Nothing
# mainly regression tests against old version of BCEA::evppi()
# from version <= 2.4.5
# versus new evppi() calling voi::evppi internally
# library(BCEA)
if (interactive()) library(testthat)
if (!requireNamespace("voi", quietly = TRUE)) {
stop(
"Package \"voi (>= 1.0.1)\" must be installed to use this function.",
call. = FALSE
)
}
test_that("GAM regression (default) with vaccine data", {
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
# Run the health economic evaluation using BCEA
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
# expect_length(inp, 2)
# expect_named(inp, c("mat", "parameters"))
# expect_type(inp, "list")
# EVPPI <- BCEA::evppi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat)
# save(EVPPI, file = "tests/testthat/testdata/EVPPI_GAM_default.RData")
load(file = test_path("testdata", "EVPPI_GAM_default.RData"))
EVPPI_voi <- evppi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat)
EVPPI_voi_orig <- voi::evppi(bcea_vacc[c("e","c","k")],
inputs = inp$mat,
pars = c("beta.1.", "beta.2."),
check = TRUE)
expect_s3_class(EVPPI, "evppi")
expect_length(EVPPI, 10)
expect_type(EVPPI, "list")
expect_s3_class(EVPPI_voi, "evppi")
expect_type(EVPPI_voi, "list")
expect_equivalent(EVPPI$evppi, EVPPI_voi$evppi, tolerance = 0.001)
expect_equivalent(EVPPI_voi_orig$evppi, EVPPI_voi$evppi, tolerance = 0.001)
expect_equivalent(EVPPI$k, EVPPI_voi$k, tolerance = 0.001)
expect_equivalent(EVPPI_voi_orig$k, EVPPI_voi$k, tolerance = 0.001)
expect_equivalent(EVPPI$evi, EVPPI_voi$evi, tolerance = 0.001)
expect_equivalent(EVPPI$index, EVPPI_voi$index)
expect_equivalent(EVPPI$fitted.costs, EVPPI_voi$fitted.costs, tolerance = 0.001)
expect_equivalent(EVPPI$fitted.effects, EVPPI_voi$fitted.effects, tolerance = 0.001)
expect_equivalent(EVPPI$select, EVPPI_voi$select)
##TODO: snapshot
# plot(EVPPI)
# plot(EVPPI_voi)
rm(EVPPI)
})
test_that("Strong & Oakley with vaccine data", {
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
expect_error(evppi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat, method = "so", n.blocks = 50),
regexp = "only works for single-parameter EVPPI")
# EVPPI.so <- BCEA::evppi(bcea_vacc, "beta.1.", inp$mat, method = "so", n.blocks = 50)
# save(EVPPI.so, file = "tests/testthat/testdata/EVPPI_so_default.RData")
load(file = test_path("testdata", "EVPPI_so_default.RData"))
EVPPI.so_voi <- evppi(bcea_vacc, "beta.1.", inp$mat, method = "so", n.blocks = 50)
expect_s3_class(EVPPI.so, "evppi")
expect_length(EVPPI.so, 6)
expect_type(EVPPI.so, "list")
expect_s3_class(EVPPI.so_voi, "evppi")
expect_type(EVPPI.so_voi, "list")
expect_equivalent(EVPPI.so$evppi, EVPPI.so_voi$evppi, tolerance = 0.001)
expect_equivalent(EVPPI.so$k, EVPPI.so_voi$k, tolerance = 0.001)
expect_equivalent(EVPPI.so$evi, EVPPI.so_voi$evi, tolerance = 0.001)
expect_equivalent(EVPPI.so$index, EVPPI.so_voi$index)
rm(EVPPI.so)
})
test_that("Sadatsafavi et al with vaccine data", {
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
# Run the health economic evaluation using BCEA
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
