Type:	Package
Title:	Identification of Counterfactual Queries in Causal Models
Version:	0.1.7
Maintainer:	Santtu Tikka <santtuth@gmail.com>
Description:	Facilitates the identification of counterfactual queries in structural causal models via the ID* and IDC* algorithms by Shpitser, I. and Pearl, J. (2007, 2008) <doi:10.48550/arXiv.1206.5294>, https://jmlr.org/papers/v9/shpitser08a.html. Provides a simple interface for defining causal diagrams and counterfactual conjunctions. Construction of parallel worlds graphs and counterfactual graphs is carried out automatically based on the counterfactual query and the causal diagram. See Tikka, S. (2023) <doi:10.32614/RJ-2023-053> for a tutorial of the package.
License:	GPL (≥ 3)
Encoding:	UTF-8
URL:	https://github.com/santikka/cfid
RoxygenNote:	7.2.3
Suggests:	covr, dagitty, igraph, mockery, testthat (≥ 3.0.0)
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2023-11-27 15:16:28 UTC; santikka
Author:	Santtu Tikka [aut, cre]
Repository:	CRAN
Date/Publication:	2023-11-27 16:00:04 UTC

The cfid package

Description

Identification of Counterfactual Queries in Causal Models

Details

This package provides tools necessary for identifying counterfactual queries in causal models. Causal graphs, counterfactual variables, and counterfactual conjunctions are defined via simple interfaces.

Counterfactuals

In simple terms, counterfactual are statements involving multiple conceptual "worlds" where the observed state of the worlds is different. As an example, consider two variables, Y = "headache", and X = "aspirin". A counterfactual statement could be "If I have a headache and did not take aspirin, would I not have a headache, had I taken aspirin instead". This statement involves two worlds: the real or "actual" world, where aspirin was not taken, and a hypothetical world, where it was taken. In more formal terms, this statement involves a counterfactual variable Y_x that attains two different values in two different worlds, forming a counterfactual conjunction: y_x \wedge y'_{x'}, where y and y' are two different values of Y, and x and x' are two different values of X.

Identifiability

Pearl's ladder of causation consists of the associational, interventional and counterfactual levels, with counterfactual being the highest level. The goal of identification is to find a transformation of a higher level query into a lower level one. For the interventional case, this transformation is known as causal effect identifiability, where interventional distributions are expressed in terms of observational quantities. Tools for this type of identification are readily available, such as in the causaleffect, dagitty, pcalg, and dosearch packages. Transformation from the highest counterfactual level, is more difficult, both conceptually and computationally, since to reach the observational level, we must first find a transformation of our counterfactual query into a interventional query, and then transform this yet again to observational. Also, there transformations may not always exist, for example in the presence of latent unobserved confounders, meaning that the queries are non-identifiable. This package deals with the first transformation, i.e., expressing the counterfactual queries in terms of interventional queries (and observational, when possible), as well as the second one, transforming interventional distributions to observational quantities.

Algorithms

Identification is carried out in terms of G and P_* and where G is a directed acyclic graph (DAG) depicting the causal model in question (a causal graph for short), and P_* is the set of all interventional distributions in causal models inducing G. Identification is carried out by the ID* and IDC* algorithms by Shpitser and Pearl (2008) which aim to convert the input counterfactual probability into an expression which can be represented solely in terms of interventional distributions. These algorithms are sound and complete, meaning that their output is always correct, and in the case of a non-identifiable counterfactual, one can always construct a counterexample, witnessing non-identifiability.

Graphs

The causal graph associated with the causal model is given via a simple text-based interface, similar to dagitty package syntax. Directed edges are given as X -> Y, and bidirected edges as ⁠X <-> Y⁠, which is a shorthand notation for latent confounders. For more details on graph construction, see dag().

Counterfactual variables and conjunctions

Counterfactual variables are defined by their name, value and the conceptual world that they belong to. A world is defined by a unique set of actions (interventions) via the do-operator (Pearl, 2009). We can define the two counterfactual variables of the headache/aspirin example as follows:

cf(var = "Y", obs = 0, sub = c(X = 0))
cf(var = "Y", obs = 1, sub = c(X = 1))

Here, var defines the name of the variable, obs gives level the variable is assigned to (not the actual value), and sub defines the vector of interventions that define the counterfactual world. For more details, see counterfactual_variable(). Counterfactual conjunctions on the other hand, are simply counterfactual statements (variables) that are observed at the same time. For more details, see counterfactual_conjunction().

