kendall Survival Twostage Helpers
alpha2spear Survival Twostage Helpers
as.character.Event Event history object
as.matrix.Event Event history object
ascertained_pairs Concordance Probability from Twostage Model

-- B --

basecumhaz Plotting the baselines of stratified Cox
baseplot Plotting the baselines of stratified Cox
bicomprisk Estimation of Concordance in Bivariate Competing Risks Data
bicompriskData 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.
binreg Binomial Regression for Censored Competing Risks Data
binregATE Average Treatment Effect for Censored Competing Risks Data using Binomial Regression
binregCasewise Estimate Casewise Concordance Using Binomial Regression
binregG G-Estimator for Binomial Regression Model (Standardized Estimates)
binregRatio Percentage of Years Lost Due to a Cause Regression
binregt Binomial Regression for Censored Competing Risks Data
binregTSR Two-Stage Randomization for Survival or Competing Risks Data
biprobit Bivariate Probit model
biprobit.time Bivariate Probit model
biprobit.vector Bivariate Probit model
blocksample Block sampling
bmt The Bone Marrow Transplant Data
BootmediatorSurv Mediation analysis in survival context
bplot Plotting the baselines of stratified Cox
bptwin Liability model for twin data
bptwin.time Liability model for twin data

-- C --

calgb8923 CALGB 8923, twostage randomization SMART design
casewise Estimate Casewise Concordance from prodlim Objects
casewise_bin Casewise Concordance from Concordant/Discordant Counts
cif Cumulative Incidence with Robust Standard Errors
cif-nonpar Non-parametric Cumulative Incidence Functions
cifreg Cumulative Incidence Function (CIF) Regression
cifregFG Fine-Gray Cumulative Incidence Function Regression
cif_yearslost Restricted Mean Time Lost for Competing Risks
ClaytonOakes Clayton-Oakes model with piece-wise constant hazards
cluster.index Finds subjects related to same cluster
cluster_index Finds subjects related to same cluster
coarse_clust Coarsen Cluster Identifiers
concordance.cor Concordance Computes concordance and casewise concordance
concordanceCor Concordance Computes concordance and casewise concordance
concordanceTwinACE Concordance Probability from Twostage Model
concordanceTwostage Concordance Probability from Twostage Model
conftype Robust Baseline Hazard Standard Errors
cor_cif Cross-odds-ratio, OR or RR risk regression for competing risks
countID Finds subjects related to same cluster
count_history Compute cumulative event counts as time-dependent covariates
CPH_HPN_CRBSI Rates for HPN program for patients of Copenhagen Cohort
cpred Fast approximation
cumContr Goodness-of-Fit for Cox Covariates (Linearity)
cumoddsreg Cumulative Odds Regression for Discrete Time Data
cumsumstrata Stratified Cumulative and Summary Operations

-- 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
diabetes The Diabetic Retinopathy Data
diffstrata Cumulative Incidence Function (CIF) Regression
dInterval Discrete Time-to-Event Analysis with Interval Censoring
divide_conquer Split a data set and run function
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
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
drop.specials Remove Special Terms from a Formula
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 --

Event Event history object
eventpois Extract survival estimates from lifetable analysis
event_split event_split (SurvSplit).
event_split2 Event split with two time-scales, time and gaptime
extendCums Extend Cumulative Hazard Functions to Common Time Range

-- F --

familyclusterWithProbands_index Finds all pairs within a cluster (famly) with the proband (case/control)
familycluster_index Finds all pairs within a cluster (family)
fast.approx Fast approximation
fast.cluster Fast Cluster Index Conversion
fast.pattern Fast pattern
fast.reshape Fast reshape
faster.reshape Fast Reshape from Long to Wide Format
FGprediid Cumulative Incidence Function (CIF) Regression
folds Generate Random Fold Indices for Cross-Validation
force.same.cens Force Same Censoring Within Clusters
force_same_cens Force Same Censoring Within Clusters
format.Event Event history object

-- G --

glm_IPTW IPTW GLM, Inverse Probabibilty of Treatment Weighted GLM
GLprediid Recurrent Events Regression with Terminal Event
gof.phreg Goodness-of-Fit for Cox PH Regression (Proportionality)
gofFG Cumulative Incidence Function (CIF) Regression
gofM_phreg Goodness-of-Fit for Cox Covariates (Model Matrix)
gofZ_phreg Goodness-of-Fit for Cox Covariates (Linearity)
Grandom.cif Non-parametric Cumulative Incidence Functions
Grandom_cif Additive Random effects model for competing risks data for polygenetic modelling
grouptable Create Group Contingency Table from Clustered Data

-- H --

haplo haplo fun data
haplo_surv_discrete Discrete Time-to-Event Haplotype Analysis
hfactioncpx12 hfaction, subset of block randomized study HF-ACtion from WA package

