Author: Gregor de Cillia

# Model based Imputation Methods

#### Gregor de Cillia

This vignette showcases the functions `regressionImp()` and `rangerImpute()`, which can both be used to generate imputations for several variables in a dataset using a formula interface.

## Data

For data, a subset of `sleep` is used. The columns have been selected deliberately to include some interactions between the missing values.

    library(VIM)
    dataset <- sleep[, c("Dream", "NonD", "BodyWgt", "Span")]
    dataset$BodyWgt <- log(dataset$BodyWgt)
    dataset$Span <- log(dataset$Span)
    aggr(dataset)

    str(dataset)
    #> 'data.frame':    62 obs. of  4 variables:
    #>  $ Dream  : num  NA 2 NA NA 1.8 0.7 3.9 1 3.6 1.4 ...
    #>  $ NonD   : num  NA 6.3 NA NA 2.1 9.1 15.8 5.2 10.9 8.3 ...
    #>  $ BodyWgt: num  8.803 0 1.2194 -0.0834 7.8427 ...
    #>  $ Span   : num  3.65 1.5 2.64 NA 4.23 ...

## Imputation

In order to invoke the imputation methods, a formula is used to specify which variables are to be estimated and which variables should be used as regressors. We will start by imputing `NonD` based in `BodyWgt` and `Span`.

    imp_regression <- regressionImp(NonD ~ BodyWgt + Span, dataset)
    #> There still missing values in variable NonD . Probably due to missing values in the regressors.
    imp_ranger <- rangerImpute(NonD ~ BodyWgt + Span, dataset)
    aggr(imp_regression, delimiter = "_imp")

We can see that for `regrssionImp()` there are still missings in `NonD` for all observations where `Span` is unobserved. This is because the regression model could not be applied to those observations. The same is true for the values imputed via `rangerImpute()`.

## Diagnosing the results

As we can see in the next two plots, the correlation structure of `NonD` and `BodyWgt` is preserved by both imputation methods. In the case of `regressionImp()` all imputed values almost follow a straight line. This suggests that the variable `Span` had little to no effect on the model.

    imp_regression[, c("NonD", "BodyWgt", "NonD_imp")] |>
      marginplot(delimiter = "_imp")

For `rangerImpute()` on the other hand, `Span` played an important role in the generation of the imputed values.

    imp_ranger[, c("NonD", "BodyWgt", "NonD_imp")] |>
      marginplot(delimiter = "_imp")

    imp_ranger[, c("NonD", "Span", "NonD_imp")] |>
      marginplot(delimiter = "_imp")

## Imputing multiple variables

To impute several variables at once, the formula in `rangerImpute()` and `regressionImp()` can be specified with more than one column name in the left hand side.

    imp_regression <- regressionImp(Dream + NonD ~ BodyWgt + Span, dataset)
    #> There still missing values in variable Dream . Probably due to missing values in the regressors.
    #> There still missing values in variable NonD . Probably due to missing values in the regressors.
    imp_ranger <- rangerImpute(Dream + NonD ~ BodyWgt + Span, dataset)
    aggr(imp_regression, delimiter = "_imp")

Again, there are missings left for both `Dream` and `NonD`.

## Performance of method

In order to validate the performance of `regressionImp()` the `iris` dataset is used. Firstly, some values are randomly set to `NA`.

    library(reactable)

    data(iris)
    df <- iris
    colnames(df) <- c("S.Length","S.Width","P.Length","P.Width","Species")
    # randomly produce some missing values in the data
    set.seed(1)
    nbr_missing <- 50
    y <- data.frame(row=sample(nrow(iris),size = nbr_missing,replace = T),
                    col=sample(ncol(iris)-1,size = nbr_missing,replace = T))
    y<-y[!duplicated(y),]
    df[as.matrix(y)]<-NA

    aggr(df)

    sapply(df, function(x)sum(is.na(x)))
    #> S.Length  S.Width P.Length  P.Width  Species
    #>       12       10       13       12        0

We can see that there are missings in all variables and some observations reveal missing values on several points. In the next step we perform a multiple variable imputation and `Species` serves as a regressor.

    imp_regression <- regressionImp(S.Length + S.Width + P.Length + P.Width ~ Species, df)
    aggr(imp_regression, delimiter = "imp")

The plot indicates that all missing values have been imputed by the `regressionImp()` algorithm. The following table displays the rounded first five results of the imputation for all variables.