tests/testthat/test-plots.R

In UUPharmacometrics/xpose: Diagnostics for Pharmacometric Models

prediction_plot_functions <- c('dv_vs_pred', 'dv_vs_ipred', 'dv_vs_idv', 
                               'ipred_vs_idv', 'pred_vs_idv', 'dv_preds_vs_idv')
residual_plot_functions   <- c('res_vs_idv', 'res_vs_pred', 'absval_res_vs_idv', 
                               'absval_res_vs_pred', 'res_distrib', 'res_qq') 
iteration_plot_functions  <- c('prm_vs_iteration', 'grd_vs_iteration')
parameter_plot_functions  <- c('prm_distrib', 'prm_qq')
eta_plot_functions        <- c('eta_distrib', 'eta_qq')
cov_plot_functions        <- c('cov_distrib', 'cov_qq')
kinetic_plot_functions    <- c('amt_vs_idv')
individual_plot_functions <- c('ind_plots')

plot_functions <- c(prediction_plot_functions, residual_plot_functions, 
                    iteration_plot_functions, parameter_plot_functions, 
                    eta_plot_functions, cov_plot_functions, 
                    individual_plot_functions, kinetic_plot_functions)

not_sim_functions <- plot_functions[!grepl('iteration|prm_|eta_|cov_|res_qq|res_distrib|amt_|pred|ind_plots', plot_functions)]
distribution_functions <- plot_functions[grepl('(prm|eta|cov|res)_(distrib|qq)', plot_functions)]

# Simulation only xpdb
xpdb_sim_only <- xpose_data(file = 'sim.lst', dir = 'data', quiet = TRUE)

# Missing all output files except grd
xpdb_mis_file <- xpose_data(file = 'sim.lst', dir = 'data', 
                            ignore = c('data', 'summary'), quiet = TRUE,
                            extra_files = '.phi')
# No output files at all
xpdb_no_file <- xpose_data(file = 'sim.lst', dir = 'data', quiet = TRUE,
                           ignore = c('data', 'files', 'summary'))

# Tests start here --------------------------------------------------------

test_that_for_all(plot_functions, 'errors are returned when xpdb_ex_pk is missing', {
  expect_error(.plot_function())
})

test_that_for_all(plot_functions, 'errors are returned when length .problem is > 1', {
  expect_error(.plot_function(xpdb_ex_pk, .problem = 1:2),  regexp = 'must be of length 1')
})

test_that_for_all(plot_functions, 'errors are returned a .problem not in the data', {
  expect_error(.plot_function(xpdb_ex_pk, .problem = 99),  regexp = '99 not found in')
})


test_that_for_all(plot_functions, 'xpose plot objects are returned with appropriate xpdb_ex_pk', {
  expect_true(is.xpose.plot(.plot_function(xpdb_ex_pk)))
})

test_that_for_all(residual_plot_functions, 'xpose plot objects are returned with appropriate xpdb_ex_pk and muliple residuals', {
  expect_true(is.xpose.plot(.residual_plot_function(xpdb_ex_pk, res = c('CWRES', 'IWRES'))))
})

test_that_for_all(not_sim_functions, 'no error occurs when xpdb is from a simulation only', {
  expect_error(.not_sim_function(xpdb_sim_only), NA)
})

test_that_for_all(iteration_plot_functions, 'have proper error check', {
  expect_error(.iteration_plot_function(xpdb_no_file), 
               regexp = 'No `files` slot could be found in this xpdb')
  expect_error(.iteration_plot_function(xpdb_mis_file), 
               regexp = 'File extension.+not found in model output files')
})  

test_that_for_all(distribution_functions, 'have proper error check', {
  expect_error(.distribution_function(xpdb_sim_only), 
               regexp = 'Column.+ not available')
  expect_error(.distribution_function(xpdb_no_file), 
               regexp = 'No `data` slot could be found in this xpdb')
  expect_error(xpdb_ex_pk %>% filter(ITERATION == 0, .source = 'ext') %>% prm_vs_iteration(),
               regexp = 'No parameters varying across ITERATION were found')
  expect_error(xpdb_ex_pk %>% mutate(ETA1 = 0, ETA2 = 0, ETA3 = 0) %>% eta_qq(drop_fixed = TRUE),
               regexp = 'No non-fixed variables available for plotting')
  expect_true(is.xpose.plot(xpdb_ex_pk %>% 
                              mutate(ETA1 = 0, ETA2 = 0, ETA3 = 0) %>% 
                              eta_qq(drop_fixed = FALSE)))
})