Package index • TwoTimeScales

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'

predict_haz2ts_pointwise(): Point-wise prediction hazard 2 time scale

predict_haz2ts(): Prediction method for objects of class 'haz2ts'

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

predict_cif2ts_pointwise(): Point-wise prediction of cumulative incidence over 2 time scale

predict_comprisks2ts(): Predict overall survival and cumulative incidence functions