impute_missing_values: Impute missing values in a dataframe and add missingness...

In ck37r: Chris Kennedy's R Toolkit

Description

Impute missing values, using knn by default or alternatively median-impute numerics, mode-impute factors. Add missingness indicators.

Usage

impute_missing_values(
  data,
  type = "standard",
  add_indicators = TRUE,
  prefix = "miss_",
  skip_vars = NULL,
  all_vars = FALSE,
  remove_constant = TRUE,
  remove_collinear = TRUE,
  values = NULL,
  h2o_glrm = NULL,
  glrm_k = 10L,
  verbose = FALSE
)

Arguments

data	Dataframe or matrix.
type	"knn" or "standard" (median/mode). NOTE: knn will result in the data being centered and scaled!
add_indicators	Add a series of missingness indicators.
prefix	String to add at the beginning of the name of each missingness indicator.
skip_vars	List of variable names to exclude from the imputation.
all_vars	Calculate imputation value for all variables, in cases where the imputation info may be used for future datasets.
remove_constant	Remove constant missingness indicators, if applicable.
remove_collinear	Remove collinear missingness indicators, if applicable.
values	Named list with imputation value to use from another dataset.
h2o_glrm	Optional h2o glrm model for imputing on new data (e.g. test set)
glrm_k	Number of principal components to estimate (up to the # of columns in the data).
verbose	If True display extra information during execution.

Value

List with the following elements:

• $data - imputed dataset.

• $impute_info - if knn, caret preprocess element for imputing test data.

• $impute_values - if standard, list of imputation values for each variable.

See Also

missingness_indicators preProcess

Examples

# Load a test dataset.
data(PimaIndiansDiabetes2, package = "mlbench")

# Check for missing values.
colSums(is.na(PimaIndiansDiabetes2))

# Impute missing data and add missingness indicators.
# Don't impute the outcome though.
result = impute_missing_values(PimaIndiansDiabetes2, skip_vars = "diabetes")

# Confirm we have no missing data.
colSums(is.na(result$data))


#############
# K-nearest neighbors imputation

result2 = impute_missing_values(PimaIndiansDiabetes2, type = "knn",
                                skip_vars = "diabetes")

# Confirm we have no missing data.
colSums(is.na(result2$data))

ck37r documentation built on Feb. 6, 2020, 5:09 p.m.