Package: mstate 0.3.3

Hein Putter

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>.

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

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mstate.pdf |mstate.html✨
mstate/json (API)
NEWS

# Install 'mstate' in R:
install.packages('mstate', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hputter/mstate/issues

Datasets:
  • 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
  • ebmt1 - Data from the European Society for Blood and Marrow Transplantation
  • ebmt2 - Data from the European Society for Blood and Marrow Transplantation
  • ebmt3 - Data from the European Society for Blood and Marrow Transplantation
  • ebmt4 - Data from the European Society for Blood and Marrow Transplantation
  • prothr - Abnormal prothrombin levels in liver cirrhosis

On CRAN:

11.59 score 7 stars 49 packages 282 scripts 8.4k downloads 108 mentions 37 exports 7 dependencies

Last updated 5 months agofrom:3dfa315b25. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-win-x86_64OKNov 08 2024
R-4.5-linux-x86_64OKNov 08 2024
R-4.4-win-x86_64OKNov 08 2024
R-4.4-mac-x86_64OKNov 08 2024
R-4.4-mac-aarch64OKNov 08 2024
R-4.3-win-x86_64OKNov 08 2024
R-4.3-mac-x86_64OKNov 08 2024
R-4.3-mac-aarch64OKNov 08 2024

Exports:absorbingcrprepCuminccutLMmsELOSetm2msdataeventsexpand.covshaz_functionis.circularLMAJMarkovTestmodify_transMatmsbootmsboot.relsurvmsboot.relsurv.bootmsdata2etmmsfitmsfit.relsurvmsprepmssampleoptimal_weights_matrixoptimal_weights_multiplepathsprobtransredrankto.trans2tra2transtrans.comprisktrans.illdeathtrans2Qtrans2tratransMatvarHaz.fixedvis.mirror.ptvis.multiple.ptxsect

Dependencies:data.tablelatticeMatrixRColorBrewerrlangsurvivalviridisLite

Using mstate for the analyses of Putter et al. (Stat Med 2007)

Rendered fromTutorial.Rnwusingutils::Sweaveon Nov 08 2024.

Last update: 2024-07-05
Started: 2014-05-30

Visualising multi-state models using mstate

Edouard F. Bonneville

Rendered fromvisuals_demo.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2021-07-09
Started: 2020-09-15

Readme and manuals

Help Manual

Help pageTopics
Data preparation, estimation and prediction in multi-state modelsmstate-package mstate
Data from the Amsterdam Cohort Studies on HIV infection and AIDSaidssi aidssi2
BMT data from Klein and Moeschbergerbmt
Function to create weighted data set for competing risks analysescrprep crprep.default
Calculate nonparametric cumulative incidence functions and associated standard errorsCuminc print.Cuminc
Cut a multi-state data set at a landmark time pointcutLMms
Data from the European Society for Blood and Marrow Transplantation (EBMT)EBMT cause of death data ebmt2
Data from the European Society for Blood and Marrow Transplantation (EBMT)EBMT data ebmt4
Data from the European Society for Blood and Marrow Transplantation (EBMT)EBMT platelet recovery data ebmt3
Data from the European Society for Blood and Marrow Transplantation (EBMT)EBMT year of relapse data ebmt1
Expected length of stayELOS
Converts between etm and msdata formatetm2msdata tra2trans
Count number of observed transitionsevents
Expand covariates in competing risks dataset in stacked formatexpand.covs expand.covs.default
Expand covariates in multi-state dataset in long formatexpand.covs.msdata
Helper function that calculates excess and population hazards for a given transitionhaz_function
Abnormal prothrombin levels in liver cirrhosisLiver cirrhosis data prothr
Landmark Aalen-Johansen methodLMAJ
Log-rank based test for the validity of the Markov assumptionMarkovTest optimal_weights_matrix optimal_weights_multiple
Upgrade the transMat object for the multi-state/relsurv setting.modify_transMat
Bootstrap function in multi-state modelsmsboot
Bootstrap function for upgraded multi-state models using relsurvmsboot.relsurv
Default theta function used for msboot.relsurvmsboot.relsurv.boot
msdata to etm formatmsdata2etm
Compute subject-specific transition hazards with (co-)variancesmsfit
Extend a multi-state model using relative survivalmsfit.relsurv
Function to prepare dataset for multi-state modeling in long format from dataset in wide formatmsprep
Sample paths through a multi-state modelmssample
Find all possible trajectories through a given multi-state modelpaths
Plot method for Cuminc objectsplot.Cuminc
Plot method for a MarkovTest objectplot.MarkovTest
Plot method for an msfit objectplot.msfit
Plot method for a probtrans objectplot.probtrans
Print method for a MarkovTest objectprint.MarkovTest
Print method for a msdata objectprint.msdata
Print method for summary.msfit objectprint.summary.msfit
Print method for a summary.probtrans objectprint.summary.probtrans
Compute subject-specific or overall transition probabilities with standard errorsprobtrans
Reduced rank proportional hazards model for competing risks and multi-state modelsredrank
Summary method for a summary.Cuminc objectsummary.Cuminc
Summary method for an msfit objectsummary.msfit
Summary method for a probtrans objectsummary.probtrans
Convert transition matrix from mstate to etm formattrans2tra
Help functions for transition matrixabsorbing is.circular to.trans2 trans2Q transhelp
Define transition matrix for multi-state modeltrans.comprisk trans.illdeath transMat
Upgrade the varHaz objectvarHaz.fixed
Mirror plot comparing two probtrans objectsvis.mirror.pt
Visualise multiple probtrans objectsvis.multiple.pt
Make a cross-section of multi-state data at a given time pointxsect