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Description

Quantile G-Computation Extensions for Effect Measure Modification.

G-computation for a set of time-fixed exposures with quantile-based basis functions, possibly under linearity and homogeneity assumptions. Effect measure modification in this method is a way to assess how the effect of the mixture varies by a binary, categorical or continuous variable. Reference: Alexander P. Keil, Jessie P. Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and Alexandra J. White (2019) A quantile-based g-computation approach to addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.

qgcompint: quantile g-computation with effect measure modification

Quick start

devtools::install_github("alexpkeil1/qgcompint")
library(qgcomp)
library(qgcompint)
 set.seed(40)
dat <- data.frame(y=runif(50),
                  x1=runif(50),
                  x2=runif(50),
                  z=rbinom(50,1,0.5),
                  r=rbinom(50,1,0.5))
	 
 # quantile g-computation without effect measure modification
 qfit <- qgcomp.noboot(f=y ~ z + x1 + x2, 
           expnms = c('x1', 'x2'), 
           data=dat, q=2, 
           family=gaussian())
 # no output given here          
	 
 # with effect measure modification by Z
 (qfitemm <- qgcomp.emm.noboot(f=y ~ z + x1 + x2,
           emmvar="z", 
           expnms = c('x1', 'x2'), 
           data=dat, q=2, 
           family=gaussian()))



> ## Qgcomp weights/partial effects at z = 0
> Scaled effect size (positive direction, sum of positive coefficients = 0)
> None

> Scaled effect size (negative direction, sum of negative coefficients = -0.278)
>    x2    x1 
> 0.662 0.338 

> ## Qgcomp weights/partial effects at z = 1
> Scaled effect size (positive direction, sum of positive effects = 0.0028)
> x1 
>  1 

> Scaled effect size (negative direction, sum of negative effects = -0.0128)
> x2 
>  1 

> Mixture slope parameters (Delta method CI):

> 			  Estimate Std. Error Lower CI Upper CI t value  Pr(>|t|)
> (Intercept)  0.58062    0.11142  0.36224  0.79900  5.2112 4.787e-06
> psi1        -0.27807    0.20757 -0.68490  0.12876 -1.3397    0.1872
> z           -0.10410    0.15683 -0.41148  0.20329 -0.6637    0.5103
> z:mixture    0.26811    0.26854 -0.25822  0.79444  0.9984    0.3235

> Estimate (CI), z=1: 
> -0.0099575 (-0.34389, 0.32398)
	

Current package capabilities/limitations

  • Single modifiers only (e.g. interaction terms between a modifier and the mixture can only be estimated for a single modifier at a time). This also implies that no interaction terms between the modifier and other covariates can be considered.
  • linear only specifications (i.e. linear effects of a mixture, but not covariates) for Cox model

Interpretation

  • coefficients
    • psi1 coefficient: effect of the mixture in the referent category of the effect measure modifier (z in this case)
    • z coefficient: main effect of the effect measure modifier (will change based on name of effect measure modifier)
    • z:mixture coefficient: interaction term between the effect measure modifier and the entire mixture
  • weights/partial effects (only given if effect measure modifier is binary)
    • first set of weights/sum of negative/positive coefficients: - weights: proportion of positive/negative partial effect in the reference stratum effect measure modifier (here, z=0)
      • partial effect: sum of main term coefficients for exposure in a given direction (these will sum to psi1, the effect estimate in the reference stratum effect measure modifier (here, z=0))
    • second set:
      • weights: proportion of positive/negative partial effect in the index stratum effect measure modifier (here, z=1)
      • partial effect: sum of main term coefficients + interaction term coefficients for exposure in a given direction (these will sum to the mixture effect estimate in the index stratum effect measure modifier (here, z=1))
  • Additional estimates (only given if effect measure modifier is binary): The effect of the mixture in the index category of the effect measure modifier (here, z=1)
Metadata

Version

0.7.0

License

Unknown

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