tests/testthat/test-glm.R

In JointAI: Joint Analysis and Imputation of Incomplete Data

library("JointAI")

skip_on_cran()

cat("ON CRAN:", testthat:::on_cran(), "\n")

if (identical(Sys.getenv("NOT_CRAN"), "true")) {
  set_seed(1234)
  wideDF <- JointAI::wideDF

  # poisson variables
  wideDF$P1 <- rpois(nrow(wideDF), 3)
  wideDF$P2 <- rpois(nrow(wideDF), 2)
  wideDF$P2[sample.int(nrow(wideDF), 20)] <- NA

  # gamma variables
  wideDF$L1mis <- wideDF$L1
  wideDF$L1mis[sample.int(nrow(wideDF), 20)] <- NA

  wideDF$Be1 <- plogis(rnorm(nrow(wideDF)))
  wideDF$Be2 <- plogis(rnorm(nrow(wideDF)))
  wideDF$Be2[sample.int(nrow(wideDF), size = 20)] <- NA


  run_glm_models <- function() {
    sink(tempfile())
    on.exit(sink())
    invisible(force(suppressWarnings({

      models = list(
        # no covariates
        m0a1 = lm_imp(y ~ 1, data = wideDF, n.adapt = 5, n.iter = 10,
                      seed = 2020, warn = FALSE, mess = FALSE),
        m0a2 = glm_imp(y ~ 1, family = gaussian(link = "identity"),
                       data = wideDF, n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m0a3 = glm_imp(y ~ 1, family = gaussian(link = "log"),
                       data = wideDF, n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m0a4 = glm_imp(y ~ 1, family = gaussian(link = "inverse"),
                       data = wideDF, n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),

        m0b1 = glm_imp(B1 ~ 1, family = binomial(link = "logit"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m0b2 = glm_imp(B1 ~ 1, family = binomial(link = "probit"),
                       data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m0b3 = glm_imp(B1 ~ 1, family = binomial(link = "log"), data = wideDF,
                       n.adapt = 150, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m0b4 = glm_imp(B1 ~ 1, family = binomial(link = "cloglog"),
                       data = wideDF,
                       n.adapt = 50, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),

        m0c1 = glm_imp(L1 ~ 1, family = Gamma(link = "inverse"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m0c2 = glm_imp(L1 ~ 1, family = Gamma(link = "log"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),

        m0d1 = glm_imp(P1 ~ 1, family = poisson(link = "log"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m0d2 = glm_imp(P1 ~ 1, family = poisson(link = "identity"),
                       data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),

        m0e1 = lognorm_imp(L1 ~ 1, data = wideDF,
                           n.adapt = 5, n.iter = 10, seed = 2020,
                           warn = FALSE, mess = FALSE),
        m0f1 = betareg_imp(Be1 ~ 1, data = wideDF,
                           n.adapt = 5, n.iter = 10, seed = 2020,
                           warn = FALSE, mess = FALSE),

        # only complete
        m1a = lm_imp(y ~ C1, data = wideDF, n.adapt = 5, n.iter = 10,
                     seed = 2020, warn = FALSE, mess = FALSE),
        m1b = glm_imp(B1 ~ C1, data = wideDF, n.adapt = 5, n.iter = 10,
                      seed = 2020, family = binomial(),
                      warn = FALSE, mess = FALSE),
        m1c = glm_imp(L1 ~ C1, data = wideDF, n.adapt = 5, n.iter = 10,
                      seed = 2020, family = Gamma(),
                      warn = FALSE, mess = FALSE),
        m1d = glm_imp(P1 ~ C1, data = wideDF, n.adapt = 5, n.iter = 10,
                      seed = 2020, family = poisson(),
                      warn = FALSE, mess = FALSE),

        m1e = lognorm_imp(L1 ~ C1, data = wideDF,
                          n.adapt = 5, n.iter = 10, seed = 2020,
                          warn = FALSE, mess = FALSE),
        m1f = betareg_imp(Be1 ~ C1, data = wideDF,
                          n.adapt = 5, n.iter = 10, seed = 2020,
                          warn = FALSE, mess = FALSE),


