tests/testthat/test-span_table.R

In ruminate: A Pharmacometrics Data Transformation and Analysis Tool

library(onbrand)
test_that("Spanning tables", {
  # First we need to create some data.
  # This will read in a test dataset:
  DS = readxl::read_excel(
    path  = system.file(package="formods",
                        "test_data",
                        "TEST_DATA.xlsx"),
    sheet = "DATA")

  # This will filter the dataset down and modify the formatting
  DS = dplyr::filter(DS, EVID == 0)                          |>
    dplyr::filter(ID <= 20)                                  |>
    dplyr::select(ID, TIME, DV, CMT)                         |>
    dplyr::mutate(CMT  = ifelse(.data[["CMT"]] == "C_ng_ml",
                                "Test Article",
                                .data[["CMT"]]))              |>
    dplyr::select(ID, TIME, DV, CMT)                         |>
    dplyr::mutate(CMT = ifelse(.data[["CMT"]] == "BM_ng_ml",
                               "Biomarker",
                               .data[["CMT"]]))               |>
    dplyr::rename(Analyte = "CMT")                           |>
    dplyr::mutate(DV = ifelse(.data[["DV"]] == 0, "BQL", .data[["DV"]]))

  # This represents the large table we want to split up into smaller tables
  wide_df = tidyr::pivot_wider(DS,
                               values_from = "DV",
                               names_from  = "ID")               |>
    dplyr::arrange(Analyte, TIME)     |>
    dplyr::mutate(TIME = as.character(.data[["TIME"]]))

  # The first two columns represent the rows
  # that are common across the tables:
  row_common = wide_df[,1:2]

  # The remaining columns represent the body of the table:
  table_body = wide_df[,3:ncol(wide_df)]

  # Next we create matrices that contain the header
  # information for each component above:
  row_common_head = matrix(
    data  = c("Time", "Analyte",
              "(hr)", "(ng/ml)"),
    ncol  = 2,
    byrow = TRUE)

  table_body_head = matrix(
    data  = c(rep("Subject ID", times=ncol(table_body)),
              names(table_body)),
    ncol  = ncol(table_body),
    byrow = TRUE)


  # This builds all of the tables:
  span_res = span_table(table_body      = table_body,
                        row_common      = row_common,
                        table_body_head = table_body_head,
                        row_common_head = row_common_head,
                        notes_detect    = c("BQL"))


  expect_true(span_res[["isgood"]])


  # Checking headers
  span_res = span_table(table_body      = table_body,
                        row_common      = row_common,
                        table_body_head = NULL,
                        row_common_head = row_common_head,
                        notes_detect    = c("BQL"))
  expect_false(span_res[["isgood"]])

  span_res = span_table(table_body      = table_body,
                        row_common      = row_common,
                        table_body_head = table_body_head,
                        row_common_head = NULL,
                        notes_detect    = c("BQL"))
  expect_false(span_res[["isgood"]])

  # checking table body columns
  span_res = span_table(table_body      = table_body[,1:(ncol(table_body)-1)],
                        row_common      = row_common,
                        table_body_head = table_body_head,
                        row_common_head = row_common_head,
                        notes_detect    = c("BQL"))
  expect_false(span_res[["isgood"]])

  span_res = span_table(table_body      = table_body,
                        row_common      = row_common[,1:(ncol(row_common)-1)],
                        table_body_head = table_body_head,
                        row_common_head = row_common_head,
                        notes_detect    = c("BQL"))
  expect_false(span_res[["isgood"]])

  # Missing body or common rows
  span_res = span_table(table_body      = table_body,
                        row_common      = NULL,
                        table_body_head = table_body_head,
                        row_common_head = row_common_head,
                        notes_detect    = c("BQL"))
  expect_false(span_res[["isgood"]])

  span_res = span_table(table_body      = NULL,
                        row_common      = row_common,
                        table_body_head = table_body_head,
                        row_common_head = row_common_head,
                        notes_detect    = c("BQL"))
  expect_false(span_res[["isgood"]])


})