Using multiple imputation with regmedint

## knitr configuration: http://yihui.name/knitr/options#chunk_options
library(knitr)
showMessage <- FALSE
showWarning <- TRUE
set_alias(w = "fig.width", h = "fig.height", res = "results")
opts_chunk$set(comment = "##", error= TRUE, warning = showWarning, message = showMessage,
               tidy = FALSE, cache = FALSE, echo = TRUE,
               fig.width = 7, fig.height = 7,
               fig.path = "man/figures")

Missing data is the norm in real-life data analysis. Multiple imputation via the mice package is a popular option in R. Here we introduce simple missingness and demonstrate use of regmedint along with mice.

Missing data generation

For demonstration purpose, missing data is introduced here.

set.seed(138087069)
library(regmedint)
library(tidyverse)
## Prepare dataset
data(vv2015)
vv2015 <- vv2015 %>%
    select(-cens) %>%
    ## Generate exposure-dependent missing of mediator
    mutate(logit_p_m_miss = -1 + 0.5 * x,
           p_m_miss = exp(logit_p_m_miss) / (1 + exp(logit_p_m_miss)),
           ## Indicator draw
           ind_m_miss = rbinom(n = length(p_m_miss), size = 1, prob = p_m_miss),
           m_true = m,
           m = if_else(ind_m_miss == 1L, as.numeric(NA), m))

Truth fit

Taking the advantage of the simulated setting, the true model is fit here.

regmedint_true <-
    regmedint(data = vv2015,
              ## Variables
              yvar = "y",
              avar = "x",
              mvar = "m_true",
              cvar = c("c"),
              eventvar = "event",
              ## Values at which effects are evaluated
              a0 = 0,
              a1 = 1,
              m_cde = 1,
              c_cond = 0.5,
              ## Model types
              mreg = "logistic",
              yreg = "survAFT_weibull",
              ## Additional specification
              interaction = TRUE,
              casecontrol = FALSE)
summary(regmedint_true)

Naive complete case analysis

regmedint_cca <- vv2015 %>%
    filter(!is.na(m)) %>%
    regmedint(data = .,
              ## Variables
              yvar = "y",
              avar = "x",
              mvar = "m",
              cvar = c("c"),
              eventvar = "event",
              ## Values at which effects are evaluated
              a0 = 0,
              a1 = 1,
              m_cde = 1,
              c_cond = 0.5,
              ## Model types
              mreg = "logistic",
              yreg = "survAFT_weibull",
              ## Additional specification
              interaction = TRUE,
              casecontrol = FALSE)
summary(regmedint_cca)

Multiple imputation

This specific data setting is a little tricky in that the outcome variable is a censored survival time variable. Here we will use a log transformed survival time.

library(mice)
vv2015_mod <- vv2015 %>%
    mutate(log_y = log(y)) %>%
    select(x,m,c,log_y,event)
## Run mice
vv2015_mice <- mice(data = vv2015_mod, m = 50, printFlag = FALSE)
## Object containig 50 imputed dataset
vv2015_mice

After creating such MI datasets, mediation analysis can be performed in each dataset.

## Fit in each MI dataset
vv2015_mice_regmedint <-
    vv2015_mice %>%
    ## Stacked up dataset
    mice::complete("long") %>%
    as_tibble() %>%
    mutate(y = exp(log_y)) %>%
    group_by(.imp) %>%
    ## Nested data frame
    nest() %>%
    mutate(fit = map(data, function(data) {
        regmedint(data = data,
                  ## Variables
                  yvar = "y",
                  avar = "x",
                  mvar = "m",
                  cvar = c("c"),
                  eventvar = "event",
                  ## Values at which effects are evaluated
                  a0 = 0,
                  a1 = 1,
                  m_cde = 1,
                  c_cond = 0.5,
                  ## Model types
                  mreg = "logistic",
                  yreg = "survAFT_weibull",
                  ## Additional specification
                  interaction = TRUE,
                  casecontrol = FALSE)
    })) %>%
    ## Extract point estimates and variance estimates
    mutate(coef_fit = map(fit, coef),
           vcov_fit = map(fit, vcov))
vv2015_mice_regmedint

The results can be combined using the mitools package.

regmedint_mi <- mitools::MIcombine(results = vv2015_mice_regmedint$coef_fit,
                                   variances = vv2015_mice_regmedint$vcov_fit)
regmedint_mi_summary <- summary(regmedint_mi)

Comparison

We can observe the MI estimtates are generally more in alignment with the true estimates than the complete-case analysis estimates.

cbind(true = coef(regmedint_true),
      cca = coef(regmedint_cca),
      mi = regmedint_mi_summary$results)


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regmedint documentation built on May 12, 2021, 9:06 a.m.