        # only incomplete
        m2a = lm_imp(y ~ C2, data = wideDF, n.adapt = 5, n.iter = 10,
                     seed = 2020,
                     warn = FALSE, mess = FALSE),
        m2b = glm_imp(B2 ~ C2, data = wideDF, n.adapt = 5, n.iter = 10,
                      seed = 2020,
                      family = binomial(),
                      warn = FALSE, mess = FALSE),
        m2c = glm_imp(L1mis ~ C2, data = wideDF, n.adapt = 5, n.iter = 10,
                      seed = 2020,
                      family = Gamma(),
                      warn = FALSE, mess = FALSE),
        m2d = glm_imp(P2 ~ C2, data = wideDF, n.adapt = 5, n.iter = 10,
                      seed = 2020,
                      family = poisson(),
                      warn = FALSE, mess = FALSE),

        m2e = lognorm_imp(L1mis ~ C2, data = wideDF,
                          n.adapt = 5, n.iter = 10, seed = 2020,
                          warn = FALSE, mess = FALSE),
        m2f = betareg_imp(Be2 ~ C2, data = wideDF,
                          n.adapt = 5, n.iter = 10, seed = 2020,
                          warn = FALSE, mess = FALSE),


        # as covariate
        m3a = lm_imp(C1 ~ C2 + B2 + P2 + L1mis + Be2, data = wideDF,
                     n.adapt = 5, n.iter = 10, seed = 2020,
                     models = c(P2 = "glm_poisson_log",
                                L1mis = "glm_gamma_inverse",
                                Be2 = "beta"),
                     warn = FALSE, mess = FALSE),

        m3b = lm_imp(C1 ~ C2 + B2 + P2 + L1mis, data = wideDF,
                     n.adapt = 5, n.iter = 10, seed = 2020,
                     models = c(C2 = "glm_gaussian_inverse",
                                P2 = "glm_poisson_identity",
                                B2 = "glm_binomial_probit",
                                L1mis = "lognorm"),
                     warn = FALSE, mess = FALSE),

        m3c = lm_imp(C1 ~ C2 + B2 + P2 + L1mis, data = wideDF,
                     n.adapt = 5, n.iter = 10, seed = 2020,
                     models = c(C2 = "glm_gaussian_log",
                                P2 = "glm_poisson_identity",
                                L1mis = "glm_gamma_log",
                                B2 = "glm_binomial_log"),
                     warn = FALSE, mess = FALSE),

        m3d = lm_imp(C1 ~ C2 + B2 + P2 + L1mis + Be2, data = wideDF,
                     n.adapt = 5, n.iter = 10, seed = 2020,
                     trunc = list(Be2 = c(0, 1)),
                     models = c(C2 = "glm_gaussian_log",
                                P2 = "glm_poisson_identity",
                                L1mis = "glm_gamma_log",
                                B2 = "glm_binomial_log"),
                     warn = FALSE, mess = FALSE),

        # complex structures
        m4a = lm_imp(y ~ M2 + O2 * abs(C1 - C2) + log(C1), data = wideDF,
                     n.adapt = 5, n.iter = 10, seed = 2020,
                     warn = FALSE, mess = FALSE),

        m4b = glm_imp(B1 ~ L1mis + abs(C1 - C2) + log(Be2),
                      data = wideDF, n.adapt = 5, n.iter = 10, seed = 2020,
                      models = c(C2 = "glm_gaussian_log",
                                 L1mis = "glm_gamma_inverse",
                                 Be2 = "beta"),
                      family = binomial(),
                      warn = FALSE, mess = FALSE),

