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Extending-TrialEmulation

Source: vignettes/Extending-TrialEmulation.Rmd
Extending-TrialEmulation.Rmd

Introduction

Due to the extensive use of classes, TrialEmulation can be expanded by the user to fit their own specific needs.

This document gives a quick overview of the extensible classes, the current implementations and the requirements for adding your own child classes.

This vignette describes two areas where new functionality could be implemented: regression model fitting and data storage.

Model fitters

Classes and Slots

Three classes are required implementing a model fitter:

  • te_model_fitter: Parent class. This class is virtual so no object can be created with this class. It exists to allow the definition of child classes.
    • @save_path A path to a directory for saving models
  • te_outcome_fitted: Parent class. This class contains the results of the fitting an outcome model. A class inheriting from te_outcome_fitted must be defined for a new model fitter implementation.
    • @model: A list containing the fitted model objects
    • @summary: A list of data frames containing a summary of the fitted model (tidy, glance) and the saved file (save_path)
  • te_weights_fitted: Parent class. This class contains the results of the fitting a weight model.
    • @label: A label which is supplied to the fitting function to describe the model
    • @summary: A list of data frames containing a summary of the fitted model (tidy, glance) and the saved file (save_path)
    • @fitted: The fitted values (predicted probabilities)

Currently only one model fitter class is implemented:

  • te_stats_glm_logit: Models are fit using stats::glm(..., family = binomial("logit"))
    • @save_path A path to a directory for saving models
  • te_stats_glm_logit_outcome_fitted: The results of fitting the pooled logistic regression model.
    • @model: list containing model, the result of glm(), and vcov, the robust covariance matrix
    • @summary: list of data frames tidy, glance and save_path

User Constructor

A user constructor is required to specify the model fitter type in set_censor_weight_model(), set_switch_weight_model() and set_outcome_model(). Each is specified independently. The user constructor should have arguments for any required model fitting (hyper-)parameters as well as a path for saving the model objects.

See stats_glm_logit() for a simple implementation.

Methods

There are 3 generic methods that are required when implementing a new model, fit_weights_model(), fit_outcome_model(), and predict().

fit_weights_model

This method uses the model object to fit a model for probability of censoring and returns the fitted probabilities which are later combined and used to construct the inverse probability of censoring weights. The method should also save the fitted model object to disk if a save path is specified.

  • Arguments
    • object: the te_model_fitter object
    • data: data.frame containing the outcome (here the censoring indicator) and covariate data
    • formula: the model formula
    • label: a character label describing the model to be attached to the result
  • Returns: a te_weights_fitted object containing a summary of the fitted model and the fitted probabilities.

fit_outcome_model

This method fits the outcome model. object, data, formula, weights = NULL - Arguments - object: the te_model_fitter object - data: data.frame containing the outcome and covariate data - formula: the model formula - weights: a numeric vector containing weights for all observations in data - Returns: The fitted model as an object inheriting from a te_outcome_fitted child class corresponding to the fitter model class used. This object contains a summary of the results as well as the raw result from the model.

predict

This method calculates the marginal survival or cumulative incidences based on the outcome model object. The method should take the baseline covariates and construct data for assigned_treatment = 0 and 1 as well as the follow up times given in predict_times.

  • Arguments
    • object: the fitted model object inheriting from te_outcome_fitted, eg te_stats_glm_logit_outcome_fitted
    • newdata: a data.frame containing baseline covariates to predict probabilities for
    • predict_times: a contiguous numeric vector of times to calculate predictions for
    • type: a string indicating the type of prediction to calculate: "cum_inc" or "survival"
    • conf_int: logical indicating whether or not to calculate the 95% confidence interval
    • samples: an integer giving the number of iterations used to calculate the confidence interval using a sampling approach
  • Returns: a list containing the predicted values for assigned treatment 0, 1 and the difference between them.

Data Stores

The sequence of target trials dataset is much larger than the input longitudinal data. If the original input data is already large compared to the available system memory, an alternative data storage mechanism might be desirable. Currently the package offers data.table, csv, and duckdb. Here we describe the implementation of “data stores”.