# voi::evppi only works for single-parameter EVPPI
# EVPPI.sad <- BCEA::evppi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat, method = "sad", n.seps = 1)
# save(EVPPI.sad, file = "tests/testthat/testdata/EVPPI_sad_default.RData")
# load(file = test_path("testdata", "EVPPI_sad_default.RData"))
# TODO: error
# EVPPI.sal <- BCEA::evppi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat, method = "sal", n.seps = 1)
expect_error(evppi(bcea_vacc, param_idx = c("beta.1.", "beta.2."), inp$mat, method = "sal", n.seps = 1),
regexp = "only works for single-parameter EVPPI")
# voiEVPPI.sad <- voi::evppi(outputs = bcea_vacc[c("e","c","k")], inputs = inp$mat,
# pars = c("beta.1.", "beta.2."), method = "sal", n.seps = 1)
# EVPPI.sad <- BCEA::evppi(bcea_vacc, "beta.2.", inp$mat, method = "sad", n.seps = 1)
# save(EVPPI.sad, file = "tests/testthat/testdata/EVPPI_sad_default.RData")
load(file = test_path("testdata", "EVPPI_sad_default.RData"))
EVPPI.sad_voi <- evppi(bcea_vacc, "beta.2.", inp$mat, method = "sad", n.seps = 1)
EVPPI.sal_voi <- evppi(bcea_vacc, "beta.1.", inp$mat, method = "sal", n.seps = 1)
expect_s3_class(EVPPI.sad, "evppi")
expect_length(EVPPI.sad, 6)
expect_type(EVPPI.sad, "list")
expect_s3_class(EVPPI.sad_voi, "evppi")
expect_type(EVPPI.sad_voi, "list")
expect_equivalent(EVPPI.sad$evppi, EVPPI.sad_voi$evppi, tolerance = 0.001)
expect_equivalent(EVPPI.sad$k, EVPPI.sad_voi$k, tolerance = 0.001)
expect_equivalent(EVPPI.sad$evi, EVPPI.sad_voi$evi, tolerance = 0.001)
expect_equivalent(EVPPI.sad$index, EVPPI.sad_voi$index)
##TODO: snapshot
# plot(EVPPI.so)
# plot(EVPPI.sad)
# plot(EVPPI.so_voi)
# plot(EVPPI.sad_voi)
rm(EVPPI.sad)
})
test_that("Select parameters by position with vaccine data", {
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
# Run the health economic evaluation using BCEA
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
# evppi_idx <- BCEA::evppi(he = bcea_vacc, param_idx = 39:40, input = inp$mat)
# save(evppi_idx, file = "tests/testthat/testdata/EVPPI_idx.RData")
load(file = test_path("testdata", "EVPPI_idx.RData"))
evppi_idx_voi <- evppi(he = bcea_vacc, param_idx = 39:40, input = inp$mat)
expect_s3_class(evppi_idx, "evppi")
expect_length(evppi_idx, 10)
expect_type(evppi_idx, "list")
expect_s3_class(evppi_idx_voi, "evppi")
expect_type(evppi_idx_voi, "list")
})
test_that("INLA/SPDE with vaccine data", {
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
# Run the health economic evaluation using BCEA
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
skip_if_not_installed("INLA")
skip("INLA is crashing")
if (require("INLA")) {
# EVPPI_inla <- BCEA::evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "inla")
# save(EVPPI_inla, file = "tests/testthat/testdata/EVPPI_inla_default.RData")
load(file = test_path("testdata", "EVPPI_inla_default.RData"))
EVPPI_inla_voi <- evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "inla")
expect_s3_class(EVPPI_inla, "evppi")
expect_length(EVPPI_inla, 10)
expect_type(EVPPI_inla, "list")
expect_s3_class(EVPPI_inla_voi, "evppi")
expect_type(EVPPI_inla_voi, "list")
}
})
test_that("Different argument formats with vaccine data", {
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
# Run the health economic evaluation using BCEA
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
# GAM regression
# EVPPI_gam <- BCEA::evppi(he = bcea_vacc, param_idx = 39:40, input = inp$mat, method = "GAM")
# save(EVPPI_gam, file = "tests/testthat/testdata/EVPPI_gam.RData")
load(file = test_path("testdata", "EVPPI_gam.RData"))