-- I --

IC.phreg Influence Functions for phreg objects
iidBaseline Influence Functions or IID Decomposition of Baseline
IIDrecreg Recurrent Events Regression with Terminal Event
iidRecurrent Marginal mean estimation for recurrent events with a terminal event
ilap Inverse Laplace Transform Helper
indexstrata Fast approximation
indexstratarightR Cumulative Incidence Function (CIF) Regression
Interval Discrete Time-to-Event Analysis with Interval Censoring
interval_logitsurv_discrete Discrete Time-to-Event Analysis with Interval Censoring
invsubdist Simulation of Output from Cumulative Incidence Regression Model
ipw Inverse Probability of Censoring Weights
ipw2 Inverse Probability of Censoring Weights

-- J --

jumptimes Extract Event (Jump) Times

-- K --

kendall.ClaytonOakes.twin.ace Concordance Probability from Twostage Model
kendall_ClaytonOakes_twin_ace Concordance Probability from Twostage Model
kendall_normal_twin_ace Concordance Probability from Twostage Model
km Kaplan-Meier with Robust Standard Errors
kmplot Plotting the baselines of stratified Cox

-- L --

lifecourse Life-course plot
lifetable Life table
lifetable.formula Life table
lifetable.matrix Life table
LinSpline Simple linear spline
lin_approx Simulation of Piecewise Constant Hazard Model (Cox)
logitATE Average Treatment Effect for Censored Competing Risks Data using Binomial Regression
logitIPCW Binomial Regression for Censored Competing Risks Data
logitIPCWATE Average Treatment Effect for Censored Competing Risks Data using Binomial Regression
logitSurv Proportional Odds Survival Model
loglikMVN Multivariate normal distribution function
logrankRecurrentBase Logrank-type test for comparing recurrent event marginal means between groups

-- M --

make_pairwise_design Concordance Probability from Twostage Model
marks Recurrent Events Regression with Terminal Event
matdoubleindex Stratified Cumulative and Summary Operations
matplot.mets.twostage Survival Twostage Helpers
mdi Stratified Cumulative and Summary Operations
mediatorSurv Mediation analysis in survival context
medweight Computes mediation weights
melanoma The Melanoma Survival Data
mena Menarche data set
mets.options Set global options for 'mets'
migr Migraine data
mlogit Multinomial Regression Based on phreg
multcif Multivariate Cumulative Incidence Function example data set
mystrata Finds subjects related to same cluster
mystrata2index Finds subjects related to same cluster

-- N --

nonparcuminc Non-parametric Cumulative Incidence Functions
normalATE Average Treatment Effect for Censored Competing Risks Data using Binomial Regression
np np data set
npc Non-parametric Cumulative Incidence Functions

-- O --

or.cif Cross-odds-ratio, OR or RR risk regression for competing risks
or2prob Estimate parameters from odds-ratio
or_cif Non-parametric Cumulative Incidence Functions

-- P --

p11.binomial.twostage.RV Concordance Probability from Twostage Model
p11_binomial_twostage_RV Concordance Probability from Twostage Model
pairRisk Finds subjects related to same cluster
pbvn Multivariate normal distribution function
pcif Extract survival estimates from lifetable analysis
phreg Fast Cox Proportional Hazards Regression
phreg.par Weibull-Cox regression
phreg_IPTW IPTW Cox Regression (Inverse Probability of Treatment Weighted)
phreg_rct Lu-Tsiatis More Efficient Log-Rank for Randomized Studies with Baseline Covariates
phreg_weibull Weibull-Cox regression
piecewise_data Survival Twostage Helpers
piecewise_twostage Survival Twostage Helpers
plack.cif2 plack Computes concordance for or.cif based model, that is Plackett random effects model
plack_cif plack Computes concordance for or.cif based model, that is Plackett random effects model
plot.phreg Plotting the baselines of stratified Cox
plotConfRegion Plotting the baselines of stratified Cox
plotConfregion Plotting the baselines of stratified Cox
plotConfRegionSE Plotting the baselines of stratified Cox
plotcr Non-parametric Cumulative Incidence Functions
plotstrata Plotting the baselines of stratified Cox
plotSurvd Discrete Time-to-Event Analysis with Interval Censoring
plot_twin Scatter plot function
pmvn Multivariate normal distribution function
predict Multinomial Regression Based on phreg
predict.mlogit Predictions from Multinomial Regression
predict.phreg Predictions from Proportional Hazards Model
predictCumhaz Fast approximation
predictGLM Reporting OR (exp(coef)) from glm with binomial link and glm predictions
predictlogitSurvd Discrete Time-to-Event Analysis with Interval Censoring
predictPairPlack Non-parametric Cumulative Incidence Functions
predictSurvd Discrete Time-to-Event Analysis with Interval Censoring
print.casewise prints Concordance test
print.Event Event history object
prob_exceed_recurrent Estimate the probability of exceeding k recurrent events by time t
prt Prostate data set

