Package 'tmle3mopttx'

Title: Targeted Maximum Likelihood Estimation of the Mean under Optimal Individualized Treatment
Description: This package estimates the optimal individualized treatment rule for the categorical treatment using Super Learner (sl3). In order to avoid nested cross-validation, it uses split-specific estimates of Q and g to estimate the rule as described by Coyle et al. In addition, it provides the Targeted Maximum Likelihood estimates of the mean performance using CV-TMLE under such estimated rules. This is an adapter package for use with the tmle3 framework and the tlverse software ecosystem for Targeted Learning.
Authors: Ivana Malenica [aut, cre] , Jeremy Coyle [aut, cph] , Mark van der Laan [aut, ths], Haodong Li [ctb]
Maintainer: Ivana Malenica <[email protected]>
License: GPL-3
Version: 1.0.0
Built: 2024-10-29 02:46:02 UTC
Source: https://github.com/tlverse/tmle3mopttx

Help Index

Make SL of multivariate learners

Description

Make SL of multivariate learners

Usage

create_mv_learners(learners)

Arguments

learners

List of learners supporting multivariate prediction.

Mock data set with Binary Treatment

Description

A dataset with a simple data structure O = (A, Y, W), where exposure (A) and outcome (Y) are binary. This is a simple dataset designed specifically to illustrate the TMLE estimation procedure.

Usage

data_bin

Format

A data.frame with 5 columns.

Y

A binary variable representing an outcome of interest.

A

A binary variable representing an intervention of interest.

W1

A continuous variable representing a covariate of interest.

W2

A continuous variable representing a covariate of interest.

W3

A continuous variable representing a covariate of interest.

Mock data set with Categorical Treatment

Description

A dataset with a simple data structure O = (A, Y, W), where outcome (Y) is binary and treatment (A) is categorical. This is a simple dataset designed specifically to illustrate the TMLE estimation procedure.

Usage

data_cat

Format

A data.frame with 6 columns.

Y

A binary variable representing an outcome of interest.

A

A binary variable representing an intervention of interest.

W1

A continuous variable representing a covariate of interest.

W2

A continuous variable representing a covariate of interest.

W3

A continuous variable representing a covariate of interest.

W4

A continuous variable representing a covariate of interest.

Mock data set with Categorical Treatment and rare treatment

Description

A dataset with a simple data structure O = (A, Y, W), where outcome (Y) is binary and treatment (A) is categorical, with one of the categories having low probability. This is a simple dataset designed specifically to illustrate the TMLE estimation procedure with realistic intervention.

Usage

data_cat_realistic

Format

A data.frame with 6 columns.

Y

A binary variable representing an outcome of interest.

A

A binary variable representing an intervention of interest.

W1

A categorical variable representing a covariate of interest.

W2

A categorical variable representing a covariate of interest.

W3

A categorical variable representing a covariate of interest.

W4

A categorical variable representing a covariate of interest.

Mock data set for Variable Importance Analysis with Categorical Treatment

Description

A dataset with a simple data structure O = (A, Y, W), where outcome (Y) is binary and treatment (A) is categorical. This is a simple dataset designed specifically to illustrate the TMLE estimation procedure.

Usage

data_cat_vim

Format

A data.frame with 6 columns.

Y

A binary variable representing an outcome of interest.

A

A binary variable representing an intervention of interest.

W1

A categorical variable representing a covariate of interest.

W2

A categorical variable representing a covariate of interest.

W3

A categorical variable representing a covariate of interest.

W4

A categorical variable representing a covariate of interest.

Dynamic Likelihood Factor

Description

Dynamic Likelihood Factor built on top of LF_base.

Format

An R6Class object inheriting from LF_base.

Value

LF_base object.

Super class

tmle3::LF_base -> LF_rule

Methods

Public methods

Inherited methods

Method new()

Usage
LF_rule$new(name, type = "density", rule_fun, ...)

