skrmdb: Package to estimate ED50

context("ReedMuench")

#All Good
test_that("examples work", {
  y    <- c(0, 1, 2, 3, 4)
  n    <- c(4, 4, 4, 4, 4)
  x    <- c(1, 2, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 3)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

# monotinicity
test_that("examples work", {
  y    <- c(0, 1, 2, 1, 4)
  n    <- c(4, 4, 4, 4, 4)
  x    <- c(1, 2, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 3.66666666666)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

# uneven
test_that("examples work", {
  y    <- c(0, 2, 3, 4)
  n    <- c(4, 4, 4, 4)
  x    <- c(1, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 3.2)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

# bracket
test_that("examples work", {
  y    <- c(0, 1, 2, 3, 4)
  n    <- c(8, 8, 8, 8, 8)
  x    <- c(1, 2, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 4.33333333)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

test_that("examples work", {
  y    <- c(4, 5, 6, 7, 8)
  n    <- c(8, 8, 8, 8, 8)
  x    <- c(1, 2, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 1.66666666666)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

# monotincity + reversed
test_that("examples work", {
  y    <- c(4, 1, 2, 1, 0)
  n    <- c(4, 4, 4, 4, 4)
  x    <- c(1, 2, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 2.3333333)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

# bracket + uneven
test_that("examples work", {
  y    <- c(0, 1, 2, 4)
  n    <- c(8, 8, 8, 8)
  x    <- c(1, 2, 3, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 4.4)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

test_that("examples work", {
  y    <- c(4, 5, 6, 8)
  n    <- c(8, 8, 8, 8)
  x    <- c(1, 2, 3, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 1.555555555)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

# monotinicity + bracket
test_that("examples work", {
  y    <- c(0, 1, 2, 1, 4)
  n    <- c(8, 8, 8, 8, 8)
  x    <- c(1, 2, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 4.63636363636)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

#  + reversed
test_that("examples work", {
  y    <- c(4, 1, 2, 1, 0) + 4
  n    <- c(8, 8, 8, 8, 8)
  x    <- c(1, 2, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 4.11111)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

# monotinicity + uneven
test_that("examples work", {
  y    <- c(0, 2, 1, 4)
  n    <- c(4, 4, 4, 4)
  x    <- c(1, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 4)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

#   + reversed
test_that("examples work", {
  y    <- c(4, 1, 2, 0)
  n    <- c(4, 4, 4, 4)
  x    <- c(1, 2, 3, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 2)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

# monotinicity + uneven + bracket
test_that("examples work", {
  y    <- c(0, 2, 1, 4)
  n    <- c(4, 4, 4, 4) + 4
  x    <- c(1, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 4.72727272)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

test_that("examples work", {
  y    <- c(4, 1, 3, 0)
  n    <- c(4, 4, 4, 4) + 4
  x    <- c(1, 2, 3, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 1.36363636)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

test_that("examples work", {
  y    <- c(0, 2, 1, 4) + 4
  n    <- c(4, 4, 4, 4) + 4
  x    <- c(1, 3, 4, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed   = 2)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})

test_that("examples work", {
  y    <- c(4, 1, 2, 0) + 4
  n    <- c(4, 4, 4, 4) + 4
  x    <- c(1, 2, 3, 5)
  dt   <- data.frame(dead = y, total = n, dil = x)
  resa <- suppressWarnings(ReedMuench(y = y, x = x, n = n))
  resb <- ReedMuench(y + n ~ x)
  resc <- ReedMuench(dead + total ~ dil, dt)
  res  <- list(eval = "Reed-Muench",
               ed = 4)

  expect_s3_class(resa, "skrmdb")
  expect_s3_class(resb, "skrmdb")
  expect_s3_class(resc, "skrmdb")
  expect_equal(resa$eval, res$eval)
  expect_equal(resb$eval, res$eval)
  expect_equal(resc$eval, res$eval)
  expect_equal(resa$ed, res$ed, tolerance = 0.0001)
  expect_equal(resb$ed, res$ed, tolerance = 0.0001)
  expect_equal(resc$ed, res$ed, tolerance = 0.0001)
})