test-reader.R
In ggPMX: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

context("Test reader parameters")
reader_help <- reader_helpers()

#------------------- read_mlx18_res start --------------------------------------
test_that("read_mlx18_res: params: path, x; result: data.table", {
  skip_on_os("windows")
  ipath <- file.path(reader_help$wd, "predictions.txt")
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  expect_error(read_mlx18_res(ipath, x[["predictions"]]))
})

test_that("read_mlx18_res: params: path is wrong, subfolder is not empty,
          file exists, endpoint; result: identical structure", {
  skip_on_os("windows")
  ipath <- file.path(reader_help$wd, "predictions.txt")
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$predictions$endpoint <- "pred"
  expect_error(read_mlx18_res(ipath, x$predictions))
})

test_that("read_mlx18_res: params: path is wrong, subfolder is not empty,
          file exists; result: identical structure", {
  skip_on_os("windows")
  ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "predictions.txt")

  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$predictions$subfolder <- "Monolix"
  x$predictions$file <- "predictions.txt"
  expect_null(read_mlx18_res(ipath, x$predictions))
})

test_that("read_mlx18_res: params: newnames, path is wrong, subfolder is not empty,
          file exists; result: identical structure", {
  skip_on_os("windows")
  ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "predictions.txt")

  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$predictions$subfolder <- "Monolix"
  x$predictions$file <- "predictions.txt"
  x$predictions$newnames <- list(
    ID = "id", TIME = "time", PRED = "poppred",
    NPDE = "npde", IPRED = "mlx_ipred", IWRES = "mlx_iwres"
  )

  r <- read_mlx18_res(ipath, x$predictions)
  expect_identical(r, NULL)
})

test_that("read_mlx18_res: params: pattern, path is wrong, subfolder is not empty,
          file exists; result: identical structure", {
  skip_on_os("windows")
  ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "finegrid.txt")

  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$finegrid$names <- list(
    ID = "ID", time = "time", popPred = "popPred",
    "indPred_mean*" = "indPred_mean*", indPred_mode = "indPred_mode",
    V6 = "V6"
  )
  x$finegrid$subfolder <- "Monolix"
  x$finegrid$file <- "finegrid.txt"
  x$finegrid$id <- "ID"
  x$finegrid$pattern <- "_obsVsPred"
  r <- read_mlx18_res(ipath, x$finegrid)
  expect_identical(r, NULL)
})

test_that("read_mlx18_res: 11params: path is wrong, subfolder is not empty,
          file exists; result: identical structure", {
  skip_on_os("windows")
  ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "finegrid.txt")

  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$finegrid$names <- list(
    ID = "ID", time = "time", popPred = "popPred",
    "indPred_mean*" = "indPred_mean*", indPred_mode = "indPred_mode",
    V6 = "V6"
  )
  x$finegrid$subfolder <- "Monolix"
  x$finegrid$file <- "finegrid.txt"
  x$finegrid$id <- "ID"
  expect_s3_class(read_mlx18_res(ipath, x$finegrid), c("data.table", "data.frame"))
})

test_that("read_mlx18_res: params: path, occ = OCC and its in file; result: error", {
  skip_on_os("windows")
  my.file <- tempfile()
  fwrite(
    data.frame(
      "IDS" = c(1, 1, 1), "time" = c(0, 0.5, 1),
      "y1" = c(2000, 0, 0), "OCC" = c(0, 130, 228),
      "meanPred" = c(1, 0, 0), "indPred_mean*" = c(87, 87, 87),
      "indPred_mode" = c(125.3, 412.5, 658.63), "popWRes" = c(0.00, 0.52, 0.69),
      "meanWRes" = c(0.15, 0.21, 0.42), "indWRes_mean*" = c(0.15, 0.21, 0.42),
      "indWRes_mode" = c(121, 132, 145), "NPDE" = c(121, 132, 145), "OCC" = c(1, 0, 1)
    ),
    my.file
  )
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$predictions$file <- basename(my.file)
  x$predictions$id <- "ID"
  expect_error(read_mlx18_res(dirname(my.file), x$predictions, occ = "OCC"))
})