# lower case method name
EVPPI_gam_voi <- evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "gam")
expect_s3_class(EVPPI_gam_voi, "evppi")
expect_type(EVPPI_gam_voi, "list")
expect_equivalent(EVPPI_gam$k, EVPPI_gam_voi$k, tolerance = 0.001)
expect_equivalent(EVPPI_gam$select, EVPPI_gam_voi$select)
# Strong et al GP regression
# EVPPI_gp <- BCEA::evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "GP")
# save(EVPPI_gp, file = "tests/testthat/testdata/EVPPI_gp.RData")
load(file = test_path("testdata", "EVPPI_gp.RData"))
# lower case method name
EVPPI_gp_voi <- evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "gp")
expect_s3_class(EVPPI_gp_voi, "evppi")
expect_type(EVPPI_gp_voi, "list")
# subsetting input PSA simulations
# set.seed(1234)
# EVPPI_psa <- BCEA::evppi(bcea_vacc, c("beta.1." , "beta.2."), inp$mat, N = 100)
# save(EVPPI_psa, file = "tests/testthat/testdata/EVPPI_psa.RData")
load(file = test_path("testdata", "EVPPI_psa.RData"))
set.seed(1234)
EVPPI_psa_voi <- evppi(bcea_vacc, c("beta.1." , "beta.2."), inp$mat, N = 100)
expect_equivalent(EVPPI_psa$select, EVPPI_psa_voi$select)
expect_equivalent(EVPPI_psa$evppi, EVPPI_psa_voi$evppi, tolerance = 0.001)
expect_equivalent(EVPPI_psa$k, EVPPI_psa_voi$k, tolerance = 0.001)
expect_equivalent(EVPPI_psa$evi, EVPPI_psa_voi$evi, tolerance = 0.001)
expect_equivalent(EVPPI_psa$index, EVPPI_psa_voi$index)
})
test_that("Mesh plotting with vaccine data", {
skip("plot = TRUE mesh plot to be snapshot")
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
# Run the health economic evaluation using BCEA
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
# # GAM regression (default)
# # plot not produced
# EVPPI <- BCEA::evppi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat, plot = TRUE)
# EVPPI_voi <- evppi_voi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat, plot = TRUE)
# EVPPI_voi_orig <- voi::evppi(bcea_vacc[c("e","c","k")], inputs = inp$mat, pars = c("beta.1.", "beta.2."), check = TRUE, plot_inla_mesh = TRUE)
#
# # INLA
# EVPPI_inla <- BCEA::evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "inla", plot = TRUE)
# EVPPI_inla_voi <- evppi_voi(he = bcea_vacc, 39:40, input = inp$mat, method = "inla", plot = TRUE)
})
test_that("Fitted values with vaccine data two parameters", {
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
# Run the health economic evaluation using BCEA
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
# GP
# set.seed(1234)
# EVPPI_gp_residuals <-
# BCEA::evppi(
# he = bcea_vacc,
# param_idx = 39:40,
# input = inp$mat,
# method = "gp",
# residuals = TRUE)
# save(EVPPI_gp_residuals, file = "tests/testthat/testdata/EVPPI_gp_residuals.RData")
load(file = test_path("testdata", "EVPPI_gp_residuals.RData"))
set.seed(1234)
EVPPI_gp_voi_residuals <-
evppi(
he = bcea_vacc,
param_idx = 39:40,
input = inp$mat,
method = "gp",
residuals = TRUE)
expect_equivalent(
EVPPI_gp_residuals$select,
EVPPI_gp_voi_residuals$select)
expect_equivalent(
EVPPI_gp_residuals$fitted.costs,
EVPPI_gp_voi_residuals$fitted.costs,
tolerance = 0.1)
expect_equivalent(
EVPPI_gp_residuals$fitted.effects,
EVPPI_gp_voi_residuals$fitted.effects,
tolerance = 0.1)
