tests/testthat/test-check_mapbayr_modeldata.R

In mapbayr: MAP-Bayesian Estimation of PK Parameters

mod <- mcode("mod",
             "
             $CMT @annotated
             GUT: gut
             CENT: central [OBS]
             ", compile = FALSE)
data <- exdata()

test_that("Compartment in data is ok with cmt defined in model", {
  faildata_mdv0 <- rbind(data, c(ID = 1, time = 30, evid = 0, amt = 0, cmt = 3, ii = 0, addl = 0, mdv = 0, DV = 15))
  expect_error(check_mapbayr_modeldata(mod, faildata_mdv0),
               "One or multiple line\\(s\\) with cmt = 3 observed in data, but only 2 compartments defined in model\\.")

  faildata_mdv1 <- rbind(data, c(ID = 1, time = 30, evid = 0, amt = 0, cmt = 3, ii = 0, addl = 0, mdv = 1, DV = 15))
  expect_error(check_mapbayr_modeldata(mod, faildata_mdv1),
               "One or multiple line\\(s\\) with cmt = 3 observed in data, but only 2 compartments defined in model\\.")

  faildata_mdv1_bis <- rbind(faildata_mdv1, c(ID = 1, time = 30, evid = 0, amt = 0, cmt = 99, ii = 0, addl = 0, mdv = 1, DV = 15))
  expect_error(check_mapbayr_modeldata(mod, faildata_mdv1_bis),
               "One or multiple line\\(s\\) with cmt = 3 99 observed in data, but only 2 compartments defined in model\\.")
})

test_that("Observation compartment in data are those defined with [OBS] in model, if any", {
  dat <- data.frame(ID = 1, mdv = 0, cmt = c(1,2))
  expect_error(check_mapbayr_modeldata(mod, dat),
               ".*One or more compartment with observation \\(mdv=0\\) in data don\\'t match those defined with \\[OBS\\] in \\$CMT\\.")
})

test_that("Cannot have more than one fit cmt in data if no [OBS] in model", {
  dat <- data.frame(ID = 1, mdv = 0, cmt = c(1,2))
  mod <- mcode("mod", "$CMT GUT CENT", compile = FALSE)
  expect_error(
    check_mapbayr_modeldata(mod, dat),
    "More than one \\`observation compartment\\` found in data\\. Consider editing model code with \\[OBS\\] in \\$CMT\\."
  )

  #Same, but if defined in 2 patients
  dat <- data.frame(ID = c(1,2), mdv = 0, cmt = c(1,2))
  expect_error(
    check_mapbayr_modeldata(mod, dat),
    "More than one \\`observation compartment\\` found in data\\. Consider editing model code with \\[OBS\\] in \\$CMT\\."
  )
})


test_that("Covariates in `$PARAM` are tagged with @covariates", {
  modcovannot <- mcode("mod",
                       "
             $PARAM TVCL = 1, BW = 70
             $PARAM @annotated @covariates
             SEX : 0 : sex
             ", compile = FALSE)
  datacovannot <- data.frame(ID = 1, BW = 80, SEX = 1)
  expect_error(check_mapbayr_modeldata(modcovannot, datacovannot),
               "Variables found both in the model \\(\\`\\$PARAM\\`\\) and in the data\\: BW\\.\\nIf these are covariates\\, please declare them with the \\`\\@annotated \\@covariates\\` tags in \\`\\$PARAM\\`\\.\\nOtherwise\\, remove them from the data\\.")
})