tests/testthat/test-shape_data.R

In rdinnager/fibre: Fast Evolutionary Trait Modelling on Phylogenies using Branch Regression Models

test_that("shape_data_inla() returns the correct data shapes", {
  
  skip("skipping for now until I work out the internals fully")
  
  data("vert_bmr", package = "phyf")
  ## 2 outcomes, 2 predictors, 2 pfcs, two latents
  dat <- hardhat::mold(lnBMR + lnGS ~ lnMass + endo + bre(phlo) + bre(phlo^2, latent = 2), 
                       data = vert_bmr,
                       blueprint = fibre_formula_blueprint(intercept = TRUE))
  c(phyfs, rate_dists, hypers, latents) %<-% purrr::transpose(dat$extras$model_info)
  shaped <- shape_data_inla(phyfs, dat$predictors,
                            dat$outcomes, latents)
  expect_true(check_inla_dims(shaped$y, shaped$dat, shaped$A,
                                 ny = 2, nlatent = 2, npredictors = 2 + 2, npfc = 2))
  
  stack_test <- INLA::inla.stack(data = list(y = shaped$y),
                                 A = list(shaped$A),
                                 effects = list(shaped$dat))
  expect_s3_class(stack_test, "inla.data.stack")
  
  ## 2 outcomes, 2 predictors, 1 pfcs, two latents
  dat <- hardhat::mold(lnBMR + lnGS ~ lnMass + endo + bre(phlo, latent = 2), 
                       data = vert_bmr,
                       blueprint = fibre_formula_blueprint(intercept = TRUE))
  c(phyfs, rate_dists, hypers, latents) %<-% purrr::transpose(dat$extras$model_info)
  shaped <- shape_data_inla(phyfs, dat$predictors,
                            dat$outcomes, latents)
  expect_true(check_inla_dims(shaped$y, shaped$dat, shaped$A,
                                 ny = 2, nlatent = 2, npredictors = 2 + 2, npfc = 1))
  
  ## 1 outcomes, 3 predictors, 2 pfcs, no latents
  dat <- hardhat::mold(lnBMR ~ lnMass + lnGS + endo + bre(phlo) + bre(phlo^2), 
                       data = vert_bmr,
                       blueprint = fibre_formula_blueprint(intercept = TRUE))
  c(phyfs, rate_dists, hypers, latents) %<-% purrr::transpose(dat$extras$model_info)
  shaped <- shape_data_inla(phyfs, dat$predictors,
                            dat$outcomes, latents)
  expect_true(check_inla_dims(shaped$y, shaped$dat, shaped$A,
                                 ny = 1, nlatent = 0, npredictors = 3 + 1, npfc = 2))
  
})