For complete examples of identifiable counterfactual queries, see identifiable(), which is the main function of the package.

References

Tikka, S. (2023). Identifying counterfactual queries with the R package cfid. The R Journal, 15(2):330–343.

Pearl, J. (1995) Causal diagrams for empirical research. Biometrika, 82(4):669–688.

Pearl, J. (2009) Causality: Models, Reasoning, and Inference. Cambridge University Press, 2nd edition.

Shpitser, I. and Pearl, J. (2007). What counterfactuals can be tested. In Proceedings of the 23rd Conference on Uncertainty in Artificial Intelligence, 352–359.

Shpitser, I. and Pearl, J. (2008). Complete identification methods for the causal hierarchy. Journal of Machine Learning Research, 9(64):1941–1979.

Makhlouf, K., Zhioua, S. and Palamidessi, C. (2021). Survey on causal-based machine learning fairness notions. arXiv:2010.09553

Causal Effect Identification

Description

Identify a causal effect of the form P(y|do(x),z) from P(v) in G.

Usage

causal_effect(g, y, x = character(0), z = character(0), v = integer(0))

Arguments

Value

An object of class query which is a list with the following components:

• id
  A logical value that is TRUE if the query is identifiable and FALSE otherwise.

• formula
  A functional object expressing the causal effect in terms of the joint probability distribution P(v) for identifiable queries or NULL if the query is not identifiable.

• data
  The available data, for causal_effect this is always "observations"

• causaleffect
  The original query P(y|do(x),z) as a probability object.

• undefined
  A logical value, this is always FALSE for causaleffect

Counterfactual Conjunction

Description

conj defines a conjunction of counterfactual statements (variables).

cf defines a counterfactual variable y_x.

Usage

counterfactual_conjunction(...)

## S3 method for class 'counterfactual_conjunction'
format(x, var_sep = " /\\ ", ...)

## S3 method for class 'counterfactual_conjunction'
print(x, ...)

## S3 method for class 'counterfactual_conjunction'
e1 + e2

## S3 method for class 'counterfactual_conjunction'
x[i]

## S3 method for class 'counterfactual_variable'
e1 + e2

conj(...)

counterfactual_variable(var, obs = integer(0L), sub = integer(0L))

## S3 method for class 'counterfactual_variable'
format(x, use_primes = TRUE, ...)

## S3 method for class 'counterfactual_variable'
print(x, ...)

cf(var, obs = integer(0L), sub = integer(0L))

Arguments

Value

conj returns an object of class counterfactual_conjunction.

cf returns an object of class counterfactual_variable.

Counterfactual Conjunctions

A counterfactual conjunction is a conjunction (or a set in some contexts) of counterfactual statements that are assumed to hold simultaneously.

For example, the statement "The value of Y was observed to be y, and the value of Y was observed to be y' under the intervention do(X = x)" consists of two variables: variable Y without intervention, and Y under the intervention do(X = x) (which is Y_x). This conjunction can be succinctly written as y \wedge y'_x.

Conjunctions can also be constructed via the alias conj or iteratively from counterfactual_variable objects (see examples).

Counterfactual Variables

Assume that Y is a single variable and X is a vector of variables. Here, The notation y_x means that the variable Y (var) attains the value y (obs) under the intervention do(X = x) (sub).

Note that different values of obs for a two variables with the same var and the same sub do not denote their actual values, but the levels (i.e., obs = 0 is different from obs = 1, but the variables do not actually attain values 0 and 1). In other words, if var is different for two counterfactual variables, but they have the same value obs, this does not mean that these variables have the same value. They will only actually have the same value if they share both var and obs.

For more information about the do-operator, see Pearl (2009). The shortcut alias cf can also be used to construct counterfactual variables.