In order to add a new data store, a child class must be defined that inherits from class te_datastore. You must also add at least a new constructor save_to_xxx() as well as new methods for save_expanded_data() and read_expanded_data().

A new method for sample_expanded_data() is optional (e.g. in case sampling is not required or the implemented method for te_datastore is sufficient, see below under sample_expanded_data), but it will be necessary for large datasets.

Classes and Slots

  • te_datastore: Parent class, placed as a place holder in trial_sequence objects before setting expansion options, will be replaced with the corresponding child class when expansion options are set.
    • @N: Number of observations

Currently the following Data Store child classes are available for saving expanded data:

  • te_datastore_csv: Expanded data is saved as csv files, one file per trial period. When reading the data, only the files corresponding to the selected trial periods are read.
    • @path: Path to temp folder containing the csv files
    • @files: Paths to all available files
    • @template: empty data.frame, used as a template when reading the data to preserve types and attributes
    • @N: inherited from te_datastore
  • te_datastore_datatable: Expanded data is saved as a data.table in memory, only viable for smaller datasets.
    • @data: data.table containing expanded data
    • @N: inherited from te_datastore
  • te_datastore_duckdb: Expanded data is saved as a DuckDB file containing all trial periods. Reading, subsetting and sampling can be done efficiently with an SQL query (currently constructed with a translator helper function).
    • @path: Path of the DuckDB file
    • @table: The table name
    • @con: A duckdb connection object, used to query and write to the database
    • @N: inherited from te_datastore

User Constructor

The user constructor function is used in set_expansion_options() to replace the te_datastore object in trial_sequence@expansion@datastore with an object of the desired child class. The user constructor allows the user to specify any parameters required for the data store, such as file path, or username/password. Saving of the data happens later when calling expand_trials() which internally calls the corresponding save_expanded_data() method.

See the following currently available constructor functions for further insights: save_to_csv(), save_to_datatable(), save_to_duckdb()

Methods

There are four generic methods that are defined for the te_datastore class.

show

This method prints a simple summary or extract from the data. Note: Since the child classes differ quite significantly from each other, every child class has its own show method. There is no show method for the te_datastore parent class.

save_expanded_data

This method defines how the expanded data gets saved. Method is chosen based on the te_datastore child class. It gets called internally by expand_trials(). For large datasets save_expanded_data() may be called multiple times, so the method must be able to “append” data in some way.

  • Arguments
    • object: a te_datastore child class object
    • data: data.table to be saved to the data store
  • Returns: a modified te_datastore child class object

read_expanded_data

This method is used for reading the expanded data into memory. The data can be subset by period or any other subset condition. It gets called internally by load_expanded_data() if p_control isn’t specified, and by sample_expanded_data() if no specific sampling method exists for a te_datastore child class.

  • Arguments
    • object: a te_datastore child class object
    • period: “integerish” vector to select trial periods, if missing defaults to NULL and selects all available trial periods
    • subset_condition: subset condition as a string, if missing defaults to NULL and skips subsetting
  • Returns: a data.table object

sample_expanded_data

This method is used for reading and sampling the expanded data. The data can be subset by period or any other subset condition plus it can be sampled using the p_control argument. It gets called internally by load_expanded_data() if p_control is specified.

If no method for the child class exists, the method of the parent class will be used instead which will read and subset the data using read_expanded_data(). Then the sampling happens in bulk, which might cause problems for large datasets. For speed or memory reasons it might be necessary to implement a more efficient method for a new child class.

  • Arguments
    • object: a te_datastore child class object
    • p_control: numeric value between 0 and 1, probability to sample a control value
    • period: integerish vector to select trial periods, if missing defaults to NULL and selects all available trial periods
    • subset_condition: subset condition as a string, if missing defaults to NULL and skips subsetting
    • seed: a seed to be used for sampling, if missing sampling is randomised
  • Returns: a data.table object