Cox proportional hazards model diagnostic plots using ggcoxdiagnostics from survminer package for comprehensive model validation.
Usage
coxdiagnostics(
data,
time,
event,
covariates,
strata_var = NULL,
show_martingale = TRUE,
show_deviance = TRUE,
show_score = FALSE,
show_schoenfeld = FALSE,
show_dfbeta = FALSE,
ox_scale = "linear.predictions",
add_smooth = TRUE,
add_reference = TRUE,
point_size = 1,
alpha_level = 0.6,
show_ph_test = TRUE,
show_model_summary = TRUE,
show_vif = TRUE,
vif_threshold = 5,
show_interpretation = TRUE,
exclude_missing = TRUE,
confidence_level = 0.95
)Arguments
- data
The data as a data frame.
- time
The time-to-event variable for survival analysis.
- event
The event indicator variable (1=event, 0=censored).
- covariates
Variables to include as covariates in the Cox model.
- strata_var
Optional variable for stratified Cox regression.
- show_martingale
Whether to show martingale residual plots.
- show_deviance
Whether to show deviance residual plots.
- show_score
Whether to show score residual plots.
- show_schoenfeld
Whether to show Schoenfeld residual plots.
- show_dfbeta
Whether to show DFBeta influence diagnostic plots.
- ox_scale
Scale for the x-axis in residual plots.
- add_smooth
Whether to add a smooth line to residual plots.
- add_reference
Whether to add a reference line at y=0.
- point_size
Size of points in diagnostic plots.
- alpha_level
Transparency level for points in plots.
- show_ph_test
Whether to display results of proportional hazards test.
- show_model_summary
Whether to display Cox regression model summary.
- show_vif
Whether to calculate and display Variance Inflation Factor (VIF) for multicollinearity assessment.
- vif_threshold
VIF threshold for multicollinearity warning.
- show_interpretation
Whether to include interpretation of diagnostic results.
- exclude_missing
Whether to exclude observations with missing values.
- confidence_level
Confidence level for statistical tests and intervals.
Value
A results object containing:
results$instructions | a html | ||||
results$model_summary | a html | ||||
results$ph_test_results | a html | ||||
results$vif_results | a html | ||||
results$martingale_plot | an image | ||||
results$deviance_plot | an image | ||||
results$score_plot | an image | ||||
results$schoenfeld_plot | an image | ||||
results$dfbeta_plot | an image | ||||
results$interpretation | a html |
Examples
# \donttest{
# Example usage:
library(survival)
#>
#> Attaching package: ‘survival’
#> The following object is masked from ‘package:ClinicoPath’:
#>
#> colon
library(survminer)
#> Loading required package: ggpubr
#>
#> Attaching package: ‘survminer’
#> The following object is masked from ‘package:survival’:
#>
#> myeloma
# Fit Cox model
cox_model <- coxph(Surv(time, status) ~ age + sex, data = data)
#> Error in terms.formula(formula, specials = ss, data = data): 'data' argument is of the wrong type
# Generate diagnostic plots
ggcoxdiagnostics(cox_model, type = "martingale")
#> Error: object 'cox_model' not found
ggcoxdiagnostics(cox_model, type = "deviance")
#> Error: object 'cox_model' not found
# }