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mstate

Data Preparation, Estimation and Prediction in Multi-State Models

Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.

Functions (43)

Cuminc

Calculate nonparametric cumulative incidence functions and associated standard errors

EBMT-cause-of-death-data

Data from the European Society for Blood and Marrow Transplantation (EBMT)

EBMT-data

Data from the European Society for Blood and Marrow Transplantation (EBMT)

EBMT-platelet-recovery-data

Data from the European Society for Blood and Marrow Transplantation (EBMT)

EBMT-year-of-relapse-data

Data from the European Society for Blood and Marrow Transplantation (EBMT)

ELOS

Expected length of stay

LMAJ

Landmark Aalen-Johansen method

Liver-cirrhosis-data

Abnormal prothrombin levels in liver cirrhosis

MarkovTest

Log-rank based test for the validity of the Markov assumption

aidssi

Data from the Amsterdam Cohort Studies on HIV infection and AIDS

bmt

BMT data from Klein and Moeschberger

crprep.default

Function to create weighted data set for competing risks analyses

cutLMms

Cut a multi-state data set at a landmark time point

etm2msdata

Converts between etm and msdata format

events

Count number of observed transitions

expand.covs

Expand covariates in competing risks dataset in stacked format

expand.covs.msdata

Expand covariates in multi-state dataset in long format

msboot

Bootstrap function in multi-state models

msdata2etm

msdata to etm format

msfit

Compute subject-specific transition hazards with (co-)variances

msprep

Function to prepare dataset for multi-state modeling in long format from dataset in wide format

mssample

Sample paths through a multi-state model

mstate-package

Data preparation, estimation and prediction in multi-state models

paths

Find all possible trajectories through a given multi-state model

plot.Cuminc

Plot method for Cuminc objects

plot.MarkovTest

Plot method for a MarkovTest object

plot.msfit

Plot method for an msfit object

plot.probtrans

Plot method for a probtrans object

print.MarkovTest

Print method for a MarkovTest object

print.msdata

Print method for a msdata object

print.summary.msfit

Print method for summary.msfit object

print.summary.probtrans

Print method for a summary.probtrans object

probtrans

Compute subject-specific or overall transition probabilities with standard errors

redrank

Reduced rank proportional hazards model for competing risks and multi-state models

summary.Cuminc

Summary method for a summary.Cuminc object

summary.msfit

Summary method for an msfit object

summary.probtrans

Summary method for a probtrans object

trans2tra

Convert transition matrix from mstate to etm format

transMat

Define transition matrix for multi-state model

transhelp

Help functions for transition matrix

vis.mirror.pt

Mirror plot comparing two probtrans objects

vis.multiple.pt

Visualise multiple probtrans objects

xsect

Make a cross-section of multi-state data at a given time point

mstate

Data Preparation, Estimation and Prediction in Multi-State Models

v0.3.1

GPL (>= 2)

Authors

Hein Putter [aut, cre], Liesbeth C. de Wreede [aut], Marta Fiocco [aut], Ronald B. Geskus [ctb], Edouard F. Bonneville [ctb], Damjan Manevski [ctb]

Initial release

2020-12-17

mstate

Functions (43)

mstate

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