tests/testthat/test-calc_QALY.R

In n8thangreen/QALY: Calculate Quality Adjusted Life Years (QALYs) Gains with Discounting and Inflated Costs

# context("Calculate QALYs")
#
#
# library(QALY)
# library(dplyr)
# library(memoise)
#
#
# test_that("Special case utilities", {
#
#   expect_equivalent(calc_QALY(utility = 0, intervals = 1), 0)
#   expect_equivalent(calc_QALY(utility = 1, intervals = 1), 1)
#
#   expect_equivalent(calc_QALY(utility = 0,
#                               intervals = 10) %>% unlist(),
#                     rep(0, 10))
#
#   expect_length(calc_QALY(utility = 1, intervals = 2) %>% unlist(), 2)
#   expect_equal(calc_QALY(utility = 1,
#                          intervals = 2,
#                          discount_rate = 0) %>% unlist(), c(1,1))
# })
#
# test_that("Discounting", {
#
#   discountfactor <- make_discount()
#
#   expect_equal(calc_QALY(utility = 1, intervals = 2) %>% unlist(),
#                c(discountfactor(), discountfactor()))
# })
#
# test_that("Population QALY calculation", {
#
#   # pop size 1
#   expect_equal(calc_QALY_population(utility = 0.9,
#                                     age = 20,
#                                     intervals = 1),
#                calc_QALY(utility = 0.9,
#                          age = 20,
#                          intervals = 1) %>% unlist())
#
#   # interval size 2
#   expect_equal(calc_QALY_population(utility = 0.9,
#                                     age = 20,
#                                     intervals = 2),
#                sum(calc_QALY(utility = 0.9,
#                              age = 20,
#                              intervals = 2) %>% unlist()))
#
#   # return list of yearly QALYs
#   expect_equal(calc_QALY_population(utility = 0.9,
#                                     age = 20,
#                                     intervals = 1,
#                                     sum_res = FALSE),
#                calc_QALY(utility = 0.9,
#                          age = 20,
#                          intervals = 1))
#
#   expect_equal(calc_QALY_population(utility = c(0.9, 0.9),
#                                     age = c(20, 20),
#                                     intervals = c(1,2),
#                                     sum_res = FALSE),
#                list(calc_QALY(utility = 0.9,
#                               age = 20,
#                               intervals = 1) %>% unlist(),
#                     calc_QALY(utility = 0.9,
#                               age = 20,
#                               intervals = 2) %>% unlist()))
#
#   # invariant
#   expect_equal(diff(calc_QALY_population(utility = c(0.9, 0.9),
#                                          age = c(20, 20),
#                                          intervals = c(1, 1))),
#                0)
#
#   expect_equal(calc_QALY_population(utility = c(1,1),
#                                     age = c(20, 20),
#                                     intervals = c(1, 1)),
#                c(0.87, 0.87))
#
#   expect_lt(calc_QALY_population(utility = 1,
#                                  age = 20,
#                                  intervals = 10),
#             calc_QALY_population(utility = 1,
#                                  age = 20,
#                                  intervals = 11))
#
#   expect_lt(calc_QALY_population(utility = 0.5,
#                                  age = 20,
#                                  intervals = 10),
#             calc_QALY_population(utility = 1,
#                                  age = 20,
#                                  intervals = 10))
#   # decreasing differences
#   expect_lt(diff(diff(calc_QALY_population(utility = c(1,1,1),
#                                            age = 20,
#                                            intervals = c(1, 2, 3)))),
#             0)
#
#
#   # expect_equivalent(calc_QALY_population(utility = list(c(0.9, 0.9),
#   #                                                       c(0.8, 0.8)),
#   #                                        age = c(20, 20),
#   #                                        intervals = c(2, 2)),
#   #                   c(1.513961, 1.317343))
#   #
#   # expect_equivalent(calc_QALY_population(utility = list(c(0.9, 0.9),
#   #                                                       c(0.8, 0.8)),
#   #                                        age = c(20, 20),
#   #                                        intervals = c(3, 3)),
#   #                   c( 2.232765, 1.942795))
#
#   expect_equivalent(calc_QALY_population(utility = list(c(0.9, 0.9),
#                                                         c(0.8, 0.8)),
#                                          age = c(20, 20),
#                                          intervals = c(1, 1)),
#                     calc_QALY_population(utility = list(0.9,
#                                                         