Package: mstate 0.3.3

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]

mstate_0.3.3.tar.gz
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mstate_0.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mstate/json (API)

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

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:

Conda:

11.09 score 16 stars 66 packages 460 scripts 12k downloads 108 mentions 40 exports 7 dependencies

Last updated from:406e585679. Checks:12 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR170
linux-devel-x86_64ERROR175
source / vignettesERROR2550
linux-release-arm64ERROR177
linux-release-x86_64ERROR172
macos-release-arm64ERROR159
macos-release-x86_64ERROR313
macos-oldrel-arm64ERROR197
macos-oldrel-x86_64ERROR394
windows-develERROR190
windows-releaseERROR177
windows-oldrelERROR189
wasm-releaseOK136

Exports:absorbingcrprepCuminccutLMmsELOSetm2msdataeventsexpand.covshaz_functionis.circularLMAJMarkovTestmodify_transMatmsbootmsboot.relsurvmsboot.relsurv.bootmsdata2etmmsfitmsfit_subjectsmsfit_subjects_to_msfitmsfit.relsurvmsprepmssampleoptimal_weights_matrixoptimal_weights_multiplepathsprobtransprobtrans_subjectsredrankto.trans2tra2transtrans.comprisktrans.illdeathtrans2Qtrans2tratransMatvarHaz.fixedvis.mirror.ptvis.multiple.ptxsect

Dependencies:data.tablelatticeMatrixRColorBrewerrlangsurvivalviridisLite

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
Compute subject-specific transition hazards for multiple subjects at oncemsfit_subjects
Obtain an 'msfit' object for a single subject from an 'msfit.subjects' object.msfit_subjects_to_msfit
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 an msfit.subjects objectplot.msfit.subjects
Plot method for a probtrans objectplot.probtrans
Plot an object of class '"probtrans.subjects"'plot.probtrans.subjects
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
Compute subject-specific transition probabilitiesprobtrans_subjects
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
Summary method for a probtrans.subjects objectsummary.probtrans.subjects
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