### Validate AR hhh4 via NE with identity W data("measlesWeserEms") ## fit with AR component as usual vaccdata <- matrix(measlesWeserEms@map$vacc2.2004, byrow = TRUE, nrow = nrow(measlesWeserEms), ncol = ncol(measlesWeserEms)) measlesModel <- list( ar = list(f = addSeason2formula(~1 + vacc2, S=2, period=52)), end = list(f = addSeason2formula(~1, S=1, period=52), offset = population(measlesWeserEms)), family = "NegBin1", data = list(vacc2 = vaccdata)) measlesFit <- hhh4(measlesWeserEms, measlesModel) ## now use an identity matrix as W in the NE component instead of AR measlesFit2 <- suppressWarnings( update(measlesFit, ar = list(f = ~-1), ne = list(f = measlesModel$ar$f, weights = diag(ncol(measlesWeserEms))), use.estimates = FALSE) ) ## compare fits test_that("AR-hhh4 agrees with using identity W in NE", { expect_equivalent(coef(measlesFit2), coef(measlesFit)) expect_equivalent(measlesFit2$cov, measlesFit$cov) expect_equal(logLik(measlesFit2), logLik(measlesFit)) expect_equal(fitted(measlesFit2), fitted(measlesFit)) })