set.seed(123)
data("data", package = "ameras")
dosevars <- paste0("V", 1:10)


# Snapshot test
binomial_combos <- Filter(
  function(x) x$family == "binomial",
  snapshot_combinations
)

for (combo in binomial_combos) {
  label <- sprintf("%s_%s_deg%d", combo$family, combo$doseRRmod, combo$deg)

  test_that(paste("snapshot:", label), {
    fit <- fit_combination(
      family = combo$family,
      Y = combo$Y,
      doseRRmod = combo$doseRRmod,
      deg = combo$deg,
      X = "X1",
      M = NULL,
      data = data,
    )
    fit <- confint(fit, type = c("wald.orig", "percentile"))
    expect_snapshot_value(
      coef(fit),
      tolerance = 1e-4,
      style = "deparse"
    )
    expect_snapshot_value(fit$RC$sd, tolerance = 1e-4, style = "deparse")
    expect_snapshot_value(fit$RC$CI, tolerance = 1e-4, style = "deparse")
    expect_snapshot(print(summary(fit)$summary_table, digits = 2))
  })
}


# Test all non-RC methods with snapshot for a basic model
for (method in setdiff(all_methods, "RC")) {
  test_that(paste("binomial snapshot:", method), {
    if (method %in% c("ERC", "MCML", "BMA")) {
      skip_on_cran()
    }

    fit <- fit_combination(
      family = "binomial",
      Y = "Y.binomial",
      doseRRmod = "EXP",
      deg = 2,
      X = NULL,
      M = NULL,
      data = data,
      methods = method,
      niter.BMA = 1000,
      nburnin.BMA = 500
    )
    fit <- confint(fit, type = c("wald.orig", "percentile"))
    expect_snapshot_value(
      coef(fit),
      tolerance = 1e-4,
      style = "deparse"
    )
    expect_snapshot_value(fit[[method]]$sd, tolerance = 1e-4, style = "deparse")
    expect_snapshot_value(fit[[method]]$CI, tolerance = 1e-4, style = "deparse")
    expect_snapshot(print(summary(fit)$summary_table, digits = 2))
  })
}


# Basic no-error check for RC and all combinations of doseRRmod, deg, and lengths of X and M

for (combo in binomial_combos) {
  for (cov_combo in covariate_combinations) {
    X_label <- if (is.null(cov_combo$X)) {
      "NULL"
    } else {
      paste(cov_combo$X, collapse = "-")
    }
    M_label <- if (is.null(cov_combo$M)) {
      "NULL"
    } else {
      paste(cov_combo$M, collapse = "-")
    }
    label <- sprintf(
      "%s_%s_deg%d_X%s_M%s",
      combo$family,
      combo$doseRRmod,
      combo$deg,
      X_label,
      M_label
    )

    test_that(label, {
      expect_no_error({
        if (length(cov_combo$M) > 0) {
          fit_combination(
            family = combo$family,
            Y = combo$Y,
            deg = combo$deg,
            doseRRmod = combo$doseRRmod,
            X = cov_combo$X,
            M = cov_combo$M,
            data = data,
            methods = "RC",
            CI = "wald.orig",
            transform = transform1,
            transform.jacobian = transform1.jacobian,
            index.t = (length(cov_combo$X) + 2):(length(cov_combo$X) +
              length(cov_combo$M) * combo$deg +
              combo$deg +
              1)
          )
        } else {
          fit_combination(
            family = combo$family,
            Y = combo$Y,
            deg = combo$deg,
            doseRRmod = combo$doseRRmod,
            X = cov_combo$X,
            M = cov_combo$M,
            data = data,
            methods = "RC",
            CI = "wald.orig"
          )
        }
      })
    })
  }
}