Method get_mean()

Usage
LF_rule$get_mean(tmle_task, fold_number)

Method get_density()

Usage
LF_rule$get_density(tmle_task, fold_number)

Method cf_values()

Usage
LF_rule$cf_values(tmle_task)

Method clone()

The objects of this class are cloneable with this method.

Usage
LF_rule$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Normalize rows

Description

Normalize rows

Usage

normalize_rows(x)

Arguments

x

Values needed to be normalized.

Learns the Optimal Rule given a tmle_task and likelihood, using Q learning.

Description

Learns the Optimal Rule given a tmle_task and likelihood, using Q learning.

Learns the Optimal Rule given a tmle_task and likelihood, using Q learning.

Super class

tmle3::tmle3_Spec -> Optimal_Rule_Q_learning

Methods

Public methods

Inherited methods

Method new()

Usage
Optimal_Rule_Q_learning$new(tmle_task, likelihood, maximize = TRUE)

Method fit_blip()

Usage
Optimal_Rule_Q_learning$fit_blip()

Method rule()

Usage
Optimal_Rule_Q_learning$rule(tmle_task, fold_number = "full")

Method clone()

The objects of this class are cloneable with this method.

Usage
Optimal_Rule_Q_learning$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Learning the Optimal Rule using the Revere framework

Description

Functions used to learn the Optimal Rule given a tmle_task and likelihood, using the Revere framework. Complements 'tmle3_Spec_mopttx_blip_revere' class.

Format

An R6Class object inheriting from tmle3_Spec.

Value

A optimal rule object inheriting from tmle3_Spec with methods for learning the optimal rule. For a full list of the available functionality, see the complete documentation of tmle3_Spec.

Parameters

- tmle_task: Task object specifying the data and node structure. - tmle_spec: Spec object of tmle3. Allows for different Specs to use the current class for learning the Optimal Rule. - likelihood: Likelihood object of tmle3, corresponding to the current estimate of the required parts of the likelihood necessary for the target parameter. - V: User-specified list of covariates used to define the rule. - options: Information on all the variables passed to the original Spec.

Super class

tmle3::tmle3_Spec -> Optimal_Rule_Revere

Methods

Public methods

Inherited methods

Method new()

Usage
Optimal_Rule_Revere$new(
  tmle_task,
  tmle_spec,
  likelihood,
  V,
  options,
  shift_grid = seq(-1, 1, by = 0.5)
)

Method factor_to_indicators()

Usage
Optimal_Rule_Revere$factor_to_indicators(x, x_vals)

Method V_data()

Usage
Optimal_Rule_Revere$V_data(tmle_task, fold = NULL)

Method DR_full()

Usage
Optimal_Rule_Revere$DR_full(v, indx)

Method blip_revere_function()

Usage
Optimal_Rule_Revere$blip_revere_function(tmle_task, fold_number)

Method bound()

Usage
Optimal_Rule_Revere$bound(cv_g)

Method fit_blip()

Usage
Optimal_Rule_Revere$fit_blip()

Method rule()

Usage
Optimal_Rule_Revere$rule(tmle_task, fold_number = "full")

Method rule_stochastic()

Usage
Optimal_Rule_Revere$rule_stochastic(tmle_task, fold_number = "full")

Method clone()

The objects of this class are cloneable with this method.

Usage
Optimal_Rule_Revere$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
library(sl3)
library(tmle3)
library(data.table)

data("data_bin")
data <- data_bin

Q_lib <- make_learner_stack("Lrnr_mean", "Lrnr_glm_fast")
g_lib <- make_learner_stack("Lrnr_mean", "Lrnr_glm_fast")
B_lib <- make_learner_stack("Lrnr_glm_fast", "Lrnr_xgboost")

metalearner <- make_learner(Lrnr_nnls)
Q_learner <- make_learner(Lrnr_sl, Q_lib, metalearner)
g_learner <- make_learner(Lrnr_sl, g_lib, metalearner)
B_learner <- make_learner(Lrnr_sl, B_lib, metalearner)

learner_list <- list(Y = Q_learner, A = g_learner, B = B_learner)

node_list <- list(W = c("W1", "W2", "W3"), A = "A", Y = "Y")

tmle_spec <- tmle3_mopttx_blip_revere(
  V = c("W1", "W2", "W3"),
  type = "blip1", learners = learner_list, maximize = TRUE,
  complex = TRUE, realistic = TRUE
)

## End(Not run)

Treatment Specific Mean with names specifying the covariates the rule depends on.

