Author: Yongshi Deng
Date: 2026-01-17

# mixgb: Multiple Imputation Through XGBoost

#### Yongshi Deng

#### 2026-01-17

## Introduction

The mixgb package provides a scalable approach to imputation for large data using XGBoost, subsampling, and predictive mean matching. It leverages XGBoost—an efficient implementation of gradient-boosted trees—to automatically capture complex interactions and non-linear relationships. Subsampling and predictive mean matching are incorporated to reduce bias and to preserve realistic imputation variability. The package accommodates a wide range of variable types and offers flexible control over subsampling and predictive matching settings.

We also recommend our package vismi (Visualisation Tools for Multiple Imputation), which offers a comprehensive set of diagnostics for assessing the quality of multiply imputed data.

## Impute missing values with `mixgb`

We first load the `mixgb` package and the `newborn` dataset, which contains 16 variables of various types (integer/numeric/factor/ordinal factor). There are 9 variables with missing values.

    library(mixgb)
    str(newborn)
    #> tibble [2,107 × 16] (S3: tbl_df/tbl/data.frame)
    #>  $ household_size                : int [1:2107] 4 3 5 4 4 3 5 3 3 3 ...
    #>  $ age_months                    : int [1:2107] 2 5 10 10 8 3 10 7 2 7 ...
    #>  $ sex                           : Factor w/ 2 levels "Male","Female": 2 1 2 2 1 1 2 2 2 1 ...
    #>  $ race                          : Factor w/ 3 levels "White","Black",..: 1 1 2 1 1 1 2 1 2 2 ...
    #>  $ ethnicity                     : Factor w/ 3 levels "Mexican-American",..: 3 1 3 3 3 3 3 3 3 3 ...
    #>  $ race_ethinicity               : Factor w/ 4 levels "Non-Hispanic White",..: 1 3 2 1 1 1 2 1 2 2 ...
    #>  $ head_circumference_cm         : num [1:2107] 39.3 45.4 43.9 45.8 44.9 42.2 45.8 NA 40.2 44.5 ...
    #>  $ recumbent_length_cm           : num [1:2107] 59.5 69.2 69.8 73.8 69 61.7 74.8 NA 64.5 70.2 ...
    #>  $ first_subscapular_skinfold_mm : num [1:2107] 8.2 13 6 8 8.2 9.4 5.2 NA 7 5.9 ...
    #>  $ second_subscapular_skinfold_mm: num [1:2107] 8 13 5.6 10 7.8 8.4 5.2 NA 7 5.4 ...
    #>  $ first_triceps_skinfold_mm     : num [1:2107] 9 15.6 7 16.4 9.8 9.6 5.8 NA 11 6.8 ...
    #>  $ second_triceps_skinfold_mm    : num [1:2107] 9.4 14 8.2 12 8.8 8.2 6.6 NA 10.9 7.6 ...
    #>  $ weight_kg                     : num [1:2107] 6.35 9.45 7.15 10.7 9.35 7.15 8.35 NA 7.35 8.65 ...
    #>  $ poverty_income_ratio          : num [1:2107] 3.186 1.269 0.416 2.063 1.464 ...
    #>  $ smoke                         : Factor w/ 2 levels "Yes","No": 2 2 1 1 1 2 2 1 2 1 ...
    #>  $ health                        : Ord.factor w/ 5 levels "Excellent"<"Very Good"<..: 1 3 1 1 1 1 1 1 2 1 ...
    colSums(is.na(newborn))
    #>                 household_size                     age_months
    #>                              0                              0
    #>                            sex                           race
    #>                              0                              0
    #>                      ethnicity                race_ethinicity
    #>                              0                              0
    #>          head_circumference_cm            recumbent_length_cm
    #>                            124                            114
    #>  first_subscapular_skinfold_mm second_subscapular_skinfold_mm
    #>                            161                            169
    #>      first_triceps_skinfold_mm     second_triceps_skinfold_mm
    #>                            124                            167
    #>                      weight_kg           poverty_income_ratio
    #>                            117                            192
    #>                          smoke                         health
    #>                              7                              0

To impute this dataset, we use the default settings. By default, the number of imputed datasets is set to `m = 5`. The data do not need to be converted to a `dgCMatrix` or one-hot encoded format, as these transformations are handled automatically by the package. Supported variable types include numeric, integer, factor, and ordinal factor.

    # use mixgb with default settings
    imp_list <- mixgb(data = newborn, m = 5)

### Customise imputation settings

We can also customise imputation settings:

- The number of imputed datasets `m`

- The number of imputation iterations `maxit`

- XGBoost hyperparameters and verbose settings. `xgb.params`, `nrounds`, `early_stopping_rounds`, `print_every_n` and `verbose`.

- Subsampling ratio. By default, `subsample = 0.7`. Users can change this value under the `xgb.params` argument.

- Predictive mean matching settings `pmm.type`, `pmm.k` and `pmm.link`.

- Whether ordinal factors should be converted to integer (imputation process may be faster) `ordinalAsInteger`

- Initial imputation methods for different types of variables `initial.num`, `initial.int` and `initial.fac`.