# SAD
# set.seed(1234)
# EVPPI_sad_residuals <-
# BCEA::evppi(
# he = bcea_vacc,
# param_idx = "beta.2.",
# input = inp$mat,
# method = "sad",
# residuals = TRUE)
# save(EVPPI_sad_residuals, file = "tests/testthat/testdata/EVPPI_sad_residuals.RData")
load(file = test_path("testdata", "EVPPI_sad_residuals.RData"))
set.seed(1234)
EVPPI_sad_voi_residuals <-
evppi(
he = bcea_vacc,
param_idx = "beta.2.",
input = inp$mat,
method = "sad",
residuals = TRUE)
# no fitted values returned
expect_null(EVPPI_sad_residuals$fitted.costs)
expect_null(EVPPI_sad_residuals$fitted.effects)
expect_null(EVPPI_sad_voi_residuals$fitted.costs)
expect_null(EVPPI_sad_voi_residuals$fitted.effects)
# GAM
# set.seed(1234)
# EVPPI_gam_residuals <-
# BCEA::evppi(
# he = bcea_vacc,
# param_idx = 39:40,
# input = inp$mat,
# method = "gam",
# residuals = TRUE)
# save(EVPPI_gam_residuals, file = "tests/testthat/testdata/EVPPI_gam_residuals.RData")
load(file = test_path("testdata", "EVPPI_gam_residuals.RData"))
set.seed(1234)
EVPPI_gam_voi_residuals <-
evppi(
he = bcea_vacc,
param_idx = 39:40,
input = inp$mat,
method = "gam",
residuals = TRUE)
expect_equivalent(
EVPPI_gam_residuals$fitted.costs,
EVPPI_gam_voi_residuals$fitted.costs,
tolerance = 0.001)
expect_equivalent(
EVPPI_gam_residuals$fitted.effects,
EVPPI_gam_voi_residuals$fitted.effects,
tolerance = 0.001)
skip_if_not_installed("INLA")
skip("INLA is crashing")
if (require("INLA")) {
# set.seed(1234)
# EVPPI_inla_residuals <- BCEA::evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "inla", residuals = TRUE)
# save(EVPPI_inla_residuals, file = "tests/testthat/testdata/EVPPI_inla_residuals.RData")
load(file = test_path("testdata", "EVPPI_inla_residuals.RData"))
set.seed(1234)
EVPPI_inla_voi_residuals <- evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "inla", residuals = TRUE)
expect_equivalent(
EVPPI_inla_residuals$select,
EVPPI_inla_voi_residuals$select)
expect_equivalent(
EVPPI_inla_residuals$fitted.costs,
EVPPI_inla_voi_residuals$fitted.costs,
tolerance = 0.1)
expect_equivalent(
EVPPI_inla_residuals$fitted.effects,
EVPPI_inla_voi_residuals$fitted.effects,
tolerance = 0.1)
}
})
test_that("Fitted values with vaccine data three parameters", {
data(Vaccine, package = "BCEA")
treats <- c("Status quo", "Vaccination")
# Run the health economic evaluation using BCEA
bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
inp <- createInputs(vaccine_mat, print_is_linear_comb = FALSE)
# GP
# set.seed(1234)
# EVPPI_gp_3_residuals <-
# BCEA::evppi(
# he = bcea_vacc,
# param_idx = 39:41,
# input = inp$mat,
# method = "gp",
# residuals = TRUE)
# save(EVPPI_gp_3_residuals, file = "tests/testthat/testdata/EVPPI_gp_3_residuals.RData")
load(file = test_path("testdata", "EVPPI_gp_3_residuals.RData"))
set.seed(1234)
EVPPI_gp_voi_residuals <-
evppi(
he = bcea_vacc,
param_idx = 39:41,
input = inp$mat,
method = "gp",
residuals = TRUE)
expect_equivalent(
EVPPI_gp_3_residuals$fitted.costs,
EVPPI_gp_voi_residuals$fitted.costs,
tolerance = 0.1)
expect_equivalent(
EVPPI_gp_3_residuals$fitted.effects,
EVPPI_gp_voi_residuals$fitted.effects,
tolerance = 0.1)
# GAM
# set.seed(1234)
# EVPPI_gam_3_residuals <-
# BCEA::evppi(
# he = bcea_vacc,
# param_idx = 39:41,
# input = inp$mat,
# method = "gam",
# residuals = TRUE)
# save(EVPPI_gam_3_residuals, file = "tests/testthat/testdata/EVPPI_gam_3_residuals.RData")
load(file = test_path("testdata", "EVPPI_gam_3_residuals.RData"))
