tests/testthat/test-stan_emax.R

In rstanemax: Emax Model Analysis with 'Stan'

library(dplyr)

test.data <- exposure.response.sample.with.cov

set.seed(123)

test.fit <- stan_emax(resp ~ conc,
  data = test.data,
  chains = 2, iter = 1000, refresh = 0
)

test.fit.nls <- nls(resp ~ e0 + emax * conc / (ec50 + conc),
  data = test.data,
  start = list(
    e0 = 10,
    emax = 100,
    ec50 = 100
  )
)

test.fit.cov <- stan_emax(
  formula = resp ~ conc, data = test.data,
  param.cov = list(emax = "cov2", ec50 = "cov3", e0 = "cov1"),
  chains = 2, iter = 1000,
  refresh = 0
)

## Run with non-numeric covariates
test.data.2 <-
  mutate(test.data,
    cov1 = ifelse(cov1 == 1, "x1", "x0"),
    cov3 = 5
  )
test.fit.cov2 <- stan_emax(
  formula = resp ~ conc, data = test.data.2,
  param.cov = list(emax = "cov2", ec50 = "cov3", e0 = "cov1"),
  chains = 2, iter = 1000,
  refresh = 0
)

## Fix emax and e0
test.data.3 <-
  mutate(test.data,
    cov3 = ifelse(cov1 == 1, "x1", "x0"),
    cov1 = "aa",
    cov2 = 5
  )
test.fit.fix.emax <- stan_emax(
  formula = resp ~ conc, data = test.data.3,
  emax.fix = 80, e0 = 0,
  param.cov = list(emax = "cov2", ec50 = "cov3", e0 = "cov1"),
  chains = 2, iter = 1000,
  refresh = 0
)


##########
context("stan_emax.R")

tdata1 <- create_standata(data.frame(), gamma.fix = 2, e0.fix = 2)
tdata2 <- create_standata(data.frame(), gamma.fix = NULL, e0.fix = NULL)

test_that("wrong input for create_standata", {
  expect_error(
    create_standata(data.frame(), gamma.fix = 0, e0.fix = 2),
    "gamma.fix must be NULL or positive numeric"
  )
})

test_that("create standata", {
  expect_equal(tdata1$gamma_fix_flg, 1)
  expect_equal(tdata1$gamma_fix_value, 2)
  expect_equal(tdata2$gamma_fix_flg, 0)
  expect_is(tdata2$gamma_fix_value, "numeric")

  expect_equal(tdata1$e0_fix_flg, 1)
  expect_equal(tdata1$e0_fix_value, 2)
  expect_equal(tdata2$e0_fix_flg, 0)
  expect_is(tdata2$e0_fix_value, "numeric")
})


test_that("emax model run", {
  coef.stan <- rstan::summary(test.fit$stanfit, pars = c("e0", "emax", "ec50"))$summary[, 6]
  coef.nls <- coef(test.fit.nls)
  expect_is(test.fit, "stanemax")
  expect_equal(dim(test.fit$stanfit), c(500, 2, 428))
  expect_equal(coef.stan / coef.nls, c(`e0[1]` = 1, `emax[1]` = 1, `ec50[1]` = 1), tolerance = 0.1)
})


test_that("emax model run with covs", {
  coef.stan <- rstan::summary(test.fit.cov$stanfit, pars = c("e0", "emax", "ec50"))$summary[, 6]
  expect_equal(length(coef.stan), 7)
})


test_that("emax model run with Emax and E0 fixed", {
  coef.stan <- rstan::summary(test.fit.fix.emax$stanfit, pars = c("e0", "emax", "ec50"))$summary[, 6]
  expect_equal(coef.stan[1:2], c(`e0[1]` = 0, `emax[1]` = 80))
})

test_that("print.stanemax works correctly", {
  expect_output(print.stanemax(test.fit.cov2), "---- Emax model fit with rstanemax ----")
})