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Data

reccolon2ts
Data from the chemotherapy for stace B/C colon cancer study

Data processing

prepare_data()
Prepare raw data by binning them in 1d or 2d
prepare_data_LMMsolver()
Process data to fit model with LMMsolver
make_bins()
Construct bins over one or more time axes
exposures_events_1d()
Bin data on one time scale
exposures_events_2d()
Bin data on two time scales
exposures_events_Lexis()
Bin data on the Lexis diagram
print(<data2ts>)
Print method for a data2ts object

One time scale

fit1ts()
Fit a smooth hazard model with one time scale
fit1tsmodel_ucminf()
Numerical optimization of the 1ts model
grid_search_1d()
Grid search for the optimal 1ts model
get_aic_fit_1d()
Return the AIC of 1ts model
get_bic_fit_1d()
Return the BIC of 1ts model
iwls_1d()
Iterative Weighted Least Squares algorithm for 1ts model
GLAM_1d_covariates()
Fit the 1d GLAM with covariates
get_hazard_1d()
Get estimated (log-)hazard values with 1 time scale
get_hazard_1d_LMM()
Get estimated (log-)hazard values with 1 time scale
get_hr()
Get the Hazard Ratios with their Standard Errors

Two time scales

fit2ts()
Fit a smooth hazard model with two time scales
fit2tsmodel_ucminf()
Numerical optimization of the 2ts model
grid_search_2d()
Grid search for the optimal 2ts model
get_aic_fit_2d()
Return the AIC of 2ts model
get_bic_fit_2d()
Return the BIC of 2ts model
getAIC_BIC_LMM()
Calculates AIC and BIC from object fitted via LMMsolver
GLAM_2d_no_covariates()
Fit the 2d GLAM without covariates
GLAM_2d_covariates()
Fit the 2d GLAM with covariates
get_hazard_2d()
Get estimated (log-)hazard surface with 2 time scales
get_hazard_2d_LMM()
Get estimated (log-)hazard surface with 2 time scales
get_hr()
Get the Hazard Ratios with their Standard Errors
haz2ts_summary()
Summary function for object of class 'haz2ts'
haz2tsLMM_summary()
Summary function for object of class 'haz2tsLMM'

Plotting functions

plot(<haz1ts>)
Plot method for a haz1ts object.
plot(<haz1tsLMM>)
Plot method for a haz1ts object.
plot(<haz2ts>)
Plot method for a haz2ts object.
plot(<haz2tsLMM>)
Plot method for a haz2tsLMM object.
plot_slices()
Plot slices of the (log-) hazard
imageplot_2ts()
Image Plot of 2ts hazard
imageplot_SE()
Image Plot of Standard Errors for the 2ts hazard
covariates_plot()
Plot of the covariates' effects

Competing risks functions

cumhaz2ts()
Cumulative hazard over two time scales
surv2ts()
Survival function with two time scales
cuminc2ts()
Cumulative incidence surface over two time scales