# Test RC with all 45 combinations of doseRRmod, deg and lengths of X and M
#
# test_that("ameras binomial ERR deg=1 methods=RC X=c(X1,X2) M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1, methods="RC", X=c("X1","X2"), M=c("M1", "M2"), doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=4:6))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=c(X1,X2) M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=2, methods="RC", X=c("X1","X2"), M=c("M1", "M2"), doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=4:9))
# })
#
# test_that("ameras binomial ERR deg=1 methods=RC X=X1 M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=1, methods="RC", X=c("X1"), M=c("M1", "M2"), doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=3:5))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=X1 M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=2, methods="RC", X=c("X1"), M=c("M1", "M2"), doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=3:8))
# })
#
# test_that("ameras binomial ERR deg=1 methods=RC X=NULL M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=1, methods="RC", X=NULL, M=c("M1", "M2"), doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=2:4))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=NULL M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=2, methods="RC", X=NULL, M=c("M1", "M2"), doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=2:7))
# })
#
#
#
#
#
#
# test_that("ameras binomial ERR deg=1 methods=RC X=c(X1,X2) M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=1, methods="RC", X=c("X1","X2"), M="M1", doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=4:5))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=c(X1,X2) M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=2, methods="RC", X=c("X1","X2"), M="M1", doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=4:7))
# })
#
# test_that("ameras binomial ERR deg=1 methods=RC X=X1 M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=1, methods="RC", X=c("X1"), M="M1", doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=3:4))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=X1 M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=2, methods="RC", X=c("X1"), M="M1", doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=3:6))
# })
#
# test_that("ameras binomial ERR deg=1 methods=RC X=NULL M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=1, methods="RC", X=NULL, M="M1", doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=2:3))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=NULL M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=2, methods="RC", X=NULL, M="M1", doseRRmod="ERR", transform=transform1, transform.jacobian=transform1.jacobian, index.t=2:5))
# })
#
#
#
#
#
#
# test_that("ameras binomial ERR deg=1 methods=RC X=c(X1,X2) M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=1, methods="RC", X=c("X1","X2"), M=NULL, doseRRmod="ERR"))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=c(X1,X2) M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=2, methods="RC", X=c("X1","X2"), M=NULL, doseRRmod="ERR"))
# })
#
# test_that("ameras binomial ERR deg=1 methods=RC X=X1 M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=1, methods="RC", X=c("X1"), M=NULL, doseRRmod="ERR"))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=X1 M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=2, methods="RC", X=c("X1"), M=NULL, doseRRmod="ERR"))
# })
#
# test_that("ameras binomial ERR deg=1 methods=RC X=NULL M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial",  dosevars=dosevars, deg=1, methods="RC", X=NULL, M=NULL, doseRRmod="ERR"))
# })
#
# test_that("ameras binomial ERR deg=2 methods=RC X=NULL M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2, methods="RC", X=NULL, M=NULL, doseRRmod="ERR"))
# })
#
#
#
#
#
# #------------------------
#
#
# test_that("ameras binomial LINEXP   methods=RC X=c(X1,X2) M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,   methods="RC", X=c("X1","X2"), M=c("M1", "M2"), doseRRmod="LINEXP", transform=transform1, transform.jacobian=transform1.jacobian, index.t=4:9))
# })
#
# test_that("ameras binomial LINEXP   methods=RC X=X1 M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,  methods="RC", X=c("X1"), M=c("M1", "M2"), doseRRmod="LINEXP", transform=transform1, transform.jacobian=transform1.jacobian, index.t=3:8))
# })
#
#
# test_that("ameras binomial LINEXP   methods=RC X=NULL M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,  methods="RC", X=NULL, M=c("M1", "M2"), doseRRmod="LINEXP", transform=transform1, transform.jacobian=transform1.jacobian, index.t=2:7))
# })
#
#
#
#
#
#
# test_that("ameras binomial LINEXP   methods=RC X=c(X1,X2) M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,   methods="RC", X=c("X1","X2"), M="M1", doseRRmod="LINEXP", transform=transform1, transform.jacobian=transform1.jacobian, index.t=4:7))
# })
#
#
# test_that("ameras binomial LINEXP   methods=RC X=X1 M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,   methods="RC", X=c("X1"), M="M1", doseRRmod="LINEXP", transform=transform1, transform.jacobian=transform1.jacobian, index.t=3:6))
# })
#
#
# test_that("ameras binomial LINEXP   methods=RC X=NULL M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_warning(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,  methods="RC", X=NULL, M="M1", doseRRmod="LINEXP", transform=transform1, transform.jacobian=transform1.jacobian, index.t=2:5))
# })
#
#
#
#
#
#
#
# test_that("ameras binomial LINEXP   methods=RC X=c(X1,X2) M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,   methods="RC", X=c("X1","X2"), M=NULL, doseRRmod="LINEXP"))
# })
#
#
# test_that("ameras binomial LINEXP   methods=RC X=X1 M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,  methods="RC", X=c("X1"), M=NULL, doseRRmod="LINEXP"))
# })
#
# test_that("ameras binomial LINEXP   methods=RC X=NULL M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars,   methods="RC", X=NULL, M=NULL, doseRRmod="LINEXP"))
# })
#
#
# # ------------------------
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=c(X1,X2) M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1,  methods="RC", X=c("X1","X2"), M=c("M1", "M2"), doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=c(X1,X2) M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2,  methods="RC", X=c("X1","X2"), M=c("M1", "M2"), doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=X1 M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1, methods="RC", X=c("X1"), M=c("M1", "M2"), doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=X1 M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2,  methods="RC", X=c("X1"), M=c("M1", "M2"), doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=NULL M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1,  methods="RC", X=NULL, M=c("M1", "M2"), doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=NULL M=c(M1,M2)", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2, methods="RC", X=NULL, M=c("M1", "M2"), doseRRmod="EXP"))
# })
#
#
#
#
#
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=c(X1,X2) M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1,  methods="RC", X=c("X1","X2"), M="M1", doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=c(X1,X2) M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2, methods="RC", X=c("X1","X2"), M="M1", doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=X1 M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1,methods="RC", X=c("X1"), M="M1", doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=X1 M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2,  methods="RC", X=c("X1"), M="M1", doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=NULL M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1,  methods="RC", X=NULL, M="M1", doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=NULL M=M1", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2,  methods="RC", X=NULL, M="M1", doseRRmod="EXP"))
# })
#
#
#
#
#
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=c(X1,X2) M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1,  methods="RC", X=c("X1","X2"), M=NULL, doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=c(X1,X2) M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2,  methods="RC", X=c("X1","X2"), M=NULL, doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=X1 M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1,  methods="RC", X=c("X1"), M=NULL, doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=X1 M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2,  methods="RC", X=c("X1"), M=NULL, doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=1 methods=RC X=NULL M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=1,  methods="RC", X=NULL, M=NULL, doseRRmod="EXP"))
# })
#
# test_that("ameras binomial  EXP deg=2 methods=RC X=NULL M=NULL", {
#   data("data", package="ameras")
#   dosevars <- paste0("V",1:10)
#   expect_no_error(ameras(data=data, family="binomial", Y="Y.binomial", dosevars=dosevars, deg=2,  methods="RC", X=NULL, M=NULL, doseRRmod="EXP"))
# })
#
#
#