Recurrent event survival analysis for subjects who can experience multiple events over time. Common in cancer recurrence, infections, hospitalizations, and chronic disease episodes. Handles gap time, calendar time, and counting process formulations.
Usage
recurrentsurvival(
subject_id,
event_time,
event_status = NULL,
terminal_event = NULL,
terminal_status = NULL,
event_type = NULL,
covariates = NULL,
stratification_vars = NULL,
model_type = "ag_model",
time_scale = "gap_time",
frailty_distribution = "gamma",
robust_variance = TRUE,
cluster_variable = NULL,
baseline_hazard_smooth = FALSE,
smoothing_bandwidth = 1,
confidence_level = 0.95,
max_events = 10,
terminal_competing = TRUE,
recurrence_plots = TRUE,
gap_time_plots = FALSE,
cumulative_hazard = TRUE,
model_diagnostics = TRUE,
goodness_of_fit = TRUE,
prediction_times = "12,24,36,60",
bootstrap_samples = 200,
convergence_tolerance = 1e-04,
max_iterations = 500,
use_reReg = FALSE,
reReg_model = "cox_LWYY",
reReg_se = "bootstrap",
reReg_B = 200,
show_event_plot = TRUE,
show_mcf_plot = TRUE,
event_plot_subjects = 20
)Arguments
- subject_id
Variable identifying unique subjects who can have multiple events
- event_time
Time variable for recurrent event occurrence
- event_status
Event status indicator for recurrent events
- terminal_event
Terminal event that stops the recurrence process
- terminal_status
Status indicator for terminal event
- event_type
Classification of different types of recurrent events
- covariates
Covariates to include in the recurrent event model
- stratification_vars
Variables for stratifying the baseline hazard
- model_type
Model specification for recurrent event data
- time_scale
Time scale specification for recurrent events
- frailty_distribution
Distribution assumption for frailty terms
- robust_variance
Whether to use robust variance estimation
- cluster_variable
Variable for clustering in variance estimation
- baseline_hazard_smooth
Whether to smooth the baseline hazard function
- smoothing_bandwidth
Bandwidth for baseline hazard smoothing
- confidence_level
Confidence level for parameter estimates
- max_events
Upper limit on events per subject for analysis
- terminal_competing
Whether to model terminal event as competing risk
- recurrence_plots
Whether to plot recurrence functions
- gap_time_plots
Whether to plot gap time distributions
- cumulative_hazard
Whether to plot cumulative hazard functions
- model_diagnostics
Whether to include model diagnostics
- goodness_of_fit
Whether to test model goodness-of-fit
- prediction_times
Time points for recurrence probability predictions
- bootstrap_samples
Number of bootstrap resamples
- convergence_tolerance
Convergence criterion for iterative algorithms
- max_iterations
Maximum number of algorithm iterations
- use_reReg
Whether to use reReg package for analysis
- reReg_model
Model specification for reReg package
- reReg_se
Standard error estimation method for reReg
- reReg_B
Bootstrap samples for reReg variance estimation
- show_event_plot
Whether to show event plot from reReg
- show_mcf_plot
Whether to show MCF plot from reReg
- event_plot_subjects
Number of subjects to display in event plot
Value
A results object containing:
results$instructions | a html | ||||
results$data_summary | a html | ||||
results$model_results | a html | ||||
results$covariate_effects | a html | ||||
results$recurrence_estimates | a html | ||||
results$gap_time_summary | a html | ||||
results$terminal_event_summary | a html | ||||
results$frailty_estimates | a html | ||||
results$model_diagnostics_summary | a html | ||||
results$goodness_of_fit_results | a html | ||||
results$event_frequency_table | a html | ||||
results$recurrence_plots | an image | ||||
results$gap_time_plots | an image | ||||
results$cumulative_hazard_plot | an image | ||||
results$event_timeline_plot | an image | ||||
results$residual_plots | an image | ||||
results$frailty_distribution_plot | an image | ||||
results$multistate_diagram | an image | ||||
results$model_comparison_plot | an image |
Examples
# Example: Cancer recurrence analysis
recurrentsurvival(
data = cancer_data,
subject_id = patient_id,
event_time = recurrence_time,
event_type = recurrence_type,
terminal_event = death,
covariates = c("age", "stage", "treatment"),
model_type = "ag_model"
)
#> Error in recurrentsurvival(data = cancer_data, subject_id = patient_id, event_time = recurrence_time, event_type = recurrence_type, terminal_event = death, covariates = c("age", "stage", "treatment"), model_type = "ag_model"): unused argument (data = cancer_data)