Data Preparation, Estimation and Prediction in Multi-State Models

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Documentation for package ‘mstate’ version 0.3.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

mstate-package	Data preparation, estimation and prediction in multi-state models
absorbing	Help functions for transition matrix
aidssi	Data from the Amsterdam Cohort Studies on HIV infection and AIDS
aidssi2	Data from the Amsterdam Cohort Studies on HIV infection and AIDS
bmt	BMT data from Klein and Moeschberger
crprep	Function to create weighted data set for competing risks analyses
crprep.default	Function to create weighted data set for competing risks analyses
Cuminc	Calculate nonparametric cumulative incidence functions and associated standard errors
cutLMms	Cut a multi-state data set at a landmark time point
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)
ebmt1	Data from the European Society for Blood and Marrow Transplantation (EBMT)
ebmt2	Data from the European Society for Blood and Marrow Transplantation (EBMT)
ebmt3	Data from the European Society for Blood and Marrow Transplantation (EBMT)
ebmt4	Data from the European Society for Blood and Marrow Transplantation (EBMT)
ELOS	Expected length of stay
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.default	Expand covariates in competing risks dataset in stacked format
expand.covs.msdata	Expand covariates in multi-state dataset in long format
haz_function	Helper function that calculates excess and population hazards for a given transition
is.circular	Help functions for transition matrix
Liver cirrhosis data	Abnormal prothrombin levels in liver cirrhosis
LMAJ	Landmark Aalen-Johansen method
MarkovTest	Log-rank based test for the validity of the Markov assumption
modify_transMat	Upgrade the transMat object for the multi-state/relsurv setting.
msboot	Bootstrap function in multi-state models
msboot.relsurv	Bootstrap function for upgraded multi-state models using relsurv
msboot.relsurv.boot	Default theta function used for msboot.relsurv
msdata2etm	msdata to etm format
msfit	Compute subject-specific transition hazards with (co-)variances
msfit.relsurv	Extend a multi-state model using relative survival
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	Data preparation, estimation and prediction in multi-state models
optimal_weights_matrix	Log-rank based test for the validity of the Markov assumption
optimal_weights_multiple	Log-rank based test for the validity of the Markov assumption
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.Cuminc	Calculate nonparametric cumulative incidence functions and associated standard errors
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
prothr	Abnormal prothrombin levels in liver cirrhosis
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
to.trans2	Help functions for transition matrix
tra2trans	Converts between etm and msdata format
trans.comprisk	Define transition matrix for multi-state model
trans.illdeath	Define transition matrix for multi-state model
trans2Q	Help functions for transition matrix
trans2tra	Convert transition matrix from mstate to etm format
transhelp	Help functions for transition matrix
transMat	Define transition matrix for multi-state model
varHaz.fixed	Upgrade the varHaz object
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