        # for prediction etc.
        m5a1 = lm_imp(y ~ C2 + B2 + B1 + O1, data = wideDF,
                      n.adapt = 5, n.iter = 10, seed = 2020,
                      warn = FALSE, mess = FALSE),
        m5a2 = glm_imp(y ~ C2 + B2 + B1 + O1, family = gaussian(link = "log"),
                       data = wideDF, n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m5a3 = glm_imp(y ~ C2 + B2 + B1 + O1,
                       family = gaussian(link = "inverse"),
                       data = wideDF, n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),

        m5b1 = glm_imp(B1 ~ C2 + B2 + C1 + O1,
                       family = binomial(link = "logit"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m5b2 = glm_imp(B1 ~ C2 + B2 + C1 + O1,
                       family = binomial(link = "probit"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m5b3 = glm_imp(B1 ~ C2 + B2 + C1 + O1,
                       family = binomial(link = "log"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m5b4 = glm_imp(B1 ~ C2 + B2 + C1 + O1,
                       family = binomial(link = "cloglog"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),

        m5c1 = glm_imp(L1 ~ C2 + B2 + B1 + O1,
                       family = Gamma(link = "inverse"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m5c2 = glm_imp(L1 ~ C2 + B2 + B1 + O1,
                       family = Gamma(link = "log"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),

        m5d1 = glm_imp(P1 ~ C2 + B2 + B1 + O1,
                       family = poisson(link = "log"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),
        m5d2 = glm_imp(P1 ~ C2 + B2 + B1 + O1,
                       family = poisson(link = "identity"), data = wideDF,
                       n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE),

        m5e1 = lognorm_imp(L1 ~ C2 + B2 + B1 + O1, data = wideDF,
                           n.adapt = 5, n.iter = 10, seed = 2020,
                           warn = FALSE, mess = FALSE),
        m5f1 = betareg_imp(Be1 ~ C2 + B2 + B1 + O1, data = wideDF,
                           n.adapt = 5, n.iter = 10, seed = 2020,
                           warn = FALSE, mess = FALSE),


        # from previous test files
        m6a = lm_imp(y ~ M2 + O2 * abs(C1 - C2) + log(C1), data = wideDF,
                     n.adapt = 5, n.iter = 5, seed = 2020,
                     warn = FALSE, mess = FALSE),
        m6b = glm_imp(B1 ~ M2 + O2 * abs(C1 - C2) +  log(C1), data = wideDF,
                      family = 'binomial', n.adapt = 5, n.iter = 5, seed = 2020,
                      warn = FALSE, mess = FALSE),
        m6c = glm_imp(C1 ~ M2 + O2 * abs(y - C2), data = wideDF,
                      family = Gamma(link = 'log'),
                      n.adapt = 5, n.iter = 5, seed = 2020,
                      warn = FALSE, mess = FALSE),
        m6d = lm_imp(SBP ~ age + gender + log(bili) + exp(creat),
                     trunc = list(bili = c(1e-5, 1e10)),
                     data = NHANES, n.adapt = 5, n.iter = 5, seed = 2020,
                     warn = FALSE, mess = FALSE),

        m6e = lm_imp(SBP ~ age + gender + log(bili) + exp(creat),
                     models = c(bili = 'lognorm', creat = 'lm'),
                     data = NHANES, n.adapt = 5, n.iter = 5, seed = 2020,
                     warn = FALSE, mess = FALSE),

        m6f = lm_imp(SBP ~ age + gender + log(bili) + exp(creat),
                     models = c(bili = 'glm_gamma_inverse', creat = 'lm'),
                     data = NHANES, n.adapt = 5, n.iter = 5, seed = 2020,
                     warn = FALSE, mess = FALSE),


        # from bug-fixes:
        # two-part trafo is pasted correctly
        mod7a = lm_imp(SBP ~ ns(age, df = 2) + gender + I(bili^2) + I(bili^3),
                       data = NHANES, n.adapt = 5, n.iter = 10, seed = 2020,
                       warn = FALSE, mess = FALSE)

