# Data Preparation, Estimation and Prediction in Multi-State Models

## 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