-- R --

random.cif Non-parametric Cumulative Incidence Functions
randomDes Twostage Survival Model for Multivariate Survival Data
random_cif Random effects model for competing risks data
ratioATE Ratio of Average Treatment Effects
rbind.Event Event history object
rchaz Simulation of Piecewise Constant Hazard Model (Cox)
rchazl Multiple Cause Piecewise Constant Hazard Simulation
rcrisk Simulation of Piecewise constant hazard models with two causes (Cox).
readmargsurv Twostage Survival Model for Multivariate Survival Data
recreg Recurrent Events Regression with Terminal Event
recregIPCW IPCW Estimator for Recurrent Events
recurrentMarginal Marginal mean estimation for recurrent events with a terminal event
recurrentMarginalPhreg Marginal mean estimation for recurrent events with a terminal event
recurrent_marginal Marginal mean estimation for recurrent events with a terminal event
recurrent_marginalAIPCW Marginal mean estimation for recurrent events with a terminal event
resmeanATE Average Treatment Effect for Restricted Mean Time
resmeanIPCW Restricted IPCW Mean for Censored Survival Data
resmean_phreg Restricted Mean for Stratified Kaplan-Meier or Cox Model
revcumsum Stratified Cumulative and Summary Operations
revcumsumstrata Stratified Cumulative and Summary Operations
rmstATE Average Treatment Effect for Restricted Mean Time
rmstIPCW Restricted IPCW Mean for Censored Survival Data
rmst_phreg Restricted Mean for Stratified Kaplan-Meier or Cox Model
rmtlRatio Percentage of Years Lost Due to a Cause Regression
rmvn Multivariate normal distribution function
robust.basehaz.phreg Robust Baseline Hazard Standard Errors
robust_phreg Fast Cox Proportional Hazards Regression
rr.cif Cross-odds-ratio, OR or RR risk regression for competing risks
rr_cif Non-parametric Cumulative Incidence Functions
rweibullcox Simulate observations from a Weibull distribution

-- S --

scalecumhaz Recurrent Events Regression with Terminal Event
scoreMVN Multivariate normal distribution function
sim_cif Simulation of Output from Cumulative Incidence Regression Model
sim_cifs Simulation of Output from Cumulative Incidence Regression Model
sim_ClaytonOakes Simulate from the Clayton-Oakes frailty model
sim_ClaytonOakesLam Simulate from the Clayton-Oakes frailty model
sim_ClaytonOakesWei Simulate from the Clayton-Oakes frailty model
sim_GLcox Simulation of Two-Stage Recurrent Events Data
sim_multistate Simulation of Illness-Death Model
sim_multistateII Illness-Death Competing Risks with Two Causes of Death
sim_phreg Simulation of Output from Cox Model
sim_phregs Simulation of Cause-Specific Cox Models
sim_rchaz Simulation of Piecewise Constant Hazard Model (Cox)
sim_recurrent Simulate recurrent events with a single event type and a terminal event
sim_recurrentII Simulate recurrent events with two event types and a terminal event
sim_recurrentTS Simulate recurrent events from a two-stage model with structured gamma frailties
sim_recurrent_list Simulate recurrent events with two event types and a terminal event
sim_recurrent_ts Simulate recurrent events from a two-stage Cox or Ghosh-Lin model
sim_subdist Simulation of Output from Cumulative Incidence Regression Model
sTRACE The TRACE study group of myocardial infarction
strata-numeric Stratified Cumulative and Summary Operations
subdist Simulation of Output from Cumulative Incidence Regression Model
summary.cor Summary for dependence models for competing risks
summary.Event Event history object
summarybase.phreg Robust Baseline Hazard Standard Errors
summaryGLM Reporting OR (exp(coef)) from glm with binomial link and glm predictions
summaryTimeobject Summarize a Time-Varying Estimate with Confidence Bands
sumstrata Stratified Cumulative and Summary Operations
survival-helpers Survival Twostage Helpers
survival.twostage Survival Twostage Helpers
survivalG G-Estimator for Cox and Fine-Gray Models
survivalGtime G-Estimator for Cox and Fine-Gray Models
survival_twostage Twostage Survival Model for Multivariate Survival Data
surv_boxarea Bivariate Survival Data on Rectangular Regions

-- T --

test_casewise Test for Independence Using Casewise Concordance
test_conc Compare Two Concordance Estimates
test_logrankRecurrent Logrank-type test for comparing recurrent event marginal means between groups
test_marginalMean Pepe-Mori Test for Marginal Mean Comparison
tetrachoric Estimate parameters from odds-ratio
tie_breaker Break ties in event times for recurrent event data
TRACE The TRACE study group of myocardial infarction
ttpd ttpd discrete survival data on interval form
tTRACE The TRACE study group of myocardial infarction
twin-design Concordance Probability from Twostage Model
twin.polygen.design Concordance Probability from Twostage Model
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
twin_polygen_design Concordance Probability from Twostage Model
twostageMLE Twostage Survival Model Fitted by Pseudo MLE
twostageREC Fitting of Two-Stage Recurrent Events Random Effects Model
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_phreg Twostage Survival Model for Multivariate Survival Data

-- V --

vecAllStrata Cumulative Incidence Function (CIF) Regression

-- W --

WA_recurrent While-Alive Estimands for Recurrent Events
WA_reg While-Alive Regression for Recurrent Events

-- misc --

[.Event Event history object