set.seed(1234)
EVPPI_gam_voi_residuals <-
evppi(
he = bcea_vacc,
param_idx = 39:41,
input = inp$mat,
method = "gam",
residuals = TRUE)
expect_equivalent(
EVPPI_gam_3_residuals$fitted.costs,
EVPPI_gam_voi_residuals$fitted.costs,
tolerance = 0.1)
expect_equivalent(
EVPPI_gam_3_residuals$fitted.effects,
EVPPI_gam_voi_residuals$fitted.effects,
tolerance = 0.1)
skip_if_not_installed("INLA")
skip("INLA is crashing")
if (require("INLA")) {
# set.seed(1234)
# EVPPI_inla_3_residuals <-
# BCEA::evppi(
# he = bcea_vacc,
# param_idx = 39:41,
# input = inp$mat,
# method = "inla",
# residuals = TRUE)
# save(EVPPI_inla_3_residuals, file = "tests/testthat/testdata/EVPPI_inla_3_residuals.RData")
load(file = test_path("testdata", "EVPPI_inla_3_residuals.RData"))
set.seed(1234)
EVPPI_inla_voi_residuals <-
evppi(
he = bcea_vacc,
param_idx = 39:41,
input = inp$mat,
method = "inla",
residuals = TRUE)
expect_equivalent(
EVPPI_inla_3_residuals$fitted.costs,
EVPPI_inla_voi_residuals$fitted.costs,
tolerance = 0.1)
expect_equivalent(
EVPPI_inla_3_residuals$fitted.effects,
EVPPI_inla_voi_residuals$fitted.effects,
tolerance = 0.1)
}
})
test_that("More that two interventions with smoking data", {
skip("more than two interventions to be revisited after {voi} update")
data(Smoking, package = "BCEA")
treats <-
c("No intervention", "Self-help",
"Individual counselling", "Group counselling")
inp <- createInputs(smoking_output, print_is_linear_comb = FALSE)
bcea_smoke <- bcea(eff, cost, ref = 4, interventions = treats, Kmax = 500) # all interventions
# bcea_smoke <- bcea(eff, cost, ref = 4, .comparison = 1, interventions = treats, Kmax = 500)
# bcea_smoke <- bcea(eff, cost, ref = 4, .comparison = c(2,3), interventions = treats, Kmax = 500)
# expect_length(inp , 2)
# expect_named(inp, c("mat", "parameters"))
# expect_type(inp, "list")
set.seed(1234)
# EVPPI_smoke <- BCEA::evppi(bcea_smoke, param_idx = c(2,3), inp$mat, h.value = 5e-7, method = "gam")
# save(EVPPI_smoke, file = "tests/testthat/testdata/EVPPI_smoke.RData")
# load(file = test_path("testdata", "EVPPI_smoke.RData"))
set.seed(1234)
EVPPI_voi <- evppi(bcea_smoke, param_idx = c(2,3), inp$mat, h.value = 5e-7, method = "gam")
# voiEVPPI <- voi::evppi(bcea_smoke[c("e","c","k")], pars = c("d.3.", "d.4."), inputs = inp$mat, h.value = 5e-7)
expect_s3_class(EVPPI_voi, "evppi")
expect_type(EVPPI_voi, "list")
##TODO: error
expect_equivalent(EVPPI_smoke$evppi, EVPPI_voi$evppi, tolerance = 0.01)
expect_equivalent(EVPPI_smoke$k, EVPPI_voi$k, tolerance = 0.001)
expect_equivalent(EVPPI_smoke$k, EVPPI_voi$k, tolerance = 0.001)
expect_equivalent(EVPPI_smoke$evi, EVPPI_voi$evi, tolerance = 0.001)
expect_equivalent(EVPPI_smoke$select, EVPPI_voi$select)
expect_equivalent(EVPPI_smoke$index, EVPPI_voi$index)
##TODO: error
##TODO: seems like the wrong order of columns?
## what is the correct order? label columns?
expect_equivalent(EVPPI_smoke$fitted.costs, EVPPI_voi$fitted.costs, tolerance = 0.001)
expect_equivalent(EVPPI_smoke$fitted.effects, EVPPI_voi$fitted.effects, tolerance = 0.001)
# plot(EVPPI_voi)
})
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