Description
Quantile G-Computation Extensions for Effect Measure Modification.
Description
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>.
README.md
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
- psi1 coefficient: effect of the mixture in the referent category of the effect measure modifier (
- 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
))
- 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,
- 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
))
- weights: proportion of positive/negative partial effect in the index stratum effect measure modifier (here,
- first set of weights/sum of negative/positive coefficients: - weights: proportion of positive/negative partial effect in the reference stratum effect measure modifier (here,
- 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
)