tests/testthat/testPattern.R

In campsismod: Generic Implementation of a PK/PD Model

library(testthat)

context("Test the different patterns that can be created to replace occurrences")

test_that("Pattern object works as expected", {
  str <- "ETA_KA + THETA_KA + ETA_KA + ETA_KA3 + ETA_KA"
  pattern <- Pattern("ETA_KA")
  expect_equal(pattern %>% as.character(), "ETA_KA")
  expect_equal(str %>% replaceAll(pattern, "ETA_KA2"), "ETA_KA2 + THETA_KA2 + ETA_KA2 + ETA_KA23 + ETA_KA2")
  
  str <- "HELLO"
  expect_equal(str %>% replaceAll(pattern, ""), "HELLO")
})

test_that("Variable pattern object works as expected", {
  str <- "ETA_KA + THETA_KA + ETA_KA + ETA_KA3 + ETA_KA"
  pattern <- VariablePattern("ETA_KA")
  expect_equal(pattern %>% as.character(), "ETA_KA")
  expect_equal(str %>% replaceAll(pattern, "ETA_KA2"), "ETA_KA2 + THETA_KA + ETA_KA2 + ETA_KA3 + ETA_KA2")
  
  str <- "HELLO"
  expect_equal(str %>% replaceAll(pattern, ""), "HELLO")
})

test_that("Replace occurrences in model works as expected", {
  model <- model_suite$testing$nonmem$advan1_trans1
  model <- model %>% add(LineBreak())
  model <- model %>% add(Comment("Check replacement also works in IF-statement"))
  model <- model %>% add(IfStatement("K==1", Equation("XX", "K*10")))
  model <- model %>% replaceAll("K", "K2")
  
  expect_equal(model %>% find(Equation("K2")), Equation("K2", "THETA_K*exp(ETA_K)"))
  expect_equal(model %>% find(Ode("A_CENTRAL")), Ode("A_CENTRAL", "-K2*A_CENTRAL"))
  expect_equal(model %>% find(Ode("A_OUTPUT")), Ode("A_OUTPUT", "K2*A_CENTRAL"))
  expect_equal(model %>% find(IfStatement("K2==1", Equation("XX"))), IfStatement("K2==1", Equation("XX", "K2*10")))
})

test_that("Function replaceAll also replaces occurrences in compartment properties", {
  model <- model_suite$pk$'1cpt_fo'
  
  model <- model %>% 
    replaceAll("BIO", "BIO2")
  
  # Make sure BIO2 equation is there
  expect_equal(model %>% campsismod::find(Equation("BIO2")), Equation("BIO2", "TVBIO"))
  
  # Make sure compartment property was updated well
  expect_equal(model %>% find(Bioavailability(compartment=1)), Bioavailability(compartment=1, rhs="BIO2"))  
})