tests/testthat/test_mcmcCoefPlot.R

In BayesPostEst: Generate Postestimation Quantities for Bayesian MCMC Estimation

data("jags_logit")

test_that("Simple model runs with mcmcCoefPlot", {
  expect_silent(mcmcCoefPlot(jags_logit))
})

test_that("mcmcCoefPlot works with jags_logit", {
  ## mcmc
  expect_silent(mcmcCoefPlot(coda::as.mcmc(jags_logit)[[1]]))
})

if (require("MCMCpack", quietly = TRUE)) {
  ## fitting the model with MCMCpack
  mcmcpack_linear <- MCMCpack::MCMCregress(Y ~ X, b0 = 0, B0 = 0.001,
                                           sigma.mu = 5, sigma.var = 10,
                                           data = list(X = rnorm(100),
                                                       Y = rnorm(100, 5, 5)),
                                           seed = 1)
  ## testing
  test_that("mcmcCoefPlot works with mcmcpack", {
    expect_silent(mcmcCoefPlot(mcmcpack_linear))
  })
}

test_that("Simple model runs with mcmcCoefPlot with arguments", {
  ## running some expect silent tests for jags_logit
  expect_silent(mcmcCoefPlot(jags_logit))
  expect_silent(mcmcCoefPlot(jags_logit, pars = 'b', regex = T))
  expect_silent(mcmcCoefPlot(jags_logit, pars = 'b', ci = .9, hpdi = T, regex = T))
  
  ## test against a value
  med_df <- mcmcCoefPlot(jags_logit, pars = 'b', pointest = 'median', plot = F, regex = T)
  value <- med_df[2, 1]
  check_against <- 0.5273031
  expect_equal(value, check_against, tolerance = 1e-4)
  
  ## running one more for regex = FALSE
  expect_silent(mcmcCoefPlot(jags_logit, pars = c('b[1]', 'b[2]'), regex = FALSE))
})

test_that("Simple model runs with mcmcCoefPlot with sorting", {
  med_df <- mcmcCoefPlot(jags_logit, pars = 'b', sort = T, plot = F, regex = T)
  value <- med_df[3, 1]
  check_against <- 0.6335488
  expect_equal(value, check_against, tolerance = 1e-4)
})

test_that("mcmcCoefPlot errors work", {
  expect_error(mcmcCoefPlot(jags_logit, pointest = 'man'))
  expect_error(mcmcCoefPlot(jags_logit, hpdi = 2))
})

# dontrun(
# if (require("runjags", quietly = TRUE)) {
#   ## Generate an example runjags interactive fitted model
#   ## formatting the data for jags
#   datalist <- list(X = model.matrix(~ X1 * X2, sim_data_interactive),
#                    Y = sim_data_interactive[, 3],
#                    N = nrow(sim_data_interactive))
#   
#   ## creating jags model
#   model <- "model { 
#   for(i in 1 : N){ 
#   Y[i] ~ dnorm(beta %*% X[i, ], tau);
#   } 
#   for(i in 1:4) {
#   beta[i] ~ dnorm(0, 0.001)
#   }
#   tau ~ dexp(1)
#   }"
# 
#   ## fitting the model with runjags
#   runjags_interactive <- runjags::run.jags(model = model, monitor = c("beta", "tau"),
#                                            data = datalist, n.chains = 2, method = "rjags")
#   
#   ## testing
#   test_that("mcmcCoefPlot works with multiple object types", {
#     ## runjags
#     expect_silent(mcmcCoefPlot(runjags_interactive))
#   })
#   
#   rm(datalist, model)
# }
# )
# 
# dontrun(
# pkgs <- c("rjags", "R2WinBUGS"),
# 
# if (!all(sapply(pkgs, require, quietly = TRUE, character.only = TRUE))) {
#   ## Generate an example BUGS fitted model object
#   data(LINE, package = "rjags")
#   LINE$recompile()
#   
#   ## fitting the model with jags
#   bugs_model <- rjags::coda.samples(LINE, c("alpha", "beta", "sigma"),
#                                     n.iter = 1000)
#   bugs_model <- R2WinBUGS::as.bugs.array(sims.array = as.array(bugs_model))
#   
#   test_that("mcmcCoefPlot works with bugs", {
#     expect_silent(mcmcCoefPlot(bugs_model))
#   })
# }
# )

# Maintainer note 11/2021 - I commented out that earlier code I believe because
# of cran issues with size - Need to go in and figure out if can delete completely
# or modify