test_that("read_mlx18_res: params: path is NULL, x;
          result: error", {
  skip_on_os("windows")
  ipath <- NULL
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  expect_error(read_mlx18_res(ipath, x$predictions))
})

test_that("read_mlx18_res: params: path, x is NULL;
          result: error", {
  skip_on_os("windows")
  ipath <- file.path(reader_help$wd, "predictions.txt")
  x <- NULL
  expect_error(read_mlx18_res(ipath, x))
})
##------------------- read_mlx18_res end-----------------------------------------

#------------------- read_mlx_pred start ---------------------------------------
test_that("read_mlx_pred: params: path, x; result: identical class", {
  ipath <- file.path(reader_help$wd, "predictions.txt")
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  r <- read_mlx_pred(ipath, x$predictions)

  expect_true(inherits(r, "data.frame"))
})

test_that("read_mlx_pred: params: path, x$id is ID; result: identical class", {
  ipath <- file.path(reader_help$wd, "predictions.txt")
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$id <- "ID"
  r <- read_mlx_pred(ipath, x$predictions)

  expect_true(inherits(r, "data.frame"))
})

test_that("read_mlx_pred: params: path, occ = OCC and its in file; result: identical class", {
  my.file <- tempfile()
  write.csv(
    data.frame(
      "IDS" = c(1, 1, 1), "time" = c(0, 0.5, 1),
      "y1" = c(2000, 0, 0), "popPred" = c(0, 130, 228),
      "meanPred" = c(1, 0, 0), "indPred_mean*" = c(87, 87, 87),
      "indPred_mode" = c(125.3, 412.5, 658.63), "popWRes" = c(0.00, 0.52, 0.69),
      "meanWRes" = c(0.15, 0.21, 0.42), "indWRes_mean*" = c(0.15, 0.21, 0.42),
      "indWRes_mode" = c(121, 132, 145), "NPDE" = c(121, 132, 145), "OCC" = c(1, 0, 1)
    ),
    my.file
  )
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$id <- "IDS"
  r <- read_mlx_pred(my.file, x$predictions, occ = "OCC")
  expect_true(inherits(r, "data.frame"))
})

test_that("read_mlx_pred: params: path, occ = OCC but not such column in file;
          result: error", {
  my.file <- tempfile()
  write.csv(
    data.frame(
      "IDS" = c(1, 1, 1), "time" = c(0, 0.5, 1),
      "y1" = c(2000, 0, 0), "popPred" = c(0, 130, 228),
      "meanPred" = c(1, 0, 0), "indPred_mean*" = c(87, 87, 87),
      "indPred_mode" = c(125.3, 412.5, 658.63), "popWRes" = c(0.00, 0.52, 0.69),
      "meanWRes" = c(0.15, 0.21, 0.42), "indWRes_mean*" = c(0.15, 0.21, 0.42),
      "indWRes_mode" = c(121, 132, 145), "NPDE" = c(121, 132, 145)
    ),
    my.file
  )
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$id <- "IDS"
  expect_error(read_mlx_pred(my.file, x$predictions, occ = "OCC"))
})

test_that("read_mlx_pred: params: path, x is NULL; result: error", {
  ipath <- file.path(reader_help$wd, "predictions.txt")
  x <- NULL

  expect_error(read_mlx_pred(ipath, x$predictions))
})

test_that("read_mlx_pred: params: path is NULL, x; result: error", {
  ipath <- NULL
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]

  expect_error(read_mlx_pred(ipath, x$predictions))
})
#------------------- read_mlx_pred end------------------------------------------

