Penalized regression methods, such as lasso and elastic net, are used in many biomedical applications when simultaneous regression coefficient estimation and variable selection is desired. However, missing data complicates the implementation of these methods, particularly when missingness is handled using multiple imputation. Applying a variable selection algorithm on each imputed dataset will likely lead to different sets of selected predictors, making it difficult to ascertain a final active set without resorting to ad hoc combination rules. ‘miselect’ presents Stacked Adaptive Elastic Net (saenet) and Grouped Adaptive LASSO (galasso) for continuous and binary outcomes. They, by construction, force selection of the same variables across multiply imputed data. ‘miselect’ also provides cross validated variants of these methods.

`miselect`

can installed from Github via

```
# install.packages("devtools")
devtools::install_github("umich-cphds/miselect", build_opts = c())
```

The Github version may contain bug fixes not yet present on CRAN, so if you are experiencing issues, you may want to try the Github version of the package.

Here is how to use cross validated `saenet`

. A nice
feature of `saenet`

is that you can cross validate over
`alpha`

without having to use `foldid`

.

```
library(miselect)
library(mice)
#>
#> Attaching package: 'mice'
#> The following objects are masked from 'package:base':
#>
#> cbind, rbind
set.seed(48109)
# Using the mice defaults for sake of example only.
mids <- mice(miselect.df, m = 5, printFlag = FALSE)
dfs <- lapply(1:5, function(i) complete(mids, action = i))
# Generate list of imputed design matrices and imputed responses
x <- list()
y <- list()
for (i in 1:5) {
x[[i]] <- as.matrix(dfs[[i]][, paste0("X", 1:20)])
y[[i]] <- dfs[[i]]$Y
}
# Calculate observational weights
weights <- 1 - rowMeans(is.na(miselect.df))
pf <- rep(1, 20)
adWeight <- rep(1, 20)
alpha <- c(.5 , 1)
# Since 'Y' is a binary variable, we use 'family = "binomial"'
fit <- cv.saenet(x, y, pf, adWeight, weights, family = "binomial",
alpha = alpha)
# By default 'coef' returns the betas for (lambda.min , alpha.min)
coef(fit)
#> (Intercept) X1 X2 X3 X4 X5
#> 0.07500679 1.48805119 0.57645656 0.00000000 1.79085524 0.05315903
#> X6 X7 X8 X9 X10 X11
#> 0.00000000 1.78466568 0.00000000 -0.01937788 0.00000000 1.29382032
#> X12 X13 X14 X15 X16 X17
#> 0.00000000 0.00000000 0.00000000 -0.14915055 0.00000000 0.28699265
#> X18 X19 X20
#> 0.00000000 -0.23440273 0.00000000
```

You can supply different values of `lambda`

and
`alpha`

. Here we use the `lambda`

and
`alpha`

selected by the one standard error rule

```
coef(fit, lambda = fit$lambda.1se, alpha = fit$alpha.1se)
#> (Intercept) X1 X2 X3 X4 X5
#> 0.1180812 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> X6 X7 X8 X9 X10 X11
#> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> X12 X13 X14 X15 X16 X17
#> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> X18 X19 X20
#> 0.0000000 0.0000000 0.0000000
```

If you encounter a bug, please open an issue on the Issues tab on Github or send us an email.

For questions or feedback, please email Jiacong Du at jiacong@umich.edu or Alexander Rix alexrix@umich.edu.

Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods. Jiacong Du, Jonathan Boss, Peisong Han, Lauren J Beesley, Stephen A Goutman, Stuart Batterman, Eva L Feldman, and Bhramar Mukherjee. 2020. arXiv:2003.07398