inst/tinytest/test-formula.r

In USCbiostats/aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees

# context("Formulae")

# test_that("Formulas create the right model", {

set.seed(0772)
x <- rdrop_annotations(raphylo(50), .5)

m_mu <- aphylo_formula(x ~ mu_d)
m_mu_psi0 <- aphylo_formula(x ~ mu_d + psi)
m_mu_psi1 <- aphylo_formula(x ~ psi)
m_mu_psi2 <- aphylo_formula(x ~ psi + mu_d)


expect_equal(deparse(m_mu_psi0)[-1], deparse(m_mu_psi1)[-1])
expect_equal(deparse(m_mu_psi0)[-1], deparse(m_mu_psi2)[-1])
  
set.seed(071)
x <- rdrop_annotations(raphylo(50), .5)

expect_error(aphylo_formula(y ~ psi), "be found")
y <- 1
expect_error(aphylo_formula(y ~ psi), "should be either")

expect_error(aphylo_formula(x ~ mu_d, c(mu_d0=1, mu_d1=1, psi1=0)), "overspecified")
expect_error(aphylo_formula(x ~ mu_d, c(mu_d0=1)), "missing")

expect_error(aphylo_formula(x~mu_d(9)), "Arguments passed to")
expect_error(aphylo_formula(x~mu_d + I(x)), "supported")
  
  
set.seed(121)

x <- raphylo(30)
p <- matrix(runif(7*2), nrow=2, dimnames = NULL)

ctrl <- list(nchains=2, nsteps=500, burnin=10, conv_checker = NULL)

expect_warning(
  ans <- aphylo_mcmc(x ~ psi+ mu_d + eta + Pi, params = p, control = ctrl),
  "matched by position"
)

expect_identical(class(ans), "aphylo_estimates")
  
# aphylo_formula(x ~ psi + mu_d + mu_s + eta)$fun