Analysis of Multivariate Event Times
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Documentation for package ‘mets’ version 1.3.11
- DESCRIPTION file
- User guides, package vignettes and other documentation
- Code demos. Use demo() to run them.
- Package NEWS
- Package README
Help Pages
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 |
| binregStrata | Binomial Regression with Stratified Pseudo-Values and Censoring Adjustment |
| binregt | Binomial Regression for Censored Competing Risks Data |
| binregTSR | Two-Stage Randomization for Survival or Competing Risks Data |
| binreg_IPTW | IPTW logistic regression, Inverse Probabibilty of Treatment Weighted binreg |
| 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 |
| brier_binreg | Cross-validated Brier score for competing risks, RMST and RMTL regression using stratified leave-fold-out fits ('binregStrata') |
-- 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 --
| estimate.binregCV | Joint estimate across CV models for a binregCV object |
| 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 --
| 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.binreg | Influence curve components for binomial regression ATE |
| 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 |
| print.summary_binregCV_multi | Print method for summary_binregCV_multi objects |
| 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.binregCV | Summary method for binregCV objects |
| summary.binregCV_list | Summary method for binregCV_list objects |
| 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 |