0.8),
#                                          age = c(20, 20),
#                                          intervals = c(1, 1)))
#
#
# })
#
#
# test_that("compare with explicit calcs", {
#
#   expect_equivalent(calc_QALY(utility = 1,
#                               intervals = 3) %>% unlist(),
#                     c(1, 1/(1 + 0.035), 1/(1 + 0.035)^2))
# })
#
#
# test_that("sum_res", {
#
#   # single value
#   expect_equivalent(calc_QALY_population(utility = 0.9,
#                                          age = 20,
#                                          intervals = 1,
#                                          sum_res = TRUE),
#                     calc_QALY_population(utility = 0.9,
#                                          age = 20,
#                                          intervals = 1,
#                                          sum_res = FALSE) %>% unlist)
#
#   expect_equivalent(calc_QALY_population(utility = c(0.9,0.9),
#                                          age = 20,
#                                          intervals = c(1,2),
#                                          sum_res = TRUE),
#                     lapply(calc_QALY_population(utility = c(0.9,0.9),
#                                                 age = 20,
#                                                 intervals = c(1,2),
#                                                 sum_res = FALSE), sum) %>% unlist)
# })
#
#
# test_that("intervals as list", {
#
#   # constant intervals and single time_horizon
#   expect_equivalent(
#     calc_QALY_population(utility = list(c(0.9, 0.9),
#                                         c(0.8, 0.8)),
#                          age = c(20, 20),
#                          intervals = list(c(1,1),
#                                           c(1,1))),
#     calc_QALY_population(utility = list(c(0.9, 0.9),
#                                         c(0.8, 0.8)),
#                          age = c(20, 20),
#                          intervals = c(2, 2)))
#
#   # no discounting independent of start_delay
#   expect_equal(
#     calc_QALY(intervals = c(1,2),
#               utility = c(1,0.1),
#               age = NA,
#               start_delay = 0,
#               discount_rate = 0),
#     calc_QALY(intervals = c(1,2),
#               utility = c(1,0.1),
#               age = NA,
#               start_delay = 1,
#               discount_rate = 0))
#
#   expect_equal(
#     list(calc_QALY(intervals = c(1,1),
#                    utility = c(1,1),
#                    age = NA,
#                    start_delay = 1,
#                    discount_rate = 0) %>% unlist(),
#          calc_QALY(intervals = c(1,1),
#                    utility = c(1,1),
#                    age = NA,
#                    start_delay = 1,
#                    discount_rate = 0) %>% unlist()),
#     calc_QALY_population(
#       intervals = list(c(1,1),
#                        c(1,1)),
#       utility = list(c(1,1),
#                      c(1,1)),
#       age = NA,
#       start_delay = NA,
#       discount_rate = 0,
#       sum_res = FALSE
#     ))
#
#
#   # fractional time intervals
#   expect_equal(
#     calc_QALY(intervals = c(2, 1.2),
#               utility = c(1, 1),
#               age = NA,
#               start_delay = 0,
#               discount_rate = 0),
#     list(c(1,1), c(1,0.2)))
#
#   expect_error(
#     expect_equal(
#       calc_QALY(intervals = c(2, 1),
#                 utility = c(1, 1),
#                 age = NA,
#                 start_delay = 0,
#                 discount_rate = 0),
#       calc_QALY(intervals = c(2, 1.2),
#                 utility = c(1, 1),
#                 age = NA,
#                 start_delay = 0,
#                 discount_rate = 0)))
#
#   expect_equal(
#     calc_QALY(intervals = matrix(c(2.2, 3.3, 1.1), nrow = 1),
#               utility = c(1, 1, 1),
#               age = NA,
#               start_delay = 0,
#               discount_rate = 0),
#     calc_QALY(intervals = c(2.2, 3.3, 1.1),
#               utility = c(1, 1, 1),
#               age = NA,
#               start_delay = 0,
#               discount_rate = 0))
#
#   expect_equal(
#     calc_QALY(intervals = c(0.2, 1, 2.86),
#               utility = c(1, 1, 1),
#               age = NA,
#               start_delay = 0,
#               discount_rate = 0),
#     list(c(0.2), c(1), c(1,1,0.86)))
#
#   expect_equal(
#     calc_QALY(intervals = c(0.99, 0.5),
#               utility = c(1, 1),
#               age = NA,
#               start_delay = 0,
#               discount_rate = 0),
#     list(0.99,0.5))
#
#   expect_equal(calc_QALY(intervals = c(0.99),
#                          utility = c(1),
#                          age = NA,
#                          start_delay = 0,
#                          discount_rate = 0) %>% unlist(),
#                0.99)
#
# })
#