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multibias

Overview

The multibias package is used to adjust for multiple biases in causal inference when working with observational data. Bias here refers to the case when the associational estimate of effect does not equal the causal estimate of effect:

(P(Y=1|X=1,C=0)/P(Y=1|X=0,C=0))≠(P(YX=1=1)/P(YX=0=1))(P(Y=1|X=1,C=0) / P(Y=1|X=0,C=0)) \neq (P(Y^{X=1}=1) / P(Y^{X=0}=1))

The multibias_adjust() function outputs odds ratio estimates adjusted for any combination of: uncontrolled confounding (uc), exposure misclassification (em), outcome misclassification (om), and selection bias (sel).

The package also includes several dataframes that are useful for validating the bias adjustment methods. Each dataframe contains different combinations of bias as identified by the same prefixing system. For each bias combination, there is a dataframe with incomplete information (as would be encountered in the real world) (e.g., df_uc) and a dataframe with complete information that was used to derive the biased data (e.g., df_uc_source).

Installation 

# install from CRAN
install.packages("multibias")

# install from github using devtools
# library("devtools")
devtools::install_github("pcbrendel/multibias")

Getting started

  1. Represent the observed causal data as a data_observed object. Here you provide the data, specify the key variables, and list the biases present in the data. See list below for the different bias combinations that multibias can handle.
  2. Obtain one of the two sources for bias adjustment:
    1. Bias parameters - via the bias_params object. Values for these parameters could come from the literature, validation data, or expert opinion. Each parameter can be represented as a single value or as a probability distribution. See the bias_params documentation for the full bias models.
    2. Validation dataframe - via the data_validation object. The purpose of validation data is to use an external data source to transport the necessary causal relationships that are missing in the observed data.
  3. Run multibias_adjust() using the above inputs to obtain the bias-adjusted exposure-outcome odds ratio and confidence interval.

Possible bias adjustments

Single Bias

  • exposure misclassification
  • outcome misclassification
  • selection bias
  • uncontrolled confounding

Multiple Biases

  • exposure misclassification & selection bias
  • exposure misclassification & outcome misclassification
  • outcome misclassification & selection bias
  • uncontrolled confounding & exposure misclassificaiton
  • uncontrolled confounding & outcome misclassification
  • uncontrolled confounding & selection bias
  • uncontrolled confounding, exposure misclassification, & selection bias
  • uncontrolled confounding, outcome misclassification, & selection bias

Resources