Description

Treatment Specific Mean with names specifying the covariates the rule depends on.

Format

An R6Class object inheriting from Param_base.

Value

TSP with name of the intervention specified.

Super class

tmle3::Param_base -> Param_TSM_name

Methods

Public methods

Inherited methods

Method new()

Usage
Param_TSM_name$new(
  observed_likelihood,
  intervention_list,
  v = NULL,
  ...,
  outcome_node = "Y"
)

Method clever_covariates()

Usage
Param_TSM_name$clever_covariates(tmle_task = NULL, fold_number = "full")

Method estimates()

Usage
Param_TSM_name$estimates(tmle_task = NULL, fold_number = "full")

Method clone()

The objects of this class are cloneable with this method.

Usage
Param_TSM_name$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Q learning wrapper

Description

Q learning wrapper

Usage

Q_learning(tmle_spec_Q, learner_list, B = 1000, data, node_list)

Arguments

tmle_spec_Q

TMLE Spec initializing Q learning.
learner_list

List of algorithms used to fit Q
B

Number of bootstraps
data

Dataset used
node_list

List of nodes corresponding to Y, A and W.

Mean under the Optimal Individualized Treatment Rule

Description

O=(W,A,Y) W=Covariates A=Treatment (binary or categorical) Y=Outcome (binary or bounded continuous)

Usage

tmle3_mopttx_blip_revere(
  V = NULL,
  type = "blip1",
  learners,
  maximize = TRUE,
  complex = TRUE,
  realistic = FALSE,
  resource = 1,
  interpret = FALSE,
  likelihood_override = NULL,
  reference = NULL
)

Arguments

V

Covariates the rule depends on.
type

One of three psudo-blip versions developed to accommodate categorical treatment. "Blip1" corresponds to chosing a reference category, and defining the blip for all other categories relative to the specified reference. Note that in the case of binary treatment, "blip1" is just the usual blip. "Blip2$ corresponds to defining the blip relative to the average of all categories. Finally, "Blip3" corresponds to defining the blip relative to the weighted average of all categories.
learners

Library for Y (outcome), A (treatment), and B (blip) estimation.
maximize

Specify whether we want to maximize or minimize the mean of the final outcome.
complex

If TRUE, learn the rule using the specified covariates V. If FALSE, check if a less complex rule is better.
realistic

If TRUE, it will return a rule what is possible due to practical positivity constraints.
resource

Indicates the percent of initially estimated individuals who should be given treatment that get treatment, based on their blip estimate. If resource = 1 all estimated individuals to benefit from treatment get treatment, if resource = 0 none get treatment.
interpret

If TRUE, returns a HAL fit of the blip, explaining the rule.
likelihood_override

if estimates of the likelihood are known, override learners.
reference

reference category for blip1. Default is the smallest numerical category or factor.

Mean under the Optimal Individualized Treatment Rule, using Q learning

Description

O=(W,A,Y) W=Covariates A=Treatment (binary or categorical) Y=Outcome (binary or bounded continuous)

Usage

tmle3_mopttx_Q(maximize)

Arguments

maximize

Specify whether we want to maximize or minimize the mean of the final outcome.

