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In this example, we use the binary data from Schizophrenia data from
NIMH study, i.e. schizob, which is included in the package. As
described in Wang and Liu (2022),
the original response variable was in numerical scale. The binary
response was created using a cut-point of 3.5. The data is in a wide
format. Please note that all binary variables which is set to be imputed
should be converted into factor variables.
data(schizob)
head(schizob) %>% kbl(align = "c") %>%
kable_classic_2(full_width = F, html_font = "Cambria") %>%
column_spec(1, width = "2cm") %>%
add_header_above(c(" " = 1, "Responses at the baseline, week 1, week 3, and week 6" = 4))
| Responses at the baseline, week 1, week 3, and week 6 | ||||
|---|---|---|---|---|
| tx | y0 | y1 | y3 | y6 |
| 1 | 1 | 0 | 0 | 1 |
| 1 | 1 | 0 | 0 | 0 |
| 1 | 1 | 0 | 0 | NA |
| 1 | 0 | 0 | 0 | 0 |
| 0 | 1 | 1 | 1 | 1 |
| 1 | 1 | 1 | 1 | 1 |
Missing pattern is displayed in the following plot:
Figure 1. Missing pattern of Schizophrenia data
To impute missing values with logit model, we can set up family
argument, say, family = binomial(link = "logit"):
test = remiod(formula = y6 ~ tx + y0 + y1 + y3, data=schizob, family = binomial(link = "logit"),
trtvar = 'tx', algorithm = "jags", method = "MAR",
n.iter = 0, warn = FALSE, mess = FALSE)
print(test$mc.mar$models)
> y6 y3 y1 y0
"glm_binomial_logit" "glm_binomial_logit" "glm_binomial_logit" "glm_binomial_logit"
However, if probit models are the choice, argument models must be set
to accompany with family argument, like the following:
test.probit = remiod(formula = y6 ~ tx + y0 + y1 + y3, data=schizob, family = binomial(link = "probit"),
models = c(y0="glm_binomial_probit",y1="glm_binomial_probit",y3="glm_binomial_probit"),
trtvar = 'tx', algorithm = "jags", method = "MAR",
n.iter = 0, warn = FALSE, mess = FALSE)
print(test.probit$mc.mar$models)
> y6 y3 y1 y0
"glm_binomial_probit" "glm_binomial_probit" "glm_binomial_probit" "glm_binomial_probit"
Let’s run the Probit model with an adaptation of 10000 and 2000
iterations for 4 chains. Chains run in parallel, which is set through
doFuture package:
registerDoFuture()
plan(multisession(workers = 4))
bp.test = remiod(formula=y6 ~ tx + y0 + y1 + y3, data=schizob, family = binomial(link="probit"),
models = c(y0="glm_binomial_probit",y1="glm_binomial_probit",y3="glm_binomial_probit"),
n.iter = 2000, n.chains = 4, n.adapt = 10000, thin=1, mess=TRUE, warn=FALSE,
algorithm = "jags", trtvar = 'tx', method="MAR")
plan(sequential)
The following plot show the estimated intervals as shaded areas under
the posterior density curves for the parameters of treatment variable
tx in imputation models:
The specified set of parameters can be submitted through argument
subset with keyword selected_parms (alternatively, keyword
selected_vars, which will be available in the new release, can also be
used):
pms = c("beta[2]","alpha[2]","alpha[6]","alpha[9]")
mcsub = remiod:::get_subset(object = bp.test$mc.mar, subset=c(selected_parms = list(pms)))
color_scheme_set("purple")
mcmc_areas(
mcsub,
pars = pms,
prob = 0.95, # 95% intervals
prob_outer = 0.99, # 99%
point_est = "mean"
)
Figure 2. Intervals under the estimated posterior density curves for coefficients of tx in imputation models
Wang and Liu. 2022. “Remiod: Reference-Based Controlled Multiple Imputation of Longitudinal Binary and Ordinal Outcomes with Non-Ignorable Missingness.” arXiv 2203.02771.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.