Fits Semi-Markov models where transition intensities depend on time since last transition rather than absolute time. Suitable for processes where the 'clock' resets at each transition using SemiMarkov package.
Usage
semimarkov(
data,
time,
event,
subject,
covs,
modelType = "parametric",
transitionStructure = "progressive",
distributionType = "weibull",
estimationMethod = "ml",
timeScale = "auto",
predictionHorizons = "1, 3, 5, 10",
timePoints = "0.5, 1, 2, 3, 5",
conf = 0.95,
maxIterations = 1000,
tolerance = 1e-06,
bootstrapSamples = 500,
showTransitionRates = TRUE,
showSojournDistribution = TRUE,
showTransitionProbs = TRUE,
showStateProbabilities = TRUE,
showReliabilityAnalysis = FALSE,
showModelDiagnostics = TRUE,
showPredictions = TRUE,
showEducational = TRUE,
plotSojournDistributions = TRUE,
plotTransitionIntensities = FALSE,
plotStateProbabilities = TRUE,
plotReliabilityFunctions = 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 Semi-Markov model to fit
- transitionStructure
Structure of allowed transitions between states
- distributionType
Distribution for sojourn times in each state
- estimationMethod
Method for parameter estimation
- timeScale
Time scale for analysis and reporting
- predictionHorizons
Comma-separated list of time horizons for predictions
- timePoints
Time points for transition probability estimation
- conf
Confidence level for confidence intervals
- maxIterations
Maximum iterations for convergence
- tolerance
Convergence tolerance for optimization
- bootstrapSamples
Number of bootstrap samples for confidence intervals
- showTransitionRates
Display estimated transition rates and parameters
- showSojournDistribution
Display sojourn time distribution parameters
- showTransitionProbs
Display transition probabilities over time
- showStateProbabilities
Display state occupation probabilities
- showReliabilityAnalysis
Display reliability and survival function analysis
- showModelDiagnostics
Display goodness-of-fit and diagnostic tests
- showPredictions
Display future state predictions
- showEducational
Display educational information about Semi-Markov models
- plotSojournDistributions
Display sojourn time distribution plots
- plotTransitionIntensities
Display transition intensity functions over time
- plotStateProbabilities
Display state occupation probability plots
- plotReliabilityFunctions
Display reliability and hazard function plots
- plotModelDiagnostics
Display diagnostic and goodness-of-fit plots
Value
A results object containing:
results$todo | a html | ||||
results$educationalInfo | a html | ||||
results$modelSummary | a table | ||||
results$transitionRates | a table | ||||
results$sojournDistribution | a table | ||||
results$transitionProbabilities | a table | ||||
results$stateProbabilities | a table | ||||
results$reliabilityAnalysis | a table | ||||
results$covariateEffects | a table | ||||
results$modelDiagnostics | a table | ||||
results$predictionsTable | a table | ||||
results$methodsInfo | a html | ||||
results$interpretationGuide | a html | ||||
results$sojournDistributionPlot | an image | ||||
results$stateProbabilityPlot | an image | ||||
results$transitionIntensityPlot | an image | ||||
results$reliabilityPlot | an image | ||||
results$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)