Fits Markov multi-state models for analyzing transitions between different health states over time. Supports homogeneous and non-homogeneous models with covariate effects using mstate and msm packages.
Usage
markovmultistate(
data,
time,
event,
subject,
covs,
modelType = "homogeneous",
transitionMatrix = "progressive",
baselineHazard = "exponential",
estimationMethod = "ml",
timeUnits = "auto",
predictionTimes = "1, 3, 5",
transitionTimes = "0.5, 1, 2, 3, 5",
conf = 0.95,
maxIterations = 1000,
tolerance = 1e-06,
showTransitionIntensities = TRUE,
showTransitionProbs = TRUE,
showStateProbabilities = TRUE,
showMeanSojournTimes = TRUE,
showExpectedRewards = FALSE,
showModelFit = TRUE,
showPredictions = TRUE,
showEducational = TRUE,
plotStateProbs = TRUE,
plotTransitionProbs = FALSE,
plotHazardRatios = FALSE,
plotModelDiagnostics = FALSE
)Arguments
- data
The data as a data frame.
- time
Follow-up time variable
- event
Event/state variable indicating transitions between states
- subject
Subject identifier for longitudinal tracking
- covs
Covariates affecting transition intensities
- modelType
Type of multi-state model to fit
- transitionMatrix
Structure of allowed transitions between states
- baselineHazard
Baseline hazard function specification
- estimationMethod
Method for parameter estimation
- timeUnits
Time scale for analysis and reporting
- predictionTimes
Comma-separated list of time points for state predictions
- transitionTimes
Time points for transition probability estimation
- conf
Confidence level for confidence intervals
- maxIterations
Maximum iterations for model fitting
- tolerance
Convergence tolerance for optimization
- showTransitionIntensities
Display estimated transition intensity matrix
- showTransitionProbs
Display transition probability matrices at specified times
- showStateProbabilities
Display state occupation probabilities over time
- showMeanSojournTimes
Display expected time spent in each state
- showExpectedRewards
Display expected rewards/utilities for health economics
- showModelFit
Display model fit statistics and diagnostics
- showPredictions
Display individual and population-level predictions
- showEducational
Display educational information about multi-state models
- plotStateProbs
Display state probability plots over time
- plotTransitionProbs
Display transition probability heatmaps
- plotHazardRatios
Display hazard ratio plots for covariates
- plotModelDiagnostics
Display model diagnostic plots and residuals
Value
A results object containing:
results$todo | a html | ||||
results$educationalInfo | a html | ||||
results$modelSummary | a table | ||||
results$transitionIntensities | a table | ||||
results$transitionProbabilities | a table | ||||
results$stateProbabilities | a table | ||||
results$meanSojournTimes | a table | ||||
results$covariateEffects | a table | ||||
results$modelFitStatistics | a table | ||||
results$predictionsTable | a table | ||||
results$methodsInfo | a html | ||||
results$interpretationGuide | a html | ||||
results$stateTransitionDiagram | an image | ||||
results$stateProbabilityPlot | an image | ||||
results$transitionProbabilityPlot | an image | ||||
results$hazardRatioPlot | an image | ||||
results$diagnosticsPlot | an image |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$modelSummary$asDF
as.data.frame(results$modelSummary)