#------------------- read_mlx18_pred start -------------------------------------
test_that("read_mlx18_pred: params: path, x;
          result: identical structure", {
  ipath <- file.path(reader_help$wd, "predictions.txt")
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  r <- read_mlx18_pred(ipath, x$predictions)

  expect_identical(
    names(r),
    c("ID", "TIME", "PRED", "NPDE", "IPRED", "IWRES")
  )
})

test_that("read_mlx18_pred: params: path is wrong, subfolder is not empty,
          file exists; result: identical structure", {
  ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "predictions.txt")

  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$predictions$subfolder <- "Monolix"
  x$predictions$file <- "predictions.txt"
  r <- read_mlx18_pred(ipath, x$predictions)

  expect_identical(
    names(r),
    c("ID", "TIME", "PRED", "NPDE", "IPRED", "IWRES")
  )
})

test_that("read_mlx18_pred: params:path is wrong, subfolder is not empty,
          file doesn't exist; result: NULL", {
  ipath <- file.path(system.file(package = "ggPMX"), "testdata", "predictions.txt")

  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$predictions$subfolder <- "theophylline"
  x$predictions$file <- "predictions.txt"
  r <- read_mlx18_pred(ipath, x$predictions)

  expect_identical(
    r,
    NULL
  )
})

test_that("read_mlx18_pred: params: residuals; result: error", {
  ipath <- file.path(reader_help$wd, "predictions.txt")
  names. <- names(reader_help$conf$data)
  x <- reader_help$conf$data[names.]
  x$predictions$residuals <- x$finegrid
  x$predictions$endpoint <- pmx_endpoint(
    code = "236",
    file.code = "2"
  )
  x$predictions$id <- "ID"
  expect_error(read_mlx18_pred(ipath, x$predictions))
})
#------------------- read_mlx18_pred end----------------------------------------

#------------------- read_mlx_par_est start ------------------------------------
test_that("read_mlx_par_est: params: path, x; result: identical class and structure", {
  ipath <- file.path(reader_help$wd, "estimates.txt")
  x <- NULL
  x$sep <- ";"
  x$names <- c("params", "parameter", "s.e._lin", "r.s.e._lin", "pvalues_lin")
  r <- read_mlx_par_est(ipath, x)

  expect_identical(
    names(r),
    c("params", "parameter", "s.e._lin", "r.s.e._lin", "pvalues_lin")
  )
  expect_true(inherits(r, "data.frame"))
})

test_that("read_mlx_par_est: params: path, x$name is vector; result: identical structure", {
  ipath <- file.path(reader_help$wd, "estimates.txt")
  x <- NULL
  x$sep <- ";"
  x$names <- c("parameter name", "parameter", "SE._lin", "RSE_lin", "pValues_lin")
  r <- read_mlx_par_est(ipath, x)

  expect_identical(
    names(r),
    c("parameter name", "parameter", "SE._lin", "RSE_lin", "pValues_lin")
  )
})

test_that("read_mlx_par_est: params: path, x$name is NULL; result: identical structure", {
  ipath <- file.path(reader_help$wd, "estimates.txt")
  x <- NULL
  x$sep <- ";"
  x$names <- NULL
  r <- read_mlx_par_est(ipath, x)

  expect_identical(
    names(r),
    c("X", "parameter", "s.e._lin", "r.s.e._lin", "pvalues_lin")
  )
})

test_that("read_mlx_par_est: params: path is NULL, x;
          result: error", {
  ipath <- NULL
  x <- NULL
  x$sep <- ";"
  x$names <- c("params", "parameter", "s.e._lin", "r.s.e._lin", "pvalues_lin")

  expect_error(
    read_mlx_par_est(ipath, x)
  )
})

test_that("read_mlx_par_est: params: path, x is '' ; result: error", {
  ipath <- file.path(reader_help$wd, "estimates.txt")
  x <- NULL
  x$sep <- ""
  x$names <- c("params", "parameter", "s.e._lin", "r.s.e._lin", "pvalues_lin")

  expect_error(read_mlx_par_est(ipath, x))
})
#------------------- read_mlx_par_est end---------------------------------------