Mean under the Optimal Individualized Treatment Rule

Description

O=(W,A,Y) W=Covariates A=Treatment (binary or categorical) Y=Outcome (binary or bounded continuous)

Usage

tmle3_mopttx_vim(
  V = NULL,
  type = "blip2",
  method = "SL",
  learners = NULL,
  contrast = "linear",
  maximize = TRUE,
  complex = TRUE,
  realistic = FALSE,
  resource = 1,
  reference = NULL
)

Arguments

V

Covariates the rule depends on.
type

One of three psudo-blip versions developed to accommodate categorical treatment. "Blip1" corresponds to chosing a reference category, and defining the blip for all other categories relative to the specified reference. Note that in the case of binary treatment, "blip1" is just the usual blip. "Blip2$ corresponds to defining the blip relative to the average of all categories. Finally, "Blip3" corresponds to defining the blip relative to the weighted average of all categories.
method

Specifies which methodology to use for learning the rule. Options are "Q" for Q-learning, and "SL" for the Super-Learner approach using split-specific estimates.
learners

Library for Y (outcome), A (treatment), and B (blip) estimation.
contrast

Defined either a "linear" or "multiplicative" contrast for the delta method.
maximize

Specify whether we want to maximize or minimize the mean of the final outcome.
complex

If TRUE, learn the rule using the specified covariates V. If FALSE, check if a less complex rule is better.
realistic

If TRUE, it will return a rule what is possible due to practical positivity constraints.
resource

Indicates the percent of initially estimated individuals who should be given treatment that get treatment, based on their blip estimate. If resource = 1 all estimated individuals to benefit from treatment get treatment, if resource = 0 none get treatment.
reference

reference category for blip1. Default is the smallest numerical category or factor.

TMLE for the Mean Under the Optimal Individualized Rule

Description

The functions contained in the class define a TMLE for the Mean Under the Optimal Individualized Rule with Categorical Treatment, learned and estimated under Revere CV-TMLE. For learning the Optimal Rule, see 'Optimal_Rule_Revere' class.

Format

An R6Class object inheriting from tmle3_Spec.

Value

A tmle3 object inheriting from tmle3_Spec with methods for obtaining the TMLE for the Mean Under the Optimal Individualized Rule. For a full list of the available functionality, see the complete documentation of tmle3_Spec.

Parameters

- V: User-specified list of covariates used to define the rule. - type: Blip type, corresponding to different ways of defining the reference category in learning the blip; mostly applies to categorical treatment. Available categories include "blip1" (reference level of treatment), "blip2" (average level of treatment) and "blip3" (weighted average level of treatment). - learners: List of user-defined learners for relevant parts of the likelihood. - maximize: Should the average outcome be maximized of minimized? Default is maximize=TRUE. - complex: If TRUE, the returned mean under the Optimal Rule is based on the full set of covariates provided by the user (parameter "V"). If FALSE, simpler rules (including the static rules), are evaluated as well; the returned mean under the Optimal Rule is then a potentially more parsimonious rule, if the mean performance is similar. - realistic: If TRUE, the optimal rule returned takes into account the probability of treatment given covariates. - resource: Indicates the percent of initially estimated individuals who should be given treatment that get treatment, based on their blip estimate. If resource = 1 all estimated individuals to benefit from treatment get treatment, if resource = 0 none get treatment. - interpret: If TRUE, returns a HAL fit of the blip, explaining the rule. - reference: reference category for blip1. Default is the smallest numerical category or factor.

Super class

tmle3::tmle3_Spec -> tmle3_Spec_mopttx_blip_revere

Methods

Public methods

Inherited methods

Method new()

Usage
tmle3_Spec_mopttx_blip_revere$new(
  V = NULL,
  type,
  learners,
  maximize = TRUE,
  complex = TRUE,
  realistic = FALSE,
  resource = 1,
  interpret = FALSE,
  likelihood_override = NULL,
  reference = NULL,
  ...
)

Method vals_from_factor()

Usage
tmle3_Spec_mopttx_blip_revere$vals_from_factor(x)

Method make_tmle_task()

Usage
tmle3_Spec_mopttx_blip_revere$make_tmle_task(data, node_list, ...)

