tests/testthat/test_rw.R

In surveil: Time Series Models for Disease Surveillance

iter = 100
data(msa)

dfw <- msa[grep("Dallas", msa$MSA), ]

context("stan_rw")
test_that("cor = FALSE works with stan_rw", {    
    fit <- stan_rw(
        data = dfw[grep("Hispanic", dfw$Race), ],
        time = Year,
        iter = iter,
        cor = FALSE,
        chains = 1
    )
    expect_s3_class(fit, "surveil")
})

test_that("cor = FALSE, family = bionomial works with stan_rw", {    
    fit <- stan_rw(
        data = dfw[grep("Hispanic", dfw$Race), ],
        time = Year,
        iter = iter,
        cor = FALSE,
        family = binomial(),
        chains = 1
    )
    expect_s3_class(fit, "surveil")
})

test_that("cor = TRUE works with stan_rw", {
    fit2 <- stan_rw(
        data = dfw,
        group = Race,
        time = Year,
        iter = iter,
        chains = 1,
        cor = TRUE        
    )
    expect_s3_class(fit2, "surveil")
})

test_that("cor = TRUE, family = binomial works with stan_rw", {
    fit2 <- stan_rw(
        data = dfw,
        group = Race,
        time = Year,
        iter = iter,
        chains = 1,
        cor = TRUE,
        family = binomial()
    )
    expect_s3_class(fit2, "surveil")
})


test_that("priors work: k = 1", {
    prior <- list()
    prior$eta_1 = normal(location = -5, scale = 5)
        fit <- stan_rw(
            data = dfw[grep("Hispanic", dfw$Race), ],
            prior = prior,
            time = Year,
            iter = iter,
            chains = 1
        )
    expect_s3_class(fit, "surveil")
})

test_that("priors work: k = 3", {
    prior <- list()
    prior$eta_1 = normal(location = -6, scale = 5, k = 3)
    prior$sigma <- normal(scale = 0.5, k = 3)
    prior$omega <- lkj(2)
        fit <- stan_rw(
            data = dfw,
            prior = prior,
            time = Year,
            group = Race,
            iter = iter,
            cor = TRUE,
            chains = 1
        )
    expect_s3_class(fit, "surveil")
})


test_that("group_diff works", {
    fit2 <- stan_rw(        
        dfw,
        group = Race,
        time = Year,
        iter = iter,
        chains = 1
        )
        x <- group_diff(fit2, "Black or African American", "White")
        expect_s3_class(x, "list")
    })


test_that("group_diff works, family = binomial", {
    fit2 <- stan_rw(        
        dfw,
        group = Race,
        time = Year,
        iter = iter,
        chains = 1,
        family = binomial()
        )
        x <- group_diff(fit2, "Black or African American", "White")
        expect_s3_class(x, "list")
    })


test_that("theil.surveil works", {
    fit <- stan_rw(        
        dfw,
        group = Race,
        time = Year,
        iter = iter,
        chains = 1
    )
    x <- theil(fit)
    expect_s3_class(x, "theil")
})

test_that("theil.list works", {
    fit <- stan_rw(        
        dfw,
        group = Race,
        time = Year,
        iter = iter,
        chains = 1
    )
    flist <- list(fit, fit, fit)
    x <- theil(flist)
    expect_s3_class(x, "theil_list")
})

test_that("stand_surveil works", {
    fit <- stan_rw(cancer,
               time = Year,
               group = Age,
               iter = iter,
               chains = 1
               )
    x = standardize(fit, label = standard$age, standard$standard_pop)
    expect_s3_class(x, "stand_surveil")
    })