Impute new data with a saved mixgb imputer object
Usage
impute_new(
object,
newdata,
initial.newdata = FALSE,
pmm.k = NULL,
m = NULL,
verbose = FALSE
)Arguments
- object
A saved imputer object created by
mixgb(..., save.models = TRUE)- newdata
A data.frame or data.table. New data with missing values.
- initial.newdata
Whether to use the information from the new data to initially impute the missing values of the new data. By default, this is set to
FALSE, the original data passed tomixgb()will be used for initial imputation.- pmm.k
The number of donors for predictive mean matching. If
NULL(the default), thepmm.kvalue in the saved imputer object will be used.- m
The number of imputed datasets. If
NULL(the default), themvalue in the saved imputer object will be used.- verbose
Verbose setting for mixgb. If
TRUE, will print out the progress of imputation. Default:FALSE.
Examples
set.seed(2022)
n <- nrow(nhanes3)
idx <- sample(1:n, size = round(0.7 * n), replace = FALSE)
train.data <- nhanes3[idx, ]
test.data <- nhanes3[-idx, ]
params <- list(max_depth = 3, subsample = 0.7, nthread = 2)
mixgb.obj <- mixgb(
data = train.data, m = 2, xgb.params = params, nrounds = 10,
save.models = TRUE, save.models.folder = tempdir()
)
# obtain m imputed datasets for train.data
train.imputed <- mixgb.obj$imputed.data
train.imputed
#> [[1]]
#> age_months sex ethnicity head_circumference_cm
#> <int> <fctr> <fctr> <num>
#> 1: 2 Male Not Hispanic 40.70000
#> 2: 6 Male Not Hispanic 45.10000
#> 3: 4 Female Not Hispanic 43.00000
#> 4: 3 Male Mexican-American 43.00000
#> 5: 8 Male Mexican-American 42.70341
#> ---
#> 346: 4 Female Not Hispanic 42.30000
#> 347: 3 Female Not Hispanic 38.40000
#> 348: 10 Male Not Hispanic 45.20000
#> 349: 8 Male Not Hispanic 47.00000
#> 350: 7 Male Not Hispanic 48.20000
#> recumbent_length_cm weight_kg
#> <num> <num>
#> 1: 59.20000 6.400000
#> 2: 68.60000 8.050000
#> 3: 63.00000 7.800000
#> 4: 62.00000 6.200000
#> 5: 67.01804 7.270353
#> ---
#> 346: 65.80000 7.450000
#> 347: 58.00000 5.300000
#> 348: 75.90000 8.650000
#> 349: 74.70000 10.500000
#> 350: 72.50000 9.800000
#>
#> [[2]]
#> age_months sex ethnicity head_circumference_cm
#> <int> <fctr> <fctr> <num>
#> 1: 2 Male Not Hispanic 40.70000
#> 2: 6 Male Not Hispanic 45.10000
#> 3: 4 Female Not Hispanic 43.00000
#> 4: 3 Male Mexican-American 43.00000
#> 5: 8 Male Mexican-American 43.15326
#> ---
#> 346: 4 Female Not Hispanic 42.30000
#> 347: 3 Female Not Hispanic 38.40000
#> 348: 10 Male Not Hispanic 45.20000
#> 349: 8 Male Not Hispanic 47.00000
#> 350: 7 Male Not Hispanic 48.20000
#> recumbent_length_cm weight_kg
#> <num> <num>
#> 1: 59.20000 6.400000
#> 2: 68.60000 8.050000
#> 3: 63.00000 7.800000
#> 4: 62.00000 6.200000
#> 5: 66.67313 7.614265
#> ---
#> 346: 65.80000 7.450000
#> 347: 58.00000 5.300000
#> 348: 75.90000 8.650000
#> 349: 74.70000 10.500000
#> 350: 72.50000 9.800000
#>
# use the saved imputer to impute new data
test.imputed <- impute_new(object = mixgb.obj, newdata = test.data)
test.imputed
#> [[1]]
#> age_months sex ethnicity head_circumference_cm recumbent_length_cm
#> <int> <fctr> <fctr> <num> <num>
#> 1: 11 Male Not Hispanic 46.3 74.0
#> 2: 8 Male Not Hispanic 47.7 73.1
#> 3: 5 Male Not Hispanic 44.6 71.3
#> 4: 9 Female Not Hispanic 44.8 69.3
#> 5: 2 Female Not Hispanic 41.1 58.5
#> ---
#> 146: 8 Male Not Hispanic 47.1 71.8
#> 147: 7 Male Not Hispanic 46.3 70.0
#> 148: 4 Male Not Hispanic 44.4 66.7
#> 149: 6 Male Not Hispanic 43.1 67.8
#> 150: 7 Male Not Hispanic 46.8 73.6
#> weight_kg
#> <num>
#> 1: 9.50
#> 2: 9.75
#> 3: 7.90
#> 4: 7.65
#> 5: 5.85
#> ---
#> 146: 9.80
#> 147: 8.55
#> 148: 7.50
#> 149: 7.65
#> 150: 10.05
#>
#> [[2]]
#> age_months sex ethnicity head_circumference_cm recumbent_length_cm
#> <int> <fctr> <fctr> <num> <num>
#> 1: 11 Male Not Hispanic 46.3 74.0
#> 2: 8 Male Not Hispanic 47.7 73.1
#> 3: 5 Male Not Hispanic 44.6 71.3
#> 4: 9 Female Not Hispanic 44.8 69.3
#> 5: 2 Female Not Hispanic 41.1 58.5
#> ---
#> 146: 8 Male Not Hispanic 47.1 71.8
#> 147: 7 Male Not Hispanic 46.3 70.0
#> 148: 4 Male Not Hispanic 44.4 66.7
#> 149: 6 Male Not Hispanic 43.1 67.8
#> 150: 7 Male Not Hispanic 46.8 73.6
#> weight_kg
#> <num>
#> 1: 9.50
#> 2: 9.75
#> 3: 7.90
#> 4: 7.65
#> 5: 5.85
#> ---
#> 146: 9.80
#> 147: 8.55
#> 148: 7.50
#> 149: 7.65
#> 150: 10.05
#>