Method make_initial_likelihood()

Usage
tmle3_Spec_mopttx_blip_revere$make_initial_likelihood(
  tmle_task,
  learner_list = NULL
)

Method predict_rule()

Usage
tmle3_Spec_mopttx_blip_revere$predict_rule(tmle_task_new)

Method make_rules()

Usage
tmle3_Spec_mopttx_blip_revere$make_rules(V)

Method make_est_fin()

Usage
tmle3_Spec_mopttx_blip_revere$make_est_fin(fit, max, p.value = 0.35)

Method set_opt()

Usage
tmle3_Spec_mopttx_blip_revere$set_opt(opt)

Method set_rule()

Usage
tmle3_Spec_mopttx_blip_revere$set_rule(rule)

Method data_adapt_psi()

Usage
tmle3_Spec_mopttx_blip_revere$data_adapt_psi(data_tda, node_list, Qbar0)

Method get_blip_fit()

Usage
tmle3_Spec_mopttx_blip_revere$get_blip_fit()

Method get_blip_pred()

Usage
tmle3_Spec_mopttx_blip_revere$get_blip_pred(tmle_task, fold_number = "full")

Method make_params()

Usage
tmle3_Spec_mopttx_blip_revere$make_params(tmle_task, likelihood)

Method clone()

The objects of this class are cloneable with this method.

Usage
tmle3_Spec_mopttx_blip_revere$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
library(sl3)
library(tmle3)
library(data.table)

data("data_bin")
data <- data_bin

Q_lib <- make_learner_stack("Lrnr_mean", "Lrnr_glm_fast")
g_lib <- make_learner_stack("Lrnr_mean", "Lrnr_glm_fast")
B_lib <- make_learner_stack("Lrnr_glm_fast", "Lrnr_xgboost")

metalearner <- make_learner(Lrnr_nnls)
Q_learner <- make_learner(Lrnr_sl, Q_lib, metalearner)
g_learner <- make_learner(Lrnr_sl, g_lib, metalearner)
B_learner <- make_learner(Lrnr_sl, B_lib, metalearner)

learner_list <- list(Y = Q_learner, A = g_learner, B = B_learner)

node_list <- list(W = c("W1", "W2", "W3"), A = "A", Y = "Y")

tmle_spec <- tmle3_mopttx_blip_revere(
  V = c("W1", "W2", "W3"),
  type = "blip1", learners = learner_list, maximize = TRUE,
  complex = TRUE, realistic = TRUE
)

## End(Not run)

Defines the Mean Under the Optimal Individualized Rule with Categorical Treatment, estimated using Q learning (single step)

Description

Defines the Mean Under the Optimal Individualized Rule with Categorical Treatment, estimated using Q learning (single step)

Defines the Mean Under the Optimal Individualized Rule with Categorical Treatment, estimated using Q learning (single step)

Super class

tmle3::tmle3_Spec -> tmle3_Spec_mopttx_Q

Methods

Public methods

Inherited methods

Method new()

Usage
tmle3_Spec_mopttx_Q$new(maximize = TRUE, ...)

Method vals_from_factor()

Usage
tmle3_Spec_mopttx_Q$vals_from_factor(x)

Method make_initial_likelihood_glm()

Usage
tmle3_Spec_mopttx_Q$make_initial_likelihood_glm(tmle_task)

Method make_params()

Usage
tmle3_Spec_mopttx_Q$make_params(tmle_task, likelihood)

Method estimate()

Usage
tmle3_Spec_mopttx_Q$estimate(tmle_params, tmle_task)

Method clone()

The objects of this class are cloneable with this method.

Usage
tmle3_Spec_mopttx_Q$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Variable Importance with the Mean Under the Optimal Individualized Rule

Description

The functions contained in the class define a Variable Importance metric for the TMLE of the Mean Under the Optimal Individualized Rule with Categorical Treatment, learned and estimated under Revere CV-TMLE. For learning the Optimal Rule, see 'Optimal_Rule_Revere' class.

