tests/testthat/test-format_vpc_input_data.R

In ronkeizer/vpc: Create Visual Predictive Checks

nonmem_df <- data.frame(ID = 1, ADV = c(1, 0, 0), DV = 1)

# Check standardize_column ####

nonmem_df_id <- data.frame(id = 1, ADV = c(1, 0, 0), DV = 1)

test_that("colname must be in names(cols)", {
  expect_error(
    vpc:::standardize_column(dat=nonmem_df, cols=list(ID="ID"), colname="foo", coldesc="identifier"),
    regexp="'colname' (foo) must be in 'names(cols)'.  Available names: ID",
    fixed=TRUE
  )
})

test_that("cols[[colname]] must be in names(dat), unless (see next test)", {
  expect_error(
    vpc:::standardize_column(dat=nonmem_df, cols=list(foo="foo"), colname="foo", coldesc="identifier", what="errormsg"),
    regexp="No column for identifier indicator found in errormsg data, can't continue! Available columns: ID, ADV, DV",
    fixed=TRUE
  )
})

test_that("When the column exists and it is named the same as colname even if cols is not the same, input is returned as output", {
  expect_equal(
    vpc:::standardize_column(
      dat=nonmem_df,
      cols=list(ID="foo"),
      colname="ID",
      coldesc="identifier"
    ),
    nonmem_df
  )
})

test_that("When the column exists and it is named the same, input is returned as output", {
  expect_equal(
    vpc:::standardize_column(dat=nonmem_df, cols=list(ID="ID"), colname="ID", coldesc="identifier"),
    nonmem_df
  )
})

test_that("When the column exists and it is not named the same, input is returned with the column renamed", {
  expect_equal(
    vpc:::standardize_column(dat=nonmem_df, cols=list(id="ID"), colname="id", coldesc="identifier"),
    nonmem_df_id
  )
})

# Test format_vpc_input_data ####
formatted_nonmem_df <-
  dplyr::mutate(
    dplyr::rename(nonmem_df, id="ID", idv="ADV", dv="DV"),
    strat=factor(1)
  )

test_that("format_vpc_input_data returns the source data unmodified when lloq, uloq, strat, log_y, log_y_min, and pred_corr have no effect", {
  expect_equal(
    vpc:::format_vpc_input_data(
      dat=nonmem_df,
      cols=list(id="ID", idv="ADV", dv="DV"),
      log_y=FALSE, log_y_min=1e-3,
      lloq=NULL, uloq=NULL,
      stratify=NULL,
      what="observed",
      verbose=FALSE,
      pred_corr=FALSE
    ),
    formatted_nonmem_df
  )
})

test_that("format_vpc_input_data returns the source data modified by lloq (NA if pred_corr == FALSE)", {
  formatted_nonmem_df_lloq_nopredc <- formatted_nonmem_df
  formatted_nonmem_df_lloq_nopredc$dv <- NA_real_
  expect_equal(
    vpc:::format_vpc_input_data(
      dat=nonmem_df,
      cols=list(id="ID", idv="ADV", dv="DV"),
      log_y=FALSE, log_y_min=1e-3,
      lloq=2, uloq=NULL,
      stratify=NULL,
      what="observed",
      verbose=FALSE,
      pred_corr=FALSE
    ),
    formatted_nonmem_df_lloq_nopredc
  )
})

test_that("format_vpc_input_data returns the source data modified by lloq (lloq if pred_corr == TRUE)", {
  formatted_nonmem_df_lloq_yespredc <- formatted_nonmem_df
  formatted_nonmem_df_lloq_yespredc$dv <- NA_real_
  expect_equal(
    vpc:::format_vpc_input_data(
      dat=nonmem_df,
      cols=list(id="ID", idv="ADV", dv="DV"),
      log_y=FALSE, log_y_min=1e-3,
      lloq=2, uloq=NULL,
      stratify=NULL,
      what="observed",
      verbose=FALSE,
      pred_corr=TRUE
    ),
    formatted_nonmem_df_lloq_yespredc
  )
})

test_that("format_vpc_input_data returns the source data modified by uloq (NA if pred_corr == FALSE)", {
  formatted_nonmem_df_uloq_nopredc <- formatted_nonmem_df
  formatted_nonmem_df_uloq_nopredc$dv <- NA_real_
  expect_equal(
    vpc:::format_vpc_input_data(
      dat=nonmem_df,
      cols=list(id="ID", idv="ADV", dv="DV"),
      log_y=FALSE, log_y_min=1e-3,
      lloq=NA, uloq=0.5,
      stratify=NULL,
      what="observed",
      verbose=FALSE,
      pred_corr=FALSE
    ),
    formatted_nonmem_df_uloq_nopredc
  )
})

test_that("format_vpc_input_data returns the source data modified by uloq (uloq if pred_corr == TRUE)", {
  formatted_nonmem_df_uloq_yespredc <- formatted_nonmem_df
  formatted_nonmem_df_uloq_yespredc$dv <- NA_real_
  expect_equal(
    vpc:::format_vpc_input_data(
      dat=nonmem_df,
      cols=list(id="ID", idv="ADV", dv="DV"),
      log_y=FALSE, log_y_min=1e-3,
      lloq=NA, uloq=0.5,
      stratify=NULL,
      what="observed",
      verbose=FALSE,
      pred_corr=TRUE
    ),
    formatted_nonmem_df_uloq_yespredc
  )
})

test_that("format_vpc_input_data returns the source data modified by log_y_min", {
  formatted_nonmem_df_logy_2 <- formatted_nonmem_df
  formatted_nonmem_df_logy_2$dv <- 2
  expect_equal(
    vpc:::format_vpc_input_data(
      dat=nonmem_df,
      cols=list(id="ID", idv="ADV", dv="DV"),
      log_y=TRUE, log_y_min=2,
      lloq=NULL, uloq=NULL,
      stratify=NULL,
      what="observed",
      verbose=FALSE,
      pred_corr=TRUE
    ),
    formatted_nonmem_df_logy_2
  )
})