inst/tinytest/test-how_many_imputations.R

In howManyImputations: Calculate How many Imputations are Needed for Multiple Imputation

# basic results
library(mice)
data <- airquality
data[4:10, 3] <- rep(NA, 7)
data[1:5, 4] <- NA
data <- data[-c(5, 6)]
c <- capture.output(tempData <- mice(data, m = 5, maxit = 10, meth = "pmm"))
modelFit1 <- with(tempData, lm(Temp ~ Ozone + Solar.R + Wind))

hmi1 <- how_many_imputations(modelFit1)
expect_true(is(hmi1, "numeric"))
expect_true(hmi1 > 5)
expect_true(hmi1 < 500)

hmi2 <- how_many_imputations(pool(modelFit1))
expect_true(is(hmi2, "numeric"))
expect_equal(hmi1, hmi2)

hmi3 <- how_many_imputations(modelFit1, cv = .01)
expect_true(hmi1 < hmi3)

hmi4 <- how_many_imputations(modelFit1, alpha = .00001)
expect_true(hmi1 < hmi4)

expect_error(how_many_imputations(1),
             "must be")



# jomo
library(jomo)
library(mitools) # for the `imputationList` function
c <- capture.output(jomodata <- jomo1(airquality, nburn = 100,
                                      nbetween = 100, nimp = 5))
impdata2 <- imputationList(split(jomodata, jomodata$Imputation))
modelfit2 <- with(impdata2, lm(Temp ~ Ozone + Solar.R + Wind))
# Either can work:
hmi <- how_many_imputations(modelfit2)
expect_true(is(hmi, "numeric"))
expect_true(hmi > 5)
expect_true(hmi < 500)



# howManyImputations and how_many_imputations
library(mice)
data <- airquality
data[4:10, 3] <- rep(NA, 7)
data[1:5, 4] <- NA
data <- data[-c(5, 6)]
c <- capture.output(tempData <- mice(data, m = 5, maxit = 10, meth = "pmm"))
modelFit1 <- with(tempData, lm(Temp ~ Ozone + Solar.R + Wind))

hmi1 <- how_many_imputations(modelFit1)
hmi2 <- howManyImputations(modelFit1)
expect_identical(hmi1, hmi2)