Examples

# The conjunction described under 'details'
v1 <- cf("Y", 0)
v2 <- cf("Y", 1, c("X" = 0))
c1 <- conj(v1, v2)

# Alternative construction
c1 <- v1 + v2

# Adding further variables
v3 <- cf("X", 1)
c2 <- c1 + v3

# A specific value of a variable (a unique combination of `var` and `sub`)
# can only appear once in a given conjunction,
# otherwise the conjunction would be trivially inconsistent
v4 <- cf("Y", 0, c("X" = 0))
v5 <- cf("Y", 1, c("X" = 0))
c3 <- try(conj(v4, v5))

# Y without an assigned value or any interventions
cf("Y")

# Y with a value assignment y, but no interventions
cf("Y", 0)

# Y with a different value y', but no interventions
cf("Y", 1)

# Y with the same value as the previous under the intervention do(X = x)
cf("Y", 1, c("X" = 0))

# Y with yet another value y'', under the intervention
# do(X = x', Z = z), i.e., the intervention on X has a different value
# than the previous (x != x') and Z is also assigned the value z
cf("Y", 2, c("X" = 1, "Z" = 0))

Directed Acyclic Graph

Description

Define a directed acyclic graph (DAG) describing the causal model.

Usage

dag(x, u = character(0L))

## S3 method for class 'dag'
print(x, ...)

Arguments

Details

The syntax for x follows the dagitty package closely for compatibility. However, not all features of dagitty graphs are supported. The resulting adjacency matrix of the definition is checked for cycles.

Directed edges are defined as X -> Y meaning that there is an edge from X to Y in the graph. Edges can be combined in sequence to create paths for concise descriptions, for example X -> Y <- Z -> W.

Unobserved latent confounders are defined using bidirected edges as ⁠X <-> Y⁠ which means that there is an additional variable U[X,Y] in the graph, and the edges X <- U[X,Y] -> Y, respectively.

Different statements in x can be distinguished from one another using either semicolons, line breaks, or spaces.

Subgraphs can be defined by enclosing the definition within curly braces. For example ⁠X -> {Y Z}⁠ defines an edge from X to both Y and Z. Individual statements within a subgraph can be separated by a comma or semicolon, but this is optional. Edges can also be defined within subgraphs, and subgraphs can be nested. For example, X -> {Z -> Y} is the same definition as ⁠X -> Z; X -> Y; Z -> Y⁠. Similarly ⁠X <-> {Z -> {A B}} -> Y⁠ is the same as ⁠X <-> {Z A B} -> Y; Z -> {A B}⁠.

Note that in the context of this package, vertex labels will always be converted into upper case, meaning that typing Z or z will always represent the same variable. This is done to enforce the notation of counterfactual variables, where capital letters denote variables and small letters denote their value assignments.

Value

An object of class dag, which is a square adjacency matrix with the following attributes:

• labels
  A character vector (or a list) of vertex labels.

• latent
  A logical vector indicating latent variables.

• order
  An integer vector giving a topological order for the vertices.

• text
  A character string giving representing the DAG. .

Examples

dag("X -> {Y Z} <- W <-> G")

# Subgraphs can appear on both sides of an edge
dag("{X Z} -> {Y W}")

# Semicolons can be used to distinguish individual statements
dag("X -> Z -> Y; X <-> Y")

# Commas can be used to distinguish variables within groups if there
# are no edges within the group
dag("{X, Y, Z} -> W")

# Edges within subgraphs is supported
dag("{X -> Z} -> {Y <-> W}")

# Nested subgraphs are supported
dag("{X -> {Z -> {Y <-> W}}}")

# Line breaks are also supported for statement separation
dag("
  Z -> W
  X -> Y
")

Export Graph

Description

Convert a valid graph object into a supported external format.

Usage

export_graph(
  g,
  type = c("dagitty", "causaleffect", "dosearch"),
  use_bidirected = TRUE,
  ...
)

Arguments

Value

If type is "dagitty", returns a dagitty object. If type is "causaleffect", returns an igraph graph, with its edge attributes set according to the causaleffect package syntax. If type is "dosearch", returns a character vector of length one that describes g in the dosearch package syntax.

Identifying Functional of a Counterfactual Query

Description

Identifying functionals are more complicated probabilistic expressions that cannot be expressed as simple observational or interventional probabilities using probability().

Usage

functional(sumset = NULL, terms = NULL, numerator = NULL, denominator = NULL)

## S3 method for class 'functional'
format(x, ...)

## S3 method for class 'functional'
print(x, ...)

Arguments

Details

When formatted via print or format, the arguments are prioritized in the following order if conflicting definitions are given: (sumset, terms), (numerator, denominator).

Value

An object of class functional, which is a list containing all of the arguments of the constructor.

A character representation of the functional object in LaTeX syntax.

Identify a Counterfactual Query

Description

Determine the identifiability of a (conditional) counterfactual conjunction.