      )
    }
    )))
    models
  }

  models <- run_glm_models()
  models0 <- set0_list(models)

  test_that("models run", {
    for (k in seq_along(models)) {
      expect_s3_class(models[[k]], "JointAI")
    }
  })


  test_that("models have the correct model and analysis model type", {
    for (i in seq_along(models)) {
      expect_false(any(sapply(compare_modeltype(models), isFALSE)))
    }
  })


  test_that("there are no duplicate betas/alphas in the jagsmodel", {
    expect_null(unlist(lapply(models, find_dupl_parms)))
  })

  test_that("MCMC is mcmc.list", {
    for (i in seq_along(models)) {
      expect_s3_class(models[[i]]$MCMC, "mcmc.list")
    }
  })


  test_that("MCMC samples can be plottet", {
    for (k in seq_along(models)) {
      expect_silent(traceplot(models[[k]]))
      expect_silent(densplot(models[[k]]))
      expect_silent(plot(MC_error(models[[k]])))
    }
  })

  test_that("data_list remains the same", {
    expect_snapshot(lapply(models, "[[", "data_list"))
  })

  test_that("jagsmodel remains the same", {
    skip_on_cran()
    expect_snapshot(lapply(models, "[[", "jagsmodel"))
  })

  test_that("GRcrit and MCerror give same result", {
    skip_on_cran()
    expect_snapshot(lapply(models0, GR_crit, multivariate = FALSE))
    expect_snapshot(lapply(models0, MC_error))
  })


  test_that("summary output remained the same", {
    skip_on_cran()
    expect_snapshot(lapply(models0, print))
    expect_snapshot(lapply(models0, coef))
    expect_snapshot(lapply(models0, confint))
    expect_snapshot(lapply(models0, summary, missinfo = TRUE))
    expect_snapshot(lapply(models0, function(x) coef(summary(x))))
  })



  test_that("prediction works", {
    for (k in seq_along(models)) {
      expect_s3_class(predict(models[[k]], type = "link", warn = FALSE)$fitted,
                      "data.frame")
      expect_s3_class(predict(models[[k]], type = "response",
                              warn = FALSE)$fitted,
                      "data.frame")
    }

    # prediction without specifying the type
    expect_s3_class(predict(models$m5a1, warn = FALSE)$fitted, "data.frame")

    # prediction with newdata
    ndf <- predDF(models$m5a1, vars = ~ C2)
    expect_s3_class(ndf, "data.frame")
    expect_s3_class(predict(models$m5a1, newdata = ndf, warn = FALSE)$fitted,
                    "data.frame")
  })



  test_that("residuals", {
    for (k in seq_along(models)[9:20]) {
      expect_type(residuals(models[[k]], type = "response"),
                  "double")

      if (models[[k]]$analysis_type == "beta") {
        expect_error(residuals(models[[k]], type = "working"))
        expect_error(residuals(models[[k]], type = "pearson"))
      } else {
        expect_type(residuals(models[[k]], type = "working"),
                    "double")
        expect_type(residuals(models[[k]], type = "pearson"),
                    "double")
      }
    }
    expect_type(residuals(models$m5a1), "double")
  })


  test_that("model can be plottet", {
    for (i in seq_along(models)) {
      if (models[[i]]$analysis_type %in% c("lognorm", "beta")) {
        expect_error(plot(models[[i]]))
      } else {
        expect_silent(plot(models[[i]]))
      }
    }
  })


  test_that("wrong models give errors", {

    # cauchit link is not implemented
    expect_error(glm_imp(B1 ~ 1, family = binomial(link = "cauchit"),
                         data = wideDF, seed = 2020,
                         warn = FALSE, mess = FALSE))

    # sqrt is not an allowed link (not implemented)
    expect_error(glm_imp(P1 ~ 1, family = poisson(link = "sqrt"), data = wideDF,
                         seed = 2020,
                         warn = FALSE, mess = FALSE))

    # gives JAGS model error (no dedicated error message)
    # glm_imp(time ~ 1, family = Gamma(link = "identity"), data = wideDF,
    #                 n.adapt = 5, n.iter = 10, seed = 2020)

    # no family specified
    expect_error(glm_imp(B1 ~ C1, data = wideDF, seed = 2020,
                         warn = FALSE, mess = FALSE))

    # unknown covariate model type
    expect_error(lm_imp(C1 ~ C2 + Be2, data = wideDF,
                        n.adapt = 5, n.iter = 10, seed = 2020,
                        models = c(Be2 = "betareg"),
                        warn = FALSE, mess = FALSE))
  })
}
# Sys.setenv(IS_CHECK = "")