Format

An R6Class object inheriting from tmle3_Spec.

Value

A tmle3 object inheriting from tmle3_Spec with methods for obtaining the Variable Importance metric for the TMLE of the Mean Under the Optimal Individualized Rule. For a full list of the available functionality, see the complete documentation of tmle3_Spec.

Parameters

- V: User-specified list of covariates used to define the rule. - type: Blip type, corresponding to different ways of defining the reference category in learning the blip; mostly applies to categorical treatment. Available categories include "blip1" (reference level of treatment), "blip2" (average level of treatment) and "blip3" (weighted average level of treatment). - method: Either "SL" (for the TMLE estimate) or "Q" (for Q-learning). - learners: List of user-defined learners for relevant parts of the likelihood. - contrast: Defined either a "linear" or "multiplicative" contrast for the delta method. - maximize: Should the average outcome be maximized of minimized? Default is maximize=TRUE. - complex: If TRUE, the returned mean under the Optimal Rule is based on the full set of covariates provided by the user (parameter "V"). If FALSE, simpler rules (including the static rules), are evaluated as well; the returned mean under the Optimal Rule is then a potentially more parsimonious rule, if the mean performance is similar. - realistic: If TRUE, the optimal rule returned takes into account the probability of treatment given covariates. - resource: Indicates the percent of initially estimated individuals who should be given treatment that get treatment, based on their blip estimate. If resource = 1 all estimated individuals to benefit from treatment get treatment, if resource = 0 none get treatment.

Super classes

tmle3::tmle3_Spec -> tmle3mopttx::tmle3_Spec_mopttx_blip_revere -> tmle3_Spec_mopttx_vim

Methods

Public methods

Inherited methods

Method new()

Usage
tmle3_Spec_mopttx_vim$new(
  V = NULL,
  type = "blip2",
  method = "SL",
  learners = NULL,
  contrast = "linear",
  maximize = TRUE,
  complex = TRUE,
  realistic = FALSE,
  resource = 1,
  reference = NULL,
  ...
)

Method vals_from_factor()

Usage
tmle3_Spec_mopttx_vim$vals_from_factor(x)

Method make_tmle_task()

Usage
tmle3_Spec_mopttx_vim$make_tmle_task(data, node_list, ...)

Method set_opt()

Usage
tmle3_Spec_mopttx_vim$set_opt(opt)

Method make_params()

Usage
tmle3_Spec_mopttx_vim$make_params(tmle_task, likelihood)

Method clone()

The objects of this class are cloneable with this method.

Usage
tmle3_Spec_mopttx_vim$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
library(sl3)
library(tmle3)
library(data.table)

data("data_cat_vim")
data <- data_cat_vim
data$A <- as.integer(data$A)

lrn1 <- Lrnr_mean$new()
lrn2 <- Lrnr_glm_fast$new()
lrn3 <- Lrnr_glmnet$new()

Q_learner <- Lrnr_sl$new(learners = list(lrn1, lrn2, lrn3),
metalearner = Lrnr_nnls$new()
)

mn_metalearner <- make_learner(Lrnr_solnp,
loss_function = loss_loglik_multinomial,
learner_function = metalearner_linear_multinomial
)
g_learner <- make_learner(Lrnr_sl, list(lrn1, lrn3), 
mn_metalearner)

b_learner <- create_mv_learners(learners = list(lrn1, lrn2))

learner_list <- list(Y = Q_learner, A = g_learner, B = b_learner)

node_list <- list(W = c("W2", "W3", "W4"), 
A = c("A", "W1"), Y = "Y")

tmle_spec <- tmle3_mopttx_vim(
V = "W3", learners = learner_list, type = "blip2",
contrast = "multiplicative", maximize = FALSE,
method = "SL", complex = TRUE, realistic = FALSE
)

## End(Not run)

Get factors

Description

Get factors

Usage

vals_from_factor(x)

Arguments

x

Values from which we obtain factors.