test-set_prior.R
In rstanemax: Emax Model Analysis with 'Stan'

library(dplyr)

set.seed(0)

## Generate data ##

nsample.dose   <- 10
clearance      <- 0.5
logsd.exposure <- 0.7

dose.exposure <-
  tibble(dose = rep(c(0, 100, 1000), each = nsample.dose)) %>%
  mutate(exposure = dose / clearance * exp(rnorm(dose, 0, logsd.exposure)))

e0   <- 10
emax <- 90
ec50 <- 100
sd.response <- 10

test.data <-
  dose.exposure %>%
  mutate(response =
           e0 + emax * exposure / (ec50 + exposure) +
           rnorm(exposure, 0, sd.response))


df.model <- create_model_frame(response ~ exposure, test.data, cov.levels = covs_get_levels(test.data))
test.standata.noprior <-
  create_standata(df.model,
                  gamma.fix = 1, e0.fix = NULL)

##########
context("test-set_prior.R")

t.sdata.autoprior <- set_prior_auto(test.standata.noprior)

test_that("auto prior set", {
  expect_equal(t.sdata.autoprior$prior_ec50_mu,  156.0748, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_ec50_sig, 312.1496, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_emax_mu,  116.9879, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_emax_sig, 116.9879, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_e0_mu,    7.424736, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_e0_sig,   14.84947, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_gamma_mu, 0, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_gamma_sig,5, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_sigma_mu, 0, tolerance = 0.1)
  expect_equal(t.sdata.autoprior$prior_sigma_sig,36.84818, tolerance = 0.1)
})

t.sdata.manuprior <-
  set_prior(test.standata.noprior,
            priors = list(ec50  = c(1, 2),
                          emax  = c(3, 4),
                          e0    = c(5, 6),
                          gamma = c(7, 8),
                          sigma = c(9, 10)))

test_that("manual prior set", {
  expect_equal(t.sdata.manuprior$prior_ec50_mu,  1)
  expect_equal(t.sdata.manuprior$prior_ec50_sig, 2)
  expect_equal(t.sdata.manuprior$prior_emax_mu,  3)
  expect_equal(t.sdata.manuprior$prior_emax_sig, 4)
  expect_equal(t.sdata.manuprior$prior_e0_mu,    5)
  expect_equal(t.sdata.manuprior$prior_e0_sig,   6)
  expect_equal(t.sdata.manuprior$prior_gamma_mu, 7)
  expect_equal(t.sdata.manuprior$prior_gamma_sig,8)
  expect_equal(t.sdata.manuprior$prior_sigma_mu, 9)
  expect_equal(t.sdata.manuprior$prior_sigma_sig,10,tolerance = 0.1)

  expect_error(set_prior(test.standata.noprior, priors = list(ec50  = c(1))),
               "Priors need to be defined with length 2 numeric vectors")
  expect_error(set_prior(test.standata.noprior, priors = list(emax  = c(1,2,3))),
               "Priors need to be defined with length 2 numeric vectors")
  expect_error(set_prior(test.standata.noprior, priors = list(e0  = "test")),
               "Priors need to be defined with length 2 numeric vectors")
})