- Whether to save models for imputing newdata `save.models` and `save.vars`.

    set.seed(2026)
    # Use mixgb with chosen settings
    params <- list(
      max_depth = 5,
      subsample = 0.9,
      nthread = 2,
      tree_method = "hist"
    )

    imp_list <- mixgb(
      data = newborn, m = 10, maxit = 2,
      ordinalAsInteger = FALSE,
      pmm.type = "auto", pmm.k = 5, pmm.link = "prob",
      initial.num = "normal", initial.int = "mode", initial.fac = "mode",
      save.models = FALSE, save.vars = NULL,
      xgb.params = params, nrounds = 200, early_stopping_rounds = 10, print_every_n = 10L, verbose = 0
    )

### Tune hyperparameters

Imputation performance can be influenced by the choice of hyperparameters. While tuning a large number of hyperparameters may seem daunting, the search space can often be substantially reduced because many of them are correlated. In mixgb, the function `mixgb_cv()` is provided to tune the number of boosting rounds (`nrounds`). As XGBoost does not define a default value for `nrounds`, users must specify this parameter explicitly. The default setting in mixgb() is `nrounds = 100`; however, we recommend using `mixgb_cv()` to get an appropriate value first.

    params <- list(max_depth = 3, subsample = 0.7, nthread = 2)
    cv.results <- mixgb_cv(data = newborn, nrounds = 100, xgb.params = params, verbose = FALSE)
    cv.results$evaluation.log
    #>      iter train_rmse_mean train_rmse_std test_rmse_mean test_rmse_std
    #>     <int>           <num>          <num>          <num>         <num>
    #>  1:     1       1.2361129     0.01558786      1.2475935    0.06870012
    #>  2:     2       1.0176746     0.01717526      1.0424598    0.07874904
    #>  3:     3       0.8719048     0.02081757      0.9006647    0.08512384
    #>  4:     4       0.7729998     0.02320058      0.8114182    0.09141472
    #>  5:     5       0.7106921     0.02228392      0.7594188    0.09764968
    #>  6:     6       0.6681453     0.02403651      0.7214191    0.10517030
    #>  7:     7       0.6393555     0.02535016      0.6969163    0.10746088
    #>  8:     8       0.6172915     0.02457553      0.6825221    0.10873454
    #>  9:     9       0.5996640     0.02405186      0.6723316    0.10954086
    #> 10:    10       0.5873325     0.02603579      0.6640412    0.10883955
    #> 11:    11       0.5767323     0.02478809      0.6597094    0.11041219
    #> 12:    12       0.5696605     0.02529658      0.6550031    0.11278109
    #> 13:    13       0.5623289     0.02657183      0.6503620    0.11267360
    #> 14:    14       0.5576936     0.02601675      0.6485935    0.11352195
    #> 15:    15       0.5531543     0.02582060      0.6453916    0.11458535
    #> 16:    16       0.5492073     0.02539735      0.6439388    0.11370427
    #> 17:    17       0.5447605     0.02462400      0.6409097    0.11258197
    #> 18:    18       0.5399025     0.02563486      0.6400586    0.11189189
    #> 19:    19       0.5313389     0.02270545      0.6411977    0.11286770
    #> 20:    20       0.5292437     0.02296678      0.6421435    0.11267979
    #> 21:    21       0.5273530     0.02348606      0.6414809    0.11358972
    #> 22:    22       0.5251579     0.02400633      0.6411687    0.11479062
    #> 23:    23       0.5228063     0.02426503      0.6416890    0.11348986
    #> 24:    24       0.5184316     0.02286996      0.6424514    0.11329055
    #> 25:    25       0.5156545     0.02337316      0.6427545    0.11420816
    #> 26:    26       0.5121317     0.02295848      0.6436561    0.11287003
    #> 27:    27       0.5076351     0.02153164      0.6488316    0.10984152
    #> 28:    28       0.5037371     0.02142791      0.6492334    0.10992071
    #>      iter train_rmse_mean train_rmse_std test_rmse_mean test_rmse_std
    #>     <int>           <num>          <num>          <num>         <num>
    cv.results$response
    #> [1] "weight_kg"
    cv.results$best.nrounds
    #> [1] 18

By default, `mixgb_cv()` randomly selects an incomplete variable as the response and fits an XGBoost model using the remaining variables as predictors, based on the complete cases of the dataset. As a result, repeated runs of `mixgb_cv()` may yield different results. Users may instead explicitly specify the response variable and the set of covariates via the `response` and `select_features` arguments, respectively.

    cv.results <- mixgb_cv(
      data = newborn, nfold = 10, nrounds = 100, early_stopping_rounds = 1,
      response = "head_circumference_cm", select_features = c("age_months", "sex", "race_ethinicity", "recumbent_length_cm", "first_subscapular_skinfold_mm", "second_subscapular_skinfold_mm", "first_triceps_skinfold_mm", "second_triceps_skinfold_mm", "weight_kg"), xgb.params = params, verbose = FALSE
    )

    cv.results$best.nrounds
    #> [1] 16

We can then set `nrounds = cv.results$best.nrounds` in `mixgb()` to generate five imputed datasets.

    imp_list <- mixgb(data = newborn, m = 5, nrounds = cv.results$best.nrounds)

## Inspect multiply imputed values

Older version of mixgb package included a few visual diagnostic functions. These have now been removed from mixgb.

We recommend our standalone package vismi (Visualisation Tools for Multiple Imputation), which provides a comprehensive set of visual diagnostics for evaluating multiply imputed data.

For more details, please visit:

https://agnesdeng.github.io/vismi/

https://github.com/agnesdeng/vismi.