Package index • TrialEmulation

User Functions

initiators() stable: A wrapper function to perform data preparation and model fitting in a sequence of emulated target trials

data_preparation() stable: Prepare data for the sequence of emulated target trials

trial_msm() stable: Fit the marginal structural model for the sequence of emulated trials

case_control_sampling_trials() stable: Case-control sampling of expanded data for the sequence of emulated trials

predict(): Predict marginal cumulative incidences with confidence intervals for a target trial population

print(<TE_weight_summary>): Print a weight summary object

summary(<TE_data_prep>) summary(<TE_data_prep_sep>) summary(<TE_data_prep_dt>) summary(<TE_msm>) summary(<TE_robust>): Summary methods

Data Sets

trial_example: Example of longitudinal data for sequential trial emulation

vignette_switch_data: Example of expanded longitudinal data for sequential trial emulation

te_data_ex: Example of a prepared data object

te_model_ex: Example of a fitted marginal structural model object

data_censored: Example of longitudinal data for sequential trial emulation containing censoring

New Interface Functions

Experimental functions for the new interface

trial_sequence() experimental: Create a sequence of emulated target trials object

set_data() experimental: Set the trial data

set_censor_weight_model() experimental: Set censoring weight model

set_switch_weight_model() experimental: Set switching weight model

calculate_weights() experimental: Calculate Inverse Probability of Censoring Weights

show_weight_models() experimental: Show Weight Model Summaries

ipw_data() `ipw_data<-`(): IPW Data Accessor and Setter

weight_model_data_indices(): Data used in weight model fitting

set_expansion_options() experimental: Set expansion options

set_outcome_model() experimental: Specify the outcome model

expand_trials() experimental: Expand trials

load_expanded_data() experimental: Method to read, subset and sample expanded data

outcome_data() `outcome_data<-`(): Outcome Data Accessor and Setter

fit_msm() experimental: Fit the marginal structural model for the sequence of emulated trials

Data Storage

Control how expanded data is stored

save_to_csv(): Save expanded data as CSV

save_to_duckdb(): Save expanded data to DuckDB

save_to_datatable(): Save expanded data as a data.table

Model fitters

stats_glm_logit(): Fit outcome models using stats::glm

parsnip_model(): Fit outcome models using parsnip models

Classes

trial_sequence-class trial_sequence_PP-class trial_sequence_ITT-class trial_sequence_AT-class: Trial Sequence class

te_data-class: TrialEmulation Data Class

te_datastore-class: te_datastore

save_expanded_data(<te_datastore_duckdb>) read_expanded_data(<te_datastore_duckdb>) sample_expanded_data(<te_datastore_duckdb>): te_datastore_duckdb, functions and methods

te_model_fitter-class: Outcome Model Fitter Class

te_outcome_data-class: TrialEmulation Outcome Data Class

te_outcome_fitted-class: Fitted Outcome Model Object

te_outcome_model-class: Fitted Outcome Model Object

Internal Methods

save_expanded_data(): Method to save expanded data

read_expanded_data(): Method to read expanded data

sample_expanded_data(): Internal method to sample expanded data

fit_weights_model(): Method for fitting weight models