tests/testthat/test-plotcoda.R

In florale/multilevelcoda: Estimate Bayesian Multilevel Models for Compositional Data

skip_on_cran()

if (!requireNamespace("cmdstanr", quietly = TRUE)) {
  backend <- "rstan"
  ## if using rstan backend, models can crash on Windows
  ## so skip if on windows and cannot use cmdstanr
  skip_on_os("windows")
} else {
  if (isFALSE(is.null(cmdstanr::cmdstan_version(error_on_NA = FALSE)))) {
    backend <- "cmdstanr"
  }
}

# Packages
library(testthat)
library(multilevelcoda)
library(brms)
library(ggplot2)

# Model
#---------------------------------------------------------------------------------------------------
data(mcompd)
data(sbp)
data(psub)

cilr <- complr(data = mcompd[ID %in% 1:10, .SD[1:3], by = ID], sbp = sbp,
                parts = c("TST", "WAKE", "MVPA", "LPA", "SB"), idvar = "ID", total = 1440)

suppressWarnings(
  m <- brmcoda(complr = cilr,
               formula = Stress ~ bilr1 + bilr2 + bilr3 + bilr4 +
                 wilr1 + wilr2 + wilr3 + wilr4 + Female + (1 | ID),
               chain = 1, iter = 500, seed = 123,
               backend = backend))
foreach::registerDoSEQ()

x <- substitution(object = m, delta = 1:10,
                          ref = "grandmean",
                          level = c("between", "within"))

# Testing
#---------------------------------------------------------------------------------------------------