tests/testthat/test.fill_missing.R

In ashiklom/mvtraits: Fit multivariate models to partially missing trait data

context("Fill missing data")

ss <- function(x, y) {
  sum((y - x) ^ 2)
}

# Simulate some data
rand <- random_data_multi(frac_miss = 0.50)
nparam <- length(rand$mu)

# Fill in missing data
dat_filled <- mvnorm_fill_missing(rand$dat, rand$mu, rand$sigma)

imputed <- dat_filled
imputed[!is.na(rand$dat)] <- NA

    mu_imp <- colMeans(imputed, na.rm = TRUE)
    Sigma_imp <- cov(imputed, use = 'pairwise.complete.obs')

test_that("Imputed values are close to true values", {
  expect_lt(ss(mu_imp, rand[["mu"]]), 0.05)
  expect_lt(ss(Sigma_imp, rand[["sigma"]]), 0.1)
})

## if (exists('doplot')) {
##     testplot <- function(i, j) {
##         plot(dat[,i], dat[,j], pch = '.')
##         points(imputed[,i], imputed[,j], pch = '.', col = 'red')
##         mixtools::ellipse(mu = mu[c(i,j)], sigma = sigma[c(i,j), c(i,j)], )
##     }
##     par(mfrow = c(nparam, nparam))
##     for (i in seq_len(nparam)) {
##         for (j in seq_len(nparam)) {
##             if (i == j) {
##                 plot(0, 0, type = 'n')
##             } else {
##                 testplot(i, j)
##             }
##         }
##     }
## }