Usage

identifiable(
  g,
  gamma,
  delta = NULL,
  data = c("interventions", "observations", "both")
)

Arguments

Details

To identify a non-conditional conjunction P(\gamma), the argument delta should be NULL.

To identify a conditional conjunction P(\gamma|\delta), both gamma and delta should be specified.

First, a parallel worlds graph is constructed based on the query. In a parallel worlds graph, for each do-action that appears in \gamma (and \delta) a copy of the original graph is created with the new observational variables attaining their post-interventional values but sharing the latent variables. This graph is known as a parallel worlds graph. From the parallel worlds graph, a counterfactual graph is derived such that each variable is unique, which might not be the case in a parallel worlds graph.

Finally, the ID* (or IDC*) algorithm is applied to determine identifiability of the query. Similar to the ID and IDC algorithms for causal effects, these algorithms exploit the so called c-component factorization to split the query into smaller subproblems, which are then solved recursively. If argument data is "observations" or "both", identification of interventional probabilities in the resulting functional is further attempted in terms of the joint probability distribution by using the ID and IDC algorithms (see causal_effect).

Value

An object of class query which is a list containing one or more of the following:

• id
  A logical value that is TRUE if the query is identifiable and FALSE otherwise from the available data in g. Note that in cases where gamma itself is inconsistent, the query will be identifiable, but with probability 0.

• formula
  An object of class functional giving the identifying functional of the query in LaTeX syntax via format or print, if identifiable. This expression is given in terms of the available data. Variables bound by summation are distinguished by a superscript asterisk. For tautological statements, the resulting probability is 1, and for inconsistent statements, the resulting probability is 0. For formatting options, see format.functional() and format.probability().

• undefined
  A logical value that is TRUE if a conditional conjunction p(\gamma|\delta) is undefined, for example when p(\delta) = 0, and FALSE otherwise.

• gamma
  The original counterfactual conjunction..

• delta
  The original conditioning counterfactual conjunction.

• data
  The original data.

See Also

dag(), counterfactual_variable(), probability(), functional()

Examples

# Examples that appears in Shpitser and Pearl (2008)
g1 <- dag("X -> W -> Y <- Z <- D X <-> Y")
g2 <- dag("X -> W -> Y <- Z <- D X <-> Y X -> Y")
v1 <- cf("Y", 0, c(X = 0))
v2 <- cf("X", 1)
v3 <- cf("Z", 0, c(D = 0))
v4 <- cf("D", 0)
c1 <- conj(v1)
c2 <- conj(v2, v3, v4)
c3 <- conj(v1, v2, v3, v4)

# Identifiable conditional conjunction
identifiable(g1, c1, c2)

# Identifiable conjunction
identifiable(g1, c3)

# Non-identifiable conjunction
identifiable(g2, c3)

Import Graph

Description

Import and construct a valid DAG from an external format. Accepts dagitty graphs, igraph graphs in the causaleffect package syntax, and character strings in the dosearch package syntax.

Usage

import_graph(x)

Arguments

Value

A dag object.

Symbolic Probability Distributions

Description

Defines an interventional or observational (conditional) probability P(y|do(x),z). For formatting options, see format.probability().

Usage

probability(val = NULL, var = NULL, do = NULL, cond = NULL)

## S3 method for class 'probability'
format(x, use_do = FALSE, ...)

## S3 method for class 'probability'
print(x, ...)

Arguments

Value

An object of class probability, which is a list containing all of the arguments of the constructor.

A character representation of the probability object in LaTeX syntax.

See Also

counterfactual_variable(), functional()

Examples

# Example from Makhlouf, Zhioua and Palamidessi (2021)
g2 <- dag("C -> A -> Y; C -> Y")
v1 <- cf("Y", 0, c(A = 1))
v2 <- cf("A", 0)
c1 <- conj(v1)
c2 <- conj(v2)
f <- identifiable(g2, c1, c2)$formula

# Default, using primes and subscript notation
format(f)

# Without primes, no do-operator
format(f, use_primes = FALSE)

# Primes, with do-operator
format(f, use_do = TRUE)

# Without primes, with do-operator
format(f, use_primes = FALSE, use_do = TRUE)

Query Objects

Description

Objects of class query describe the output of identifiable and causal_effect. They are list objects with a custom print method and contain data related to the identifiability results. See identifiable and causal_effect for details.

Usage

## S3 method for class 